# HG changeset patch # User m-zytnicki # Date 1367220283 14400 # Node ID c265f13066d8bb7effd7202712ec7fd678a8991c # Parent 9bcfa7936eec139c2ac86746c4b4311ff2c4f82c Deleted selected files diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/BlatClusterLauncher.py --- a/commons/launcher/BlatClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch BlatProgramLauncher on several files in parallel on a cluster. - - -from pyRepet.launcher.AbstractClusterLauncher import * -from commons.launcher.BlatProgramLauncher import BlatProgramLauncher -from commons.core.coord.AlignUtils import AlignUtils -from commons.tools import srptBlasterMatcher - - -class BlatClusterLauncher( AbstractClusterLauncher ): - """ - Launch Blat on several files in parallel on a cluster. - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractClusterLauncher.__init__( self ) - AbstractClusterLauncher.setAcronym( self, "Blat" ) - - self._cmdLineSpecificOptions = "s:p:A" - - self._exeWrapper = "BlatProgramLauncher.py" - self._prgLauncher = BlatProgramLauncher() - self._prgLauncher.setInputFile( GENERIC_IN_FILE ) - self._prgLauncher.setClean() - self._prgLauncher.setVerbosityLevel( 1 ) - self._prgLauncher.setListFilesToKeep() - self._prgLauncher.setListFilesToRemove() - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: name of the subject file (format='fasta')" - string += "\n -p: parameters for '%s'" % ( self._prgLauncher.getProgramName() ) - string += "\n -Z: concatenate output files" - string += "\n -A: same sequences (all-by-all)" - return string - - - def getSubjectFile( self ): - return self._prgLauncher.getSubjectFile() - - - def getProgramParameters( self ): - return self._prgLauncher.getProgramParameters() - - - def processOutputFile( self, tmpFile, outFile ): - sortFile = "%s.sort" % ( tmpFile ) - AlignUtils.sortAlignFile( tmpFile, sortFile ) - if self._prgLauncher.getAllByAll(): - srptBlasterMatcher.filterRedundantMatches( sortFile, - outFile ) - os.remove( sortFile ) - else: - os.rename( sortFile, outFile ) - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - if o =="-s": - self._prgLauncher.setSubjectFile( a ) - -if __name__ == "__main__": - i = BlatClusterLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/BlatProgramLauncher.py --- a/commons/launcher/BlatProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch Blat (pairwise alignment). -# -# options: -# -h: this help -# -i: name of the input file (queries, format='fasta') -# -s: name of the subject file (format='fasta') -# -p: parameters for 'blat' (default='-d 2') -# -o: name of the output file (format='align', default=inFile+'.align') -# -c: clean -# -v: verbosity level (default=0/1) - - -import os -import sys - -from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher - - -class BlatProgramLauncher( AbstractProgramLauncher ): - """ - Launch Blat (pairwise alignment). - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractProgramLauncher.__init__( self ) - self._prgName = "blat" - self._formatInFile = "fasta" - self._sbjFile = "" - self._prgParam = "" - self._allByAll = False - - - def getHelpAsString( self ): - string = AbstractProgramLauncher.getHelpAsString(self) - string += "\nspecific options:" - string += "\n -s: name of the subject file (database, format='fasta')" - string += "\n -p: parameters for '%s'" % ( self.getProgramName() ) - string += "\n -A: same sequences (all-by-all)" - string += "\n -o: name of the output file (format='align', default=inFile+'.align')" - return string - - def getCmdLineOptions(self): - return AbstractProgramLauncher.getCmdLineOptions(self) + "s:p:Ao:" - - def setAttributesFromCmdLine( self, o, a = "" ): - AbstractProgramLauncher.setAttributesFromCmdLine(self, o, a) - if o == "-s": - self.setSubjectFile( a ) - elif o == "-p": - self.setProgramParameters( a ) - elif o == "-A": - self.setAllByAll() - elif o == "-o": - self.setOutputFile( a ) - - - def setSubjectFile( self, arg ): - self._sbjFile = arg - - - def getSubjectFile( self ): - return self._sbjFile - - - def setAllByAll( self ): - self._allByAll = True - - - def getAllByAll( self ): - return self._allByAll - - - def check( self ): - """ - Check the specific attributes before running the program. - """ - AbstractProgramLauncher.check(self) - if self._sbjFile == "": - string = "ERROR: missing subject file (-s)" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - - - def setWrapperCommandLine( self ): - """ - Set the command-line of the wrapper. - Required for BlatClusterLauncher. - """ - self._wrpCmdLine = self.getWrapperName() - self._wrpCmdLine += " -i %s" % ( self.getInputFile() ) - self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() ) - if self.getProgramParameters() != "": - self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() ) - if self.getAllByAll(): - self._wrpCmdLine += " -A" - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self._wrpCmdLine += " -o %s" % ( self.getOutputFile() ) - if self.getClean(): - self._wrpCmdLine += " -c" - self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - - - def setProgramCommandLine( self ): - """ - Set the command-line of the program. - """ - self._prgCmdLine = self.getProgramName() - self._prgCmdLine += " %s" % ( self.getSubjectFile() ) - self._prgCmdLine += " %s" % ( self.getInputFile() ) - if self.getProgramParameters() != "": - self._prgCmdLine += " %s" % ( self.getProgramParameters() ) - self._prgCmdLine += " -out=blast8" - self._prgCmdLine += " %s.blast" % ( self.getInputFile() ) - - - def setListFilesToKeep( self ): - """ - Set the list of files to keep. - """ - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self.appendFileToKeep( self.getOutputFile() ) - - - def setListFilesToRemove( self ): - """ - Set the list of files to remove. - """ - self.appendFileToRemove( "%s.blast" % ( self.getInputFile() ) ) - - - def convertBlastIntoAlign( self ): - """ - Convert a 'blast' file into the 'align' format. - """ - cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py" - cmd += " -i %s.blast" % ( self.getInputFile() ) - cmd += " -o %s" % ( self.getOutputFile() ) - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR while converting 'blast' file into 'align' format" - print string - sys.exit(1) - - - def setSummary( self ): - self._summary = "input file: %s" % ( self.getInputFile() ) - self._summary += "\nsubject file: %s" % ( self.getSubjectFile() ) - self._summary += "\nparameters: %s" % ( self.getProgramParameters() ) - if self.getAllByAll(): - self._summary += "\nall-by-all" - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self._summary += "\noutput file: %s" % ( self.getOutputFile() ) - - - def run( self ): - """ - Run the program. - """ - self.start() - - self.setProgramCommandLine() - cmd = self.getProgramCommandLine() - if self.getVerbosityLevel() > 0: - print "LAUNCH: %s" % ( cmd ) - sys.stdout.flush() - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus ) - print string - sys.exit(1) - - self.convertBlastIntoAlign() - - self.end() - - -if __name__ == "__main__": - i = BlatProgramLauncher() - i.checkAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchBlastclust.py --- a/commons/launcher/LaunchBlastclust.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,372 +0,0 @@ -#!/usr/bin/env python - -""" -Launch Blastclust on nucleotide sequences and return a fasta file. -""" - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import sys -import subprocess -from commons.core.seq.BioseqDB import BioseqDB -from commons.core.seq.Bioseq import Bioseq -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - -class LaunchBlastclust(object): - """ - Launch Blastclust on nucleotide sequences and return a fasta file. - """ - - def __init__(self, input = "", outFilePrefix = "", clean = False, verbose = 0): - """ - Constructor. - """ - self._inFileName = input - self._identityThreshold = 95 - self._coverageThreshold = 0.9 - self._bothSeq = "T" - self._filterUnclusteredSeq = False - self._outFilePrefix = outFilePrefix - self._isBlastToMap = False - self._isHeaderForTEdenovo = False - self._nbCPUs = 1 - self._clean = clean - self._verbose = verbose - self._tmpFileName = "" - - def setAttributesFromCmdLine(self): - """ - Set the attributes from the command-line. - """ - - description = "Launch Blastclust on nucleotide sequences and return a fasta file." - usage = "LaunchBlastclust.py -i inputFileName [options]" - - examples = "\nExample 1: launch Blastclust with default options, highest verbose and clean temporary files.\n" - examples += "\t$ python ./LaunchBlastclust.py -i MyBank.fa -v 2 -c" - examples += "\n\t" - examples += "\t\nExample 2: launch Blastclust with an identity threshold of 90%, rename output files and generate a map file corresponding to the fasta output.\n" - examples += "\t$ python ./LaunchBlastclust.py -i MyBank.fa -S 90 -o SpecialOutputName -m" - examples += "\n\tWARNING: Please refer to -m option limitations in the description above.\n" - - #TODO: check if the optionParser can handle '\' into strings for a better code readability in -m option - - parser = RepetOptionParser(description = description, usage = usage, version = "v1.0", epilog = examples) - parser.add_option("-i", "--input", dest = "inFileName", type = "string", help = "name of the input fasta file (nucleotides)", default = "") - parser.add_option("-L", "--length", dest = "coverageThreshold", type = "float", help = "length coverage threshold (default=0.9)", default = 0.9) - parser.add_option("-S", "--ident", dest = "identityThreshold", type = "int", help = "identity threshold (default=95)", default = 95) - parser.add_option("-b", "--both", dest = "bothSeq", type = "string", help = "require coverage on both neighbours (default=T/F)", default = "T") - parser.add_option("-f", "--filter", dest = "filterUnclusteredSeq", help = "filter unclustered sequences", default = False, action="store_true") - parser.add_option("-o", "--out", dest = "outFilePrefix", type = "string", help = "prefix of the output files (default=input fasta file name)", default = "") - parser.add_option("-m", "--map", dest = "isBlast2Map", help = "generate an additional output file in map format (Warning: only works if blastclust's fasta input headers are formated like LTRharvest fasta output)", default = False, action="store_true") - parser.add_option("", "--TEdenovoHeader", dest = "isHeaderForTEdenovo", help = "format headers for TEdenovo pipeline", default = False, action="store_true") - parser.add_option("-n", "--num", dest = "nbCPUs", type = "int", help = "number of CPU's to use (default=1)", default = 1) - parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true") - parser.add_option("-v", "--verbose", dest = "verbose", type = "int", help = "verbosity level (default=0/1/2)", default = 0) - - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setInputFileName(options.inFileName) - self.setCoverageThreshold(options.coverageThreshold) - self.setIdentityThreshold(options.identityThreshold) - self.setBothSequences(options.bothSeq) - self.setNbCPUs(options.nbCPUs) - self.setIsHeaderForTEdenovo(options.isHeaderForTEdenovo) - if options.filterUnclusteredSeq: - self.setFilterUnclusteredSequences() - if options.outFilePrefix != "": - self.setOutputFilePrefix(options.outFilePrefix) - else: - self._outFilePrefix = self._inFileName - if options.isBlast2Map: - self.setIsBlastToMap() - if options.clean: - self.setClean() - self.setVerbosityLevel(options.verbose) - - def setInputFileName(self , inFileName): - self._inFileName = inFileName - - def setCoverageThreshold(self, lengthThresh): - self._coverageThreshold = float(lengthThresh) - - def setIdentityThreshold(self, identityThresh): - self._identityThreshold = int(identityThresh) - - def setBothSequences(self, bothSeq): - self._bothSeq = bothSeq - - def setNbCPUs(self, nbCPUs): - self._nbCPUs = int(nbCPUs) - - def setFilterUnclusteredSequences(self): - self._filterUnclusteredSeq = True - - def setOutputFilePrefix(self, outFilePrefix): - self._outFilePrefix = outFilePrefix - - def setIsBlastToMap(self): - self._isBlastToMap = True - - def setIsHeaderForTEdenovo(self, isHeaderForTEdenovo): - self._isHeaderForTEdenovo = isHeaderForTEdenovo - - def setClean(self): - self._clean = True - - def setVerbosityLevel(self, verbose): - self._verbose = int(verbose) - - def setTmpFileName(self, tmpFileName): - self._tmpFileName = tmpFileName - - - def checkAttributes(self): - """ - Check the attributes are valid before running the algorithm. - """ - if self._inFileName == "": - print "ERROR: missing input file name (-i)" - sys.exit(1) - if self._outFilePrefix == "": - self._outFilePrefix = self._inFileName - self._tmpFileName = "%s_blastclust.txt" % (self._outFilePrefix) - - - def launchBlastclust(self, inFile): - """ - Launch Blastclust in command-line. - """ - if os.path.exists(os.path.basename(inFile)): - inFile = os.path.basename(inFile) - prg = "blastclust" - cmd = prg - cmd += " -i %s" % (inFile) - cmd += " -o %s" % (self._tmpFileName) - cmd += " -S %i" % (self._identityThreshold) - cmd += " -L %f" % (self._coverageThreshold) - cmd += " -b %s" % (self._bothSeq) - cmd += " -p F" - cmd += " -a %i" % (self._nbCPUs) - if self._verbose == 0: - cmd += " -v blastclust.log" - if self._verbose > 0: - print cmd - sys.stdout.flush() - process = subprocess.Popen(cmd, shell = True) - process.communicate() - if process.returncode != 0: - raise Exception("ERROR when launching '%s'" % cmd) - if self._clean and os.path.exists("error.log"): - os.remove("error.log") - if self._clean and os.path.exists("blastclust.log"): - os.remove("blastclust.log") - - - def getClustersFromTxtFile(self): - """ - Return a dictionary with cluster IDs as keys and sequence headers as values. - """ - dClusterId2SeqHeaders = {} - inF = open(self._tmpFileName, "r") - line = inF.readline() - clusterId = 1 - while True: - if line == "": - break - tokens = line[:-1].split(" ") - dClusterId2SeqHeaders[clusterId] = [] - for seqHeader in tokens: - if seqHeader != "": - dClusterId2SeqHeaders[clusterId].append(seqHeader) - line = inF.readline() - clusterId += 1 - inF.close() - if self._verbose > 0: - print "nb of clusters: %i" % (len(dClusterId2SeqHeaders.keys())) - sys.stdout.flush() - return dClusterId2SeqHeaders - - - def filterUnclusteredSequences(self, dClusterId2SeqHeaders): - """ - Filter clusters having only one sequence. - """ - for clusterId in dClusterId2SeqHeaders.keys(): - if len(dClusterId2SeqHeaders[clusterId]) == 1: - del dClusterId2SeqHeaders[clusterId] - if self._verbose > 0: - print "nb of clusters (>1seq): %i" % (len(dClusterId2SeqHeaders.keys())) - sys.stdout.flush() - return dClusterId2SeqHeaders - - - def getClusteringResultsInFasta(self, inFile): - """ - Write a fasta file whose sequence headers contain the clustering IDs. - """ - dClusterId2SeqHeaders = self.getClustersFromTxtFile() - if self._filterUnclusteredSeq: - dClusterId2SeqHeaders = self.filterUnclusteredSequences(dClusterId2SeqHeaders) - inDB = BioseqDB(inFile) - outFileName = "%s_Blastclust.fa" % (inFile) - outF = open(outFileName, "w") - for clusterId in dClusterId2SeqHeaders.keys(): - memberId = 1 - for seqHeader in dClusterId2SeqHeaders[clusterId]: - bs = inDB.fetch(seqHeader) - bs.header = "BlastclustCluster%iMb%i_%s" % (clusterId, memberId, seqHeader) - bs.write(outF) - memberId += 1 - outF.close() - - - def getLinkInitNewHeaders(self): - dNew2Init = {} - linkFileName = "%s.shortHlink" % (self._inFileName) - linkFile = open(linkFileName,"r") - line = linkFile.readline() - while True: - if line == "": - break - data = line.split("\t") - dNew2Init[data[0]] = data[1] - line = linkFile.readline() - linkFile.close() - return dNew2Init - - - def retrieveInitHeaders(self, dNewH2InitH): - tmpFaFile = "%s.shortH_Blastclust.fa" % (self._inFileName) - tmpFaFileHandler = open(tmpFaFile, "r") - outFaFile = "%s_Blastclust.fa" % (self._outFilePrefix) - outFaFileHandler = open(outFaFile, "w") - while True: - line = tmpFaFileHandler.readline() - if line == "": - break - if line[0] == ">": - tokens = line[1:-1].split("_") - initHeader = dNewH2InitH[tokens[1]] - if self._isHeaderForTEdenovo: - classif = initHeader.split("_")[0] - consensusName = "_".join(initHeader.split("_")[1:]) - clusterId = tokens[0].split("Cluster")[1].split("Mb")[0] - newHeader = "%s_Blc%s_%s" % (classif, clusterId, consensusName) - else: - newHeader = "%s_%s" % (tokens[0], initHeader) - outFaFileHandler.write(">%s\n" % (newHeader)) - else: - outFaFileHandler.write(line) - tmpFaFileHandler.close() - outFaFileHandler.close() - if self._clean: - os.remove(tmpFaFile) - - - def blastclustToMap(self, blastclustFastaOut): - """ - Write a map file from blastclust fasta output. - Warning: only works if blastclust's fasta input headers are formated like LTRharvest fasta output. - """ - fileDb = open(blastclustFastaOut , "r") - mapFilename = "%s.map" % (os.path.splitext(blastclustFastaOut)[0]) - fileMap = open(mapFilename, "w") - seq = Bioseq() - numseq = 0 - while 1: - seq.read(fileDb) - if seq.sequence == None: - break - numseq = numseq + 1 - ID = seq.header.split(' ')[0].split('_')[0] - chunk = seq.header.split(' ')[0].split('_')[1] - start = seq.header.split(' ')[-1].split(',')[0][1:] - end = seq.header.split(' ')[-1].split(',')[1][:-1] - line= '%s\t%s\t%s\t%s' % (ID, chunk, start, end) - fileMap.write(line + "\n") - - fileDb.close() - fileMap.close() - print "saved in %s" % mapFilename - - - def start(self): - """ - Useful commands before running the program. - """ - self.checkAttributes() - if self._verbose > 0: - print "START %s" % (type(self).__name__) - - - def end(self): - """ - Useful commands before ending the program. - """ - if self._verbose > 0: - print "END %s" % (type(self).__name__) - - - def run(self): - """ - Run the program. - """ - self.start() - - iCSH = ChangeSequenceHeaders(inFile = self._inFileName, format = "fasta", step = 1, outFile = "%s.shortH" % self._inFileName, linkFile = "%s.shortHlink" % self._inFileName) - iCSH.run() - - self.launchBlastclust("%s.shortH" % (self._inFileName)) - - self.getClusteringResultsInFasta("%s.shortH" % (self._inFileName)) - - dNewH2InitH = self.getLinkInitNewHeaders() - self.retrieveInitHeaders(dNewH2InitH) - - if self._isBlastToMap: - blastclustFileName = "%s_Blastclust.fa" % (self._outFilePrefix) - self.blastclustToMap(blastclustFileName) - - if self._clean: - os.remove("%s.shortH" % (self._inFileName)) - os.remove("%s.shortHlink" % (self._inFileName)) - - self.end() - -if __name__ == "__main__": - i = LaunchBlastclust() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchLastZ.py --- a/commons/launcher/LaunchLastZ.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,133 +0,0 @@ -#! /usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import sys -import os -import optparse -from commons.core.checker.CheckerUtils import CheckerUtils -from commons.core.utils.FileUtils import FileUtils -from subprocess import Popen -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess -import tempfile - -class LaunchLastZ(object): - - def __init__(self,queryFileName="", refFileName ="", outputFileName=None,outputFileFormat="axt",noTransition=True, ambiguous=None, step=1,gfextend=False, chain=False, verbosity=1 ): - self.queryFileName = queryFileName - self.refFileName = refFileName - self.outputFileName = outputFileName - self.outputFileFormat = outputFileFormat - self.noTransition = noTransition - self.step = step - self.ambiguous = ambiguous - self.gfextend = gfextend - self.chain = chain - self.verbosity = verbosity - - def setAttributesFromCmdLine(self): - description = "LaunchLastZ runs the LastZ program ." - parser = RepetOptionParser(description = description) - parser.add_option("-q", "--query", dest="queryFileName", default = None, action="store", type="string", help="input query file [compulsory] [format: fasta]") - parser.add_option("-r", "--ref", dest="refFileName", default = None, action="store", type="string", help="input ref file [compulsory] [format: fasta]") - parser.add_option("-o", "--output", dest="outputFileName", default = None, action="store", type="string", help="output file [compulsory] ") - parser.add_option("-f", "--format", dest="outputFileFormat", default = "axt", action="store", type="string", help="output file format[optional] ") - parser.add_option("-n", "--notransition", dest="noTransition", action="store_false", default=True, help="noTransition (default True) [optional] ") - parser.add_option("-a", "--ambiguous", dest="ambiguous", action="store", type="string", help="ambiguous [optional] ") - parser.add_option("-s", "--step", dest="step", default = 1, action="store", type="int", help="stepsize (default 1) [optional] ") - parser.add_option("-g", "--gfextend", dest="gfextend", action="store_true", help="extend gf (default false)[optional] ") - parser.add_option("-c", "--chain", dest="chain", action="store_true", help="chain (default false)[optional] ") - parser.add_option("-v", "--verbosity", dest="verbosity", default = 1, action="store", type="int", help="verbosity [optional] ") - (self._options, args) = parser.parse_args() - self._setAttributesFromOptions(self._options) - - def _setAttributesFromOptions(self, options): - self.queryFileName = options.queryFileName - self.refFileName = options.refFileName - self.outputFileName = options.outputFileName - self.outputFileFormat = options.outputFileFormat - self.ambiguous = options.ambiguous - self.noTransition = options.noTransition - self.step = options.step - self.gfextend = options.gfextend - self.chain = options.chain - self.verbosity = options.verbosity - - def checkOptions(self): - if self.queryFileName != "": - if not FileUtils.isRessourceExists(self.queryFileName): - raise Exception("ERROR: Query file does not exist!") - else: - raise Exception("ERROR: No specified --query option!") - if self.refFileName != "": - if not FileUtils.isRessourceExists(self.refFileName): - raise Exception("ERROR: Ref file does not exist!") - else: - raise Exception("ERROR: No specified --ref option!") - if self.outputFileName == None: - self.outputFileName = "%s_%s.axt" % (os.path.basename(self.queryFileName), os.path.basename(self.refFileName)) - - def run(self): - if not CheckerUtils.isExecutableInUserPath("lastz") : - print ("ERROR: LastZ must be in your path") - else: - self.checkOptions() - - transition = "" - if self.noTransition: - transition = "--notransition" - ambiguous = "" - if self.ambiguous is not None: - ambiguous = "--ambiguous=%s" % self.ambiguous - - gfextend = "" - if self.gfextend: - gfextend = "--gfextend" - - chain = "" - if self.chain: - chain = "--chain" - - cmd = "lastz %s[format=fasta] %s[format=fasta] --output=%s --format=%s %s %s --step=%i %s %s" % (self.refFileName, self.queryFileName, self.outputFileName - , self.outputFileFormat, ambiguous, transition,self.step, gfextend, chain) - if self.verbosity>0: - print("Running LastZ with following commands : %s" %cmd) - sys.stdout.flush() - cmd = cmd.split() - process = subprocess.Popen(cmd) - process.wait() - return process.returncode - -if __name__ == "__main__": - iLaunchLastZ = LaunchLastZ() - iLaunchLastZ.setAttributesFromCmdLine() - iLaunchLastZ.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchMCL.py --- a/commons/launcher/LaunchMCL.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,239 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.seq.FastaUtils import FastaUtils -from commons.core.coord.MatchUtils import MatchUtils -import subprocess -import os -import time -import shutil -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - -LOG_DEPTH = "repet.base" - -##Launch MCL -# -class LaunchMCL(object): - - def __init__(self, fastaFileName = "", outFilePrefix = "", inflate = 1.5, covThres = 0.0, isJoined = False, isCluster2Map = False, isClusterConsensusHeaders = False, doClean = False, verbosity = 0): - self._fastaFileName = fastaFileName - self.setOutFilePrefix(outFilePrefix) - self._inflate = inflate - self._coverageThreshold = covThres - self._isJoined = isJoined - self._isCluster2Map = isCluster2Map - self._isClusterConsensusHeaders = isClusterConsensusHeaders - self._doClean = doClean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "Launch MCL clustering program." - epilog = "\nExample: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python LaunchMCL.py -i file.fa -v 0\n" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-o", "--out", dest = "outFilePrefix", action = "store", type = "string", help = "prefix of the output files [default=input fasta file name]", default = "") - parser.add_option("-I", "--inflate", dest = "inflate", action = "store", type = "float", help = "inflate parameter of MCL [optional] [default: 1.5]", default = 1.5) - parser.add_option("-T", "--coverage", dest = "coverageThreshold", action = "store", type = "float", help = "length coverage threshold (default=0.0, 0.0 <= value <= 1.0)", default = 0.0) - parser.add_option("-j", "--join", dest = "isJoined", action = "store_true", help = "join hits after alignement [optional] [default: False]" , default = False) - parser.add_option("-m", "--map", dest = "isCluster2Map", action = "store_true", help = "generate an additional output file in map format (Warning: only works if MCL's fasta input headers are formated like LTRharvest fasta output)", default = False) - parser.add_option("", "--isClusterConsensusHeaders", dest = "isClusterConsensusHeaders", action="store_true", help = "format headers for Cluster Consensus tool", default = False) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setFastaFileName(options.fastaFileName) - self.setOutFilePrefix(options.outFilePrefix) - self.setInflate(options.inflate) - self.setCoverageThreshold(options.coverageThreshold) - self.setIsJoined(options.isJoined) - self.setIsCluster2Map(options.isCluster2Map) - self.setIsClusterConsensusHeaders(options.isClusterConsensusHeaders) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def setFastaFileName(self, fastaFileName): - self._fastaFileName = fastaFileName - - def setOutFilePrefix(self, outFilePrefix): - if outFilePrefix == "": - self._outFilePrefix = os.path.splitext(self._fastaFileName)[0] - else: - self._outFilePrefix = outFilePrefix - - def setInflate(self, inflate): - self._inflate = inflate - - def setCoverageThreshold(self, covThres): - self._coverageThreshold = float(covThres) - - def setIsJoined(self, isJoined): - self._isJoined = isJoined - - def setDoClean(self, doClean): - self._doClean = doClean - - def setIsCluster2Map(self, isCluster2Map): - self._isCluster2Map = isCluster2Map - - def setIsClusterConsensusHeaders(self, isClusterConsensusHeaders): - self._isClusterConsensusHeaders = isClusterConsensusHeaders - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self._fastaFileName == "": - self._logAndRaise("ERROR: Missing input fasta file name") - if self._isCluster2Map and self._isClusterConsensusHeaders: - self._logAndRaise("ERROR: You can't use both '--isClusterConsensusHeaders' and '-m' options") - if self._coverageThreshold > 1 or self._coverageThreshold < 0: - self._logAndRaise("ERROR: Coverage Threshold must be in [0.0 , 1.0]") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START Launch MCL") - self._log.debug("With parameters: -i %s -o %s -I %.2f -T %.2f -j %r -m %r -clusterHeaders %r " % (self._fastaFileName, self._outFilePrefix , self._inflate , self._coverageThreshold, self._isJoined, self._isCluster2Map, self._isClusterConsensusHeaders)) - #self._log.debug("With parameters: -i %s -o %s -I %.2f -T %.2f" % (self._fastaFileName, self._outFilePrefix , self._inflate , self._coverageThreshold)) - self._log.debug("Fasta file name: %s" % self._fastaFileName) - workingDir = "MCLtmpDirectory" - if os.path.exists(workingDir): - self._logAndRaise("ERROR: %s already exists." % workingDir) - os.mkdir(workingDir) - os.chdir(workingDir) - linkToFastaFile = "%s2.fa" % os.path.splitext(self._fastaFileName)[0] - os.symlink("../%s" % self._fastaFileName, self._fastaFileName) - fastaFileNameShorten = "%s.shortH" % self._fastaFileName - iChangeSequenceHeaders = ChangeSequenceHeaders(inFile=self._fastaFileName, format="fasta", step=1, outFile=fastaFileNameShorten, verbosity=self._verbosity - 1) - iChangeSequenceHeaders.run() - os.symlink(fastaFileNameShorten, linkToFastaFile) - - self._log.info("START Blaster-Matcher (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")) - cmd = "LaunchBlaster.py" - cmd += " -q %s" % fastaFileNameShorten - cmd += " -s %s" % linkToFastaFile - cmd += " -a" - cmd += " 1>&2 >> blasterMatcher.log" - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - outBlasterFileName = "%s.align" % fastaFileNameShorten - - cmd = "matcher" - cmd += " -m %s" % outBlasterFileName - cmd += " -q %s" % fastaFileNameShorten - cmd += " -s %s" % linkToFastaFile - cmd += " -a" - if self._isJoined: - cmd += " -j" - cmd += " 1>&2 >> blasterMatcher.log" - process = subprocess.Popen(cmd, shell=True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - self._log.info("END Blaster-Matcher (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")) - - outMatcherFileName = "%s.match.tab" % outBlasterFileName - inputABCFileName = "%s.shortH.abc" % os.path.splitext(fastaFileNameShorten)[0] - MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(outMatcherFileName, inputABCFileName, coverage = self._coverageThreshold) - outMCLPreprocessFileName = "MCLPreprocess.out" - - self._log.info("START MCL (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")) - cmd = "mcxload" - cmd += " -abc %s" % inputABCFileName - cmd += " --stream-mirror" - cmd += " --stream-neg-log10" - cmd += " -stream-tf 'ceil(200)'" - cmd += " -o %s" % outMCLPreprocessFileName - cmd += " -write-tab %s.tab" % outMCLPreprocessFileName - cmd += " 1>&2 > MCLpreprocess.log" - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - - outMCLFileName = "out.shortH.mcl" - cmd = "mcl" - cmd += " %s" % outMCLPreprocessFileName - cmd += " -I %s" % self._inflate - cmd += " -use-tab %s.tab" % outMCLPreprocessFileName - cmd += " -o %s" % outMCLFileName - cmd += " 1>&2 > MCL.log" - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - self._log.info("END MCL (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")) - - outFastaFileNameShorten = "%s.fa" % os.path.splitext(outMCLFileName)[0] - - FastaUtils.convertClusterFileToFastaFile(outMCLFileName, fastaFileNameShorten, outFastaFileNameShorten, "MCL", verbosity = self._verbosity - 1) - - outFastaFileName = "%s_MCL.fa" % self._outFilePrefix - linkFileName = "%s.newHlink" % self._fastaFileName - headerStyle = "A" - if self._isClusterConsensusHeaders: - headerStyle = "B" - iChangeSequenceHeaders = ChangeSequenceHeaders(inFile=outFastaFileNameShorten, format="fasta", step=2, outFile=outFastaFileName, linkFile=linkFileName, whichCluster = headerStyle, verbosity=self._verbosity - 1) - iChangeSequenceHeaders.run() - - if self._isCluster2Map: - outMapFileName = "%s_MCL.map" % self._outFilePrefix - FastaUtils.convertClusteredFastaFileToMapFile(outFastaFileName, outMapFileName) - shutil.move(outMapFileName, "..") - - shutil.move(outFastaFileName, "..") - os.chdir("..") - if self._doClean: - self._log.warning("Working directory will be cleaned") - shutil.rmtree(workingDir) - self._log.info("END Launch MCL") - -if __name__ == "__main__": - iLaunch = LaunchMCL() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchMap.py --- a/commons/launcher/LaunchMap.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,186 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.core.seq.FastaUtils import FastaUtils -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders -from commons.core.utils.FileUtils import FileUtils -import os -import subprocess - -LOG_DEPTH = "repet.tools" - -##Reference launcher implementation -# -class LaunchMap(object): - - def __init__(self, fastaFileName = "", outFileName = "", gapSize = 50, mismatchPenalty = -8, gapOpenPenalty = 16, gapExtendPenalty = 4, doClean = False, verbosity = 0): - self._fastaFileName = fastaFileName - self.setOutFileName(outFileName) - self._gapSize = gapSize - self._mismatchPenalty = mismatchPenalty - self._gapOpenPenalty = gapOpenPenalty - self._gapExtendPenalty = gapExtendPenalty - self._doClean = doClean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): -# description = "Launch template to create a launcher." -# epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" -# epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0" -# epilog += "\n\t" -# epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n" -# epilog += "\t$ python LaunchTemplate.py -i file.fa -c -v 2" -# parser = RepetOptionParser(description = description, epilog = epilog) - parser = RepetOptionParser(description = "", epilog = "") - parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: .fa_aln]", default = "") - parser.add_option("-s", "--gapSize", dest = "gapSize", action = "store", type = "int", help = "size above which a gap is not penalized anymore [optional] [default: 50]", default = 50) - parser.add_option("-m", "--mismatch", dest = "mismatch", action = "store", type = "int", help = "penalty for a mismatch [optional] [default: -8]", default = -8) - parser.add_option("-O", "--gapOpen", dest = "gapOpen", action = "store", type = "int", help = "penalty for a gap opening [optional] [default: 16]", default = 16) - parser.add_option("-e", "--gapExtend", dest = "gapExtend", action = "store", type = "int", help = "penalty for a gap extension [optional] [default: 4]", default = 4) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setFastaFileName(options.fastaFileName) - self.setOutFileName(options.outFileName) - self.setGapSize(options.gapSize) - self.setMismatchPenalty(options.mismatch) - self.setGapOpenPenalty(options.gapOpen) - self.setGapExtendPenalty(options.gapExtend) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def setFastaFileName(self, fastaFileName): - self._fastaFileName = fastaFileName - - def setOutFileName(self, outFileName): - if outFileName == "": - self._outFileName = "%s.fa_aln" % self._fastaFileName - else: - self._outFileName = outFileName - - def setGapSize(self, gapSize): - self._gapSize = gapSize - - def setMismatchPenalty(self, mismatchPenalty): - self._mismatchPenalty = mismatchPenalty - - def setGapOpenPenalty(self, gapOpenPenalty): - self._gapOpenPenalty = gapOpenPenalty - - def setGapExtendPenalty(self, gapExtendPenalty): - self._gapExtendPenalty = gapExtendPenalty - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self._fastaFileName == "": - self._logAndRaise("ERROR: Missing input fasta file name") - if not FileUtils.isRessourceExists(self._fastaFileName): - self._logAndRaise("ERROR: Input fasta file name %s doesn't exist." % self._fastaFileName) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def getMapCmd(self): - cmd = "rpt_map" - cmd += " %s.shortH" % self._fastaFileName - cmd += " %i" % self._gapSize - cmd += " %i" % self._mismatchPenalty - cmd += " %i" % self._gapOpenPenalty - cmd += " %i" % self._gapExtendPenalty - cmd += " > %s.shortH.fa_aln" % self._fastaFileName - return cmd - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START LaunchMap") - self._log.debug("Fasta file name: %s" % self._fastaFileName) - - lInitHeaders = FastaUtils.dbHeaders(self._fastaFileName, self._verbosity - 1) - - csh = ChangeSequenceHeaders() - csh.setInputFile(self._fastaFileName) - csh.setFormat("fasta") - csh.setStep(1) - csh.setPrefix("seq") - csh.setLinkFile("%s.shortHlink" % self._fastaFileName) - csh.setOutputFile("%s.shortH" % self._fastaFileName) - csh.setVerbosityLevel(self._verbosity - 1) - csh.run() - - cmd = self.getMapCmd() - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - - csh.setInputFile("%s.shortH.fa_aln" % self._fastaFileName) - csh.setFormat("fasta") - csh.setStep(2) - csh.setLinkFile("%s.shortHlink" % self._fastaFileName) - csh.setOutputFile("%s.shortH.fa_aln.initH" % self._fastaFileName) - csh.setVerbosityLevel(self._verbosity - 1) - csh.run() - - absDB = AlignedBioseqDB("%s.shortH.fa_aln.initH" % self._fastaFileName) - outFileHandler = open(self._outFileName, "w") - for header in lInitHeaders: - bs = absDB.fetch(header) - bs.upCase() - bs.write(outFileHandler) - outFileHandler.close() - if self._doClean: - os.remove("%s.shortH" % self._fastaFileName) - os.remove("%s.shortHlink" % self._fastaFileName) - os.remove("%s.shortH.fa_aln" % self._fastaFileName) - os.remove("%s.shortH.fa_aln.initH" % self._fastaFileName) - self._log.info("END Launch") - -if __name__ == "__main__": - iLaunch = LaunchMap() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchMatcher.py --- a/commons/launcher/LaunchMatcher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,168 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess - -LOG_DEPTH = "repet.tools" - -##Launch MATCHER -# -class LaunchMatcher(object): - - def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", doClean = False, verbosity = 0): - self._alignFileName = align - self._queryFileName = queryFileName - self.setSubjectFileName(subjectFileName) - self.setOutPrefix(prefix) - self._doJoin = doJoin - self._eValue = evalue - self._keepConflict = keepConflict - - self._doClean = doClean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "Launch Matcher." - epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python LaunchMatcher.py -a in.align -v 0" - epilog += "\n\t" - epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n" - epilog += "\t$ python LaunchMatcher.py -a in.align -q query.fa -s nr.fa -c -v 2" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-a", "--align", dest = "align", action = "store", type = "string", help = "input align file name [compulsory] [format: align]", default = "") - parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [optional] [format: fasta]", default = "") - parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [optional] [format: fasta]", default = "") - parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "E-value filter [default: 1e-10]", default = "1e-10") - parser.add_option("-j", "--join", dest = "doJoin", action = "store_true", help = "join matches [default: False]", default = False) - parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true", help = "keep conflicting subjects [default: False]", default = False) - parser.add_option("-o", "--outPrefix", dest = "outPrefix", action = "store", type = "string", help = "output file prefix [default: align file name]", default = "") - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setAlignFileName(options.align) - self.setQueryFileName(options.query) - self.setSubjectFileName(options.subject) - self.setEvalue(options.evalue) - self.setDoJoin(options.doJoin) - self.setKeepConflicts(options.keepConflict) - self.setOutPrefix(options.outPrefix) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def setAlignFileName(self, alignFileName): - self._alignFileName = alignFileName - - def setQueryFileName(self, queryFileName): - self._queryFileName = queryFileName - - def setSubjectFileName(self, subjectFileName): - self._subjectFileName = subjectFileName - - def setEvalue(self, evalue): - self._eValue = evalue - - def setDoJoin(self, doJoin): - self._doJoin = doJoin - - def setKeepConflicts(self, keepConflict): - self._keepConflict = keepConflict - - def setOutPrefix(self, outPrefix): - if outPrefix == "": - self._outPrefix = self._alignFileName - else: - self._outPrefix = outPrefix - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self._alignFileName == "": - self._logAndRaise("ERROR: Missing input align file name") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def _getMatcherCmd(self): - lArgs = [] - lArgs.append("-m %s" % self._alignFileName) - if self._queryFileName: - lArgs.append("-q %s" % self._queryFileName) - if self._subjectFileName: - lArgs.append("-s %s" % self._subjectFileName) - if self._doJoin: - lArgs.append("-j") - lArgs.append("-E %s" % self._eValue) - lArgs.append("-B %s" % self._outPrefix) - if self._keepConflict: - lArgs.append("-a") - lArgs.append("-v %i" % (self._verbosity - 1)) - return self._getSystemCommand("matcher", lArgs) - - def _getSystemCommand(self, prg, lArgs): - systemCmd = prg - for arg in lArgs: - systemCmd += " " + arg - return systemCmd - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START LaunchMatcher") - self._log.debug("Align file name: %s" % self._alignFileName) - self._log.debug("Query file name: %s" % self._queryFileName) - self._log.debug("Subject file name: %s" % self._subjectFileName) - #TODO: clean files -# if self._doClean: -# self._log.warning("Files will be cleaned") - cmd = self._getMatcherCmd() - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - self._log.info("END LaunchMatcher") - -if __name__ == "__main__": - iLaunch = LaunchMatcher() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchMummerPlot.py --- a/commons/launcher/LaunchMummerPlot.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,150 +0,0 @@ -#! /usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.checker.CheckerUtils import CheckerUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess -from commons.core.LoggerFactory import LoggerFactory -import os -import shutil - -LOG_DEPTH = "repet.tools" - -class LaunchMummerPlot(object): - - def __init__(self, inputFileName="", queryFileName="", refFileName ="", prefix = None, fat=False, filter=False,clean=False, verbosity=0): - self._inputFileName = inputFileName - self._queryFileName = queryFileName - self._refFileName = refFileName - self._prefix = prefix - self._fat = fat - self._filter = filter - self.doClean = clean - self.verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity) - - def setAttributesFromCmdLine(self): - description = "LaunchMummerPlot runs the MummerPlot program (part of the mummer package) ." - parser = RepetOptionParser(description = description) - parser.add_option("-i", "--input", dest="inputFileName", default = None, action="store", type="string", help="input file[mandatory] [format: delta]") - parser.add_option("-q", "--Qfile", dest="queryFileName", default = None, action="store", type="string", help="Plot an ordered set of reference sequences from Qfile [optional] [format: fasta]") - parser.add_option("-r", "--Rfile", dest="refFileName", default = None, action="store", type="string", help="Plot an ordered set of reference sequences from Rfile [optional] [format: fasta]") - parser.add_option("-p", "--prefix", dest="prefix", default = None, action="store", type="string", help="prefix name [mandatory]") - parser.add_option("-o","--fat", dest="fat",action="store_true", help="Layout sequences using fattest alignment only[optional] ") - parser.add_option("-s","--filter", dest="filter",action="store_true", help="Only display .delta alignments which represent the 'best' hit [optional] ") - parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true") - parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ") - - (self._options, args) = parser.parse_args() - self._setAttributesFromOptions(self._options) - - def _setAttributesFromOptions(self, options): - self._inputFileName = options.inputFileName - self._queryFileName = options.queryFileName - self._refFileName = options.refFileName - self._prefix = options.prefix - self._fat = options.fat - self._filter = options.filter - self.verbosity = options.verbosity - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def checkOptions(self): - if self._inputFileName != "": - if not FileUtils.isRessourceExists(self._inputFileName): - self._logAndRaise("ERROR: Query file: %s does not exist!" % self._inputFileName) - else: - self._logAndRaise("ERROR: No specified --query option!") - - if self._queryFileName != "": - if not FileUtils.isRessourceExists(self._queryFileName): - self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName) - - if self._refFileName != "": - if not FileUtils.isRessourceExists(self._refFileName): - self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName) - - def clean(self): - try: - os.remove("%s.filter" % self._prefix) - except Exception as inst: - self._log.error(inst) - try: - os.remove("%s.fplot" % self._prefix) - except Exception as inst: - self._log.error(inst) - try: - os.remove("%s.rplot" % self._prefix) - except Exception as inst: - self._log.error(inst) - - def run(self): - if not CheckerUtils.isExecutableInUserPath("mummerplot") : - self._logAndRaise("ERROR: mummerplot must be in your path") - self.checkOptions() - - ref="" - if self._refFileName != "": - ref = "-R %s" % self._refFileName - - query="" - if self._queryFileName != "": - query = "-Q %s" % self._queryFileName - - fat = "" - if self._fat: - fat = "--fat" - - filter = "" - if self._filter: - filter = "-f" - - prefix = "" - if self._prefix is not None: - prefix = "--prefix=%s" %(self._prefix) - - cmd = "mummerplot %s %s %s %s %s %s --png" % (self._inputFileName, prefix, ref, query, fat, filter) - self._log.debug("Running mummerplot with following commands : %s" %cmd) - cmd = cmd.split() - process = subprocess.Popen(cmd) - process.wait() - - self.clean() - return process.returncode - -if __name__ == "__main__": - iLaunchNucmer = LaunchMummerPlot() - iLaunchNucmer.setAttributesFromCmdLine() - iLaunchNucmer.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchNucmer.py --- a/commons/launcher/LaunchNucmer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,158 +0,0 @@ -#! /usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.checker.CheckerUtils import CheckerUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess -from commons.core.LoggerFactory import LoggerFactory -import os - -LOG_DEPTH = "repet.tools" - -class LaunchNucmer(object): - - def __init__(self,queryFileName="", refFileName ="", prefix = None, genCoords=False, showCoords = False, mum=False, maxGaps=90, minMatch=20, nooptimize=False,mincluster=65, minIdentity=50, minLength=100, verbosity=0): - self._queryFileName = queryFileName - self._refFileName = refFileName - self._prefix = prefix - self._genCoords = genCoords - self._showCoords = showCoords - self._mum = mum - self._maxgaps = maxGaps - self._minMatch = minMatch - self._nooptimize = nooptimize - self._mincluster = mincluster - self._minIdentity = minIdentity - self._minLength = minLength - self.verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity) - - def setMincluster(self, value): - self._mincluster = value - def getMincluster(self): - return self._mincluster - - mincluster = property(getMincluster, setMincluster) - - def setAttributesFromCmdLine(self): - description = "LaunchNucmer runs the Nucmer program (part of the mummer package) ." - parser = RepetOptionParser(description = description) - parser.add_option("-q", "--query", dest="queryFileName", default = "", action="store", type="string", help="input query file [compulsory] [format: fasta]") - parser.add_option("-r", "--ref", dest="refFileName", default = "", action="store", type="string", help="input ref file [compulsory] [format: fasta]") - parser.add_option("-p", "--prefix", dest="prefix", default = None, action="store", type="string", help="prefix name [optional]") - parser.add_option("-o","--gencoords", dest="genCoords",action="store_true", help="generate coords file with minimal option (show-coords -r) [optional] ") - parser.add_option("-s","--showcoords", dest="showCoords",action="store_true", help="generate coords file with: show-coords -r -c -l -d -I 50 -L 100 -T [optional] ") - parser.add_option("-m", "--mum", dest="mum", action="store_true", help="Use anchor matches that are unique in both the reference and query [optional] ") - parser.add_option("-g", "--maxgaps", dest="maxgaps", default = 90, action="store", type="int", help="Maximum gap between two adjacent matches in a cluster (default 90) [optional] ") - parser.add_option("-l", "--minmatch", dest="minMatch", default = 20, action="store", type="int", help="Minimum length of an maximal exact match (default 20) [optional] ") - parser.add_option("-n", "--nooptimize", dest="nooptimize", action="store_true", help="nooptimize (default --optimize) [optional] ") - parser.add_option("-j", "--mincluster", dest="mincluster", default = 65, action="store", type="int", help="Minimum length of a cluster of matches (default 65) [optional] ") - - parser.add_option("-i", "--minIdentity", dest="minIdentity", default = 50, action="store", type="int", help="Minimum identity for show_coords (default 50) [optional] ") - parser.add_option("-u", "--minLength", dest="minLength", default = 100, action="store", type="int", help="Minimum alignment length for show_coords (default 100) [optional] ") - parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ") - - (self._options, args) = parser.parse_args() - self._setAttributesFromOptions(self._options) - - def _setAttributesFromOptions(self, options): - self._queryFileName = options.queryFileName - self._refFileName = options.refFileName - self._prefix = options.prefix - self._genCoords = options.genCoords - self._showCoords = options.showCoords - self._mum = options.mum - self._maxgaps = options.maxgaps - self._minMatch = options.minMatch - self._nooptimize = options.nooptimize - self._mincluster = options.mincluster - - self._minIdentity = options.minIdentity - self._minLength = options.minLength - - self.verbosity = options.verbosity - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def checkOptions(self): - if self._queryFileName != "": - if not FileUtils.isRessourceExists(self._queryFileName): - self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName) - else: - self._logAndRaise("ERROR: No specified --query option!") - - if self._refFileName != "": - if not FileUtils.isRessourceExists(self._refFileName): - self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName) - else: - self._logAndRaise("ERROR: No specified --ref option!") - - def run(self): - LoggerFactory.setLevel(self._log, self.verbosity) - if not CheckerUtils.isExecutableInUserPath("nucmer") : - self._logAndRaise("ERROR: nucmer must be in your path") - self.checkOptions() - - genCoords = "" - if self._genCoords: - genCoords = "-o" - mum = "" - if self._mum: - mum = "--mum" - nooptimize = "--optimize" - if self._nooptimize: - nooptimize = "--nooptimize" - prefix = "" - if self._prefix is not None: - prefix = "--prefix=%s" %(self._prefix) - cmd = "nucmer %s %s %s %s %s -g=%d -l=%d %s -c=%d" % (self._refFileName,self._queryFileName, prefix, genCoords, mum, self._maxgaps, self._minMatch, nooptimize, self._mincluster) - self._log.debug("Running nucmer with following commands : %s" %cmd) - cmd = cmd.split() - process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - process.wait() - - if self._showCoords: - #use of os.system because redirect on process is broken in python < 3.0 - cmd = "show-coords -r -c -l -d -I %d -L %d -T %s.delta > %s.coords" % (self._minIdentity, self._minLength, self._prefix, self._prefix) - self._log.debug("Running show-coords with following commands : %s" %cmd) - os.system(cmd) - - - return process.returncode - -if __name__ == "__main__": - iLaunchNucmer = LaunchNucmer() - iLaunchNucmer.setAttributesFromCmdLine() - iLaunchNucmer.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchPhyML.py --- a/commons/launcher/LaunchPhyML.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,177 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders -import subprocess -import os -from commons.core.seq.Bioseq import Bioseq -import shutil - -LOG_DEPTH = "repet.core.launchers" - - - -class LaunchPhyML(object): - """ - Launch 'PhyML' - """ - def __init__(self, inputFileName="", outFileName="",dataType= "nt", interleavedFormat= True, nbDataSets=1, nbBootDataSets=0, substModel="HKY85", ratioTsTv=4.0, propInvSites= 0.0, nbCat=1, gammaParam=1.0, startTree="BIONJ", paramOptimisation = "tlr", clean=False, verbosity=3 ): - self.inputFileName = inputFileName - self.outFileName=outFileName - self.dataType = dataType #"nt or aa" - self._setSeqFormat(interleavedFormat) #if False -q" - self.nbDataSets = nbDataSets - self.nbBootDataSets = nbBootDataSets - self.substModel = substModel - self.ratioTsTv = ratioTsTv - self.propInvSites = propInvSites # propInvSites="e" replaced by 0.0; should be in [0-1] - self.nbCat = nbCat # Number of categories less than four or higher than eight are not recommended. - self.gammaParam = gammaParam - self.startTree = startTree #by default is BIONJ used reformatedInputFileName+"_phyml_tree.txt" instead - self.paramOptimisation = paramOptimisation # used instead of self.optTopology="y", self.optBranchRate="y" - #This option focuses on specific parameter optimisation. - #tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised. - #tl : tree topology and branch length are optimised. - #lr : branch length and rate parameters are optimised. - #l : branch length are optimised. - #r : rate parameters are optimised. - #n : no parameter is optimised. - - self._clean = clean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def _setSeqFormat(self, interleavedFormat): - if not (interleavedFormat) : - self.seqFormat = " -q" - else : - self.seqFormat = "" - - def setAttributesFromCmdLine(self): - description = "usage: LaunchPhyML.py [ options ]" - epilog = "\n -h: this help\n" - epilog += "\t -i: name of the input file (refseq is first, format='fasta')" - epilog += "\n\t" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-i", "--fasta", dest = "inputFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: .out]", default = "") - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.inputFileName = options.inputFileName - self.setOutFileName = options.outFileName - self._verbosity = options.verbosity - - def _checkOptions(self): - if self.inputFileName == "": - self._logAndRaise("ERROR: Missing input file name") - - if self.outFileName == "": - self.outFileName = "%s_phyml.newick" % (self.inputFileName) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def _shortenHeaders(self): - self.csh = ChangeSequenceHeaders() - self.csh.setInputFile(self.inputFileName) - self.csh.setFormat("fasta") - self.csh.setStep(1) - self.csh.setPrefix("seq") - self.csh.setLinkFile(self.inputFileName+".shortHlink") - self.csh.setOutputFile(self.inputFileName+".shortH") - self.csh.setVerbosityLevel(self._verbosity-1) - self.csh.run() - self.shortInputFileName = self.inputFileName+".shortH" - - def _renameHeaders(self): - self.csh.setInputFile(self.phyml_tree) - self.csh.setFormat("newick") - self.csh.setStep(2) - self.csh.setLinkFile(self.inputFileName+".shortHlink" ) - self.csh.setOutputFile(self.outFileName) - self.csh.setVerbosityLevel(self._verbosity-1) - self.csh.run() - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START LaunchPhyML") - self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName)) - - inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName)) - if not os.path.exists(inputFileName): - os.symlink(self.inputFileName, inputFileName) - self.inputFileName = inputFileName - - self._shortenHeaders() - - cmd = "sreformat phylip %s" % (self.shortInputFileName) - - with open (self.reformatedInputFileName, "w") as fPhylip : - - process = subprocess.Popen(cmd.split(' '), stdout= fPhylip , stderr=subprocess.PIPE) - self._log.debug("Running : %s" % cmd) - output = process.communicate() - self._log.debug("Output:\n%s" % output[0]) - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - - self.reformatedInputFileName = "%s.phylip" % self.shortInputFileName - self.phyml_tree = "%s_phyml_tree.txt" %self.reformatedInputFileName - cpyPhyml_tree = "%s_cpy" %self.phyml_tree - shutil.copyfile(self.phyml_tree,cpyPhyml_tree) - - cmd = "phyml -i %s -d %s%s -n %d -b %d -m %s -t %f -v %f -c %d -a %f -u %s -o %s" % (self.reformatedInputFileName, self.dataType, self.seqFormat, self.nbDataSets,self.nbBootDataSets,self.substModel, self.ratioTsTv, self.propInvSites,self.nbCat,self.gammaParam, cpyPhyml_tree , self.paramOptimisation ) - print cmd - process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE) - self._log.debug("Running : %s" % cmd) - output = process.communicate() - self._log.debug("Output:\n%s" % output[0]) - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - - self._renameHeaders() - - if self._clean: - for f in [ self.shortInputFileName, self.inputFileName+".shortHlink", self.inputFileName+".shortH.phylip",self.inputFileName+".shortH.phylip_phyml_lk.txt", self.phyml_tree ]: - os.remove(f) - os.system( "mv %s.phylip_phyml_stat.txt %s_phyml.txt" % ( self.shortInputFileName, self.inputFileName ) ) - - self._log.info("Finished running LaunchPhyML") - - diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchPromer.py --- a/commons/launcher/LaunchPromer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,147 +0,0 @@ -#! /usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.checker.CheckerUtils import CheckerUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess -from commons.core.LoggerFactory import LoggerFactory -import os - -LOG_DEPTH = "repet.tools" - -class LaunchPromer(object): - - def __init__(self,queryFileName="", refFileName ="", prefix = None, genCoords=False, showCoords = False, mum=False, maxGaps=30, minMatch=6, nooptimize=False,mincluster=20, verbosity=0): - self._queryFileName = queryFileName - self._refFileName = refFileName - self._prefix = prefix - self._genCoords = genCoords - self._showCoords = showCoords - self._mum = mum - self._maxgaps = maxGaps - self._minMatch = minMatch - self._nooptimize = nooptimize - self._mincluster = mincluster - self.verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity) - - def setMincluster(self, value): - self._mincluster = value - def getMincluster(self): - return self._mincluster - - mincluster = property(getMincluster, setMincluster) - - def setAttributesFromCmdLine(self): - description = "LaunchPromer runs the Promer program (part of the mummer package) ." - parser = RepetOptionParser(description = description) - parser.add_option("-q", "--query", dest="queryFileName", default = "", action="store", type="string", help="input query file [compulsory] [format: fasta]") - parser.add_option("-r", "--ref", dest="refFileName", default = "", action="store", type="string", help="input ref file [compulsory] [format: fasta]") - parser.add_option("-p", "--prefix", dest="prefix", default = None, action="store", type="string", help="prefix name [optional]") - parser.add_option("-o","--gencoords", dest="genCoords",action="store_true", help="generate coords file with minimal option (show-coords -r) [optional] ") - parser.add_option("-s","--showcoords", dest="showCoords",action="store_true", help="generate coords file with: show-coords -r -c -l -d -I 50 -L 100 -T [optional] ") - parser.add_option("-m", "--mum", dest="mum", action="store_true", help="Use anchor matches that are unique in both the reference and query [optional] ") - parser.add_option("-g", "--maxgaps", dest="maxgaps", default = 30, action="store", type="int", help="Maximum gap between two adjacent matches in a cluster (default 30) [optional] ") - parser.add_option("-l", "--minmatch", dest="minMatch", default = 6, action="store", type="int", help="Minimum length of an maximal exact match (default 6) [optional] ") - parser.add_option("-n", "--nooptimize", dest="nooptimize", action="store_true", help="nooptimize (default --optimize) [optional] ") - parser.add_option("-j", "--mincluster", dest="mincluster", default = 20, action="store", type="int", help="Minimum length of a cluster of matches (default 20) [optional] ") - parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ") - - (self._options, args) = parser.parse_args() - self._setAttributesFromOptions(self._options) - - def _setAttributesFromOptions(self, options): - self._queryFileName = options.queryFileName - self._refFileName = options.refFileName - self._prefix = options.prefix - self._genCoords = options.genCoords - self._showCoords = options.showCoords - self._mum = options.mum - self._maxgaps = options.maxgaps - self._minMatch = options.minMatch - self._nooptimize = options.nooptimize - self._mincluster = options.mincluster - self.verbosity = options.verbosity - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def checkOptions(self): - if self._queryFileName != "": - if not FileUtils.isRessourceExists(self._queryFileName): - self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName) - else: - self._logAndRaise("ERROR: No specified --query option!") - - if self._refFileName != "": - if not FileUtils.isRessourceExists(self._refFileName): - self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName) - else: - self._logAndRaise("ERROR: No specified --ref option!") - - def run(self): - if not CheckerUtils.isExecutableInUserPath("promer") : - self._logAndRaise("ERROR: promer must be in your path") - self.checkOptions() - - genCoords = "" - if self._genCoords: - genCoords = "-o" - mum = "" - if self._mum: - mum = "--mum" - nooptimize = "--optimize" - if self._nooptimize: - nooptimize = "--nooptimize" - prefix = "" - if self._prefix is not None: - prefix = "--prefix=%s" %(self._prefix) - - cmd = "promer %s %s %s %s %s -g=%d -l=%d %s -c=%d" % (self._refFileName,self._queryFileName, prefix, genCoords, mum, self._maxgaps, self._minMatch, nooptimize, self._mincluster) - self._log.debug("Running promer with following commands : %s" %cmd) - cmd = cmd.split() - process = subprocess.Popen(cmd) - process.wait() - - if self._showCoords: - #use of os.system because redirect on process is broken in python < 3.0 - cmd = "show-coords -r -c -l -d -I 50 -L 100 -T %s.delta > %s.coords" % (self._prefix, self._prefix) - os.system(cmd) - - return process.returncode - -if __name__ == "__main__": - iLaunchPromer = LaunchPromer() - iLaunchPromer.setAttributesFromCmdLine() - iLaunchPromer.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchRefAlign.py --- a/commons/launcher/LaunchRefAlign.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,208 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.ConfigChecker import ConfigRules -from commons.core.checker.ConfigChecker import ConfigChecker -import subprocess -import os -from commons.core.seq.Bioseq import Bioseq - -LOG_DEPTH = "repet.core.launchers" - -from commons.core.seq.BioseqDB import BioseqDB -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -class LaunchRefAlign(object): - """ - Launch 'refalign' to build a master-slave multiple sequence alignment. - """ - def __init__(self, inputFileName="", outFileName="", gapSize=10, match=10, mismatch=8, gapOpen=16, gapExtend=4, refseqName="", keepRefseq =False, verbosity=3 ): - self.inputFileName = inputFileName - self.outFileName=outFileName - self.gapSize = gapSize - self.match = match - self.mismatch = mismatch - self.gapOpen = gapOpen - self.gapExtend = gapExtend - self.gapExtend = gapExtend - self.refseqName = refseqName - self.keepRefseq = keepRefseq - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "usage: LaunchRefalign.py [ options ]" - epilog = "\n -h: this help\n" - epilog += "\t -i: name of the input file (refseq is first, format='fasta')" - epilog += "\t -r: keep the reference sequence" - epilog += "\t -o: name of the output file (default=inFileName+'.fa_aln')" - epilog += "\t -v: verbosity (default=0)" - epilog += "\n\t" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-i", "--fasta", dest = "inputFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: .out]", default = "") - parser.add_option("-r", "--keepRefseq", dest = "keepRefseq", action = "store_true", help = "keep reference sequence [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.inputFileName = options.inputFileName - self.setOutFileName = options.outFileName - self.keepRefseq = options.keepRefseq - self._verbosity = options.verbosity - - def _checkOptions(self): - if self.inputFileName == "": - self._logAndRaise("ERROR: Missing input file name") - - if self.outFileName == "": - self.outFileName = "%s.fa_aln" % (self.inputFileName) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def _prepareRefAlign(self): - self.shortInputFileName = self.inputFileName+".shortH" - self.refFileName= self.shortInputFileName + ".ref" - self.cpyFileName=self.shortInputFileName + ".cpy" - - file_db = open(self.shortInputFileName) - file_ref = open(self.refFileName,"w") - file_cpy = open(self.cpyFileName,"w") - - self._numseq=0 - while 1: - seq=Bioseq() - seq.read(file_db) - if seq.sequence==None: - break - self._numseq+=1 - if self._numseq==1: - seq.write(file_ref) - else: - seq.write(file_cpy) - file_db.close() - file_ref.close() - file_cpy.close() - - def _shortenHeaders(self): - self.csh = ChangeSequenceHeaders() - self.csh.setInputFile(self.inputFileName) - self.csh.setFormat("fasta") - self.csh.setStep(1) - self.csh.setPrefix("seq") - self.csh.setLinkFile(self.inputFileName+".shortHlink") - self.csh.setOutputFile(self.inputFileName+".shortH") - self.csh.setVerbosityLevel(self._verbosity-1) - self.csh.run() - - bsDB = BioseqDB(self.inputFileName+".shortH") - bsDB.upCase() - bsDB.save(self.inputFileName+".shortHtmp") - del bsDB - os.rename(self.inputFileName+".shortHtmp", self.inputFileName+".shortH") - - def _renameHeaders(self): - self.csh.setInputFile(self.inputFileName+".shortH.fa_aln") - self.csh.setFormat("fasta") - self.csh.setStep(2) - self.csh.setLinkFile(self.inputFileName+".shortHlink" ) - self.csh.setOutputFile(self.outFileName) - self.csh.setVerbosityLevel(self._verbosity-1) - self.csh.run() - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START LaunchRefAlign") - self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName)) - - inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName)) - if not os.path.exists(inputFileName): - os.symlink(self.inputFileName, inputFileName) - self.inputFileName = inputFileName - - self._shortenHeaders() - if self.keepRefseq: - self.refseqName="seq1" - self._prepareRefAlign() - - if self._numseq > 1: - cmd = "refalign %s %s -m %d -l %d -d %d -g %d -e %d" % (self.refFileName, self.cpyFileName, self.match, self.gapSize, self.mismatch, self.gapOpen, self.gapExtend) - - process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE) - self._log.debug("Running : %s" % cmd) - output = process.communicate() - self._log.debug("Output:\n%s" % output[0]) - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - refseqNameParam = "" - if self.refseqName != "": - refseqNameParam = "-r %s " % (self.refseqName) - outFileName = self.inputFileName+".shortH.fa_aln" - #self.cpyFileName = os.path.join(os.getcwd(),os.path.basename(self.cpyFileName)) - - self._log.info("Copy file path %s " % self.cpyFileName) - print("Copy file path %s " % self.cpyFileName) - cmd = "refalign2fasta.py -i %s.aligner %s-g d -o %s -v 1" % (self.cpyFileName, refseqNameParam, outFileName) - self._log.debug("Running : %s" % cmd) - process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE) - output = process.communicate() - self._log.debug("Output:\n%s" % output[0]) - - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - - cmd = "rm -f "+ self.refFileName + " " + self.cpyFileName + " " + self.cpyFileName + ".aligner " + self.cpyFileName + ".oriented " + self.cpyFileName + ".refalign.stat" - os.system(cmd) - - else: - self._logAndRaise("Only one sequence available") - cmd = "echo empty" - - self._renameHeaders() - - for fileName in [self.inputFileName + ".shortH", self.inputFileName + ".shortHlink", self.inputFileName + ".shortH.fa_aln"]: - os.remove(fileName) - self._log.info("END LaunchRefAlign") - return 0 - - -if __name__ == "__main__": - iLaunchRefAlign = LaunchRefAlign() - iLaunchRefAlign.setAttributesFromCmdLine() - iLaunchRefAlign.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchRefalign_old.py --- a/commons/launcher/LaunchRefalign_old.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt - -import pyRepet.launcher.programLauncher -from commons.core.seq.BioseqDB import BioseqDB -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -def help(): - print - print "usage: launchRefalign.py [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (refseq is first, format='fasta')" - print " -r: keep the reference sequence" - print " -o: name of the output file (default=inFileName+'.fa_aln')" - print " -v: verbose (default=0)" - print - - -def main(): - """ - Launch 'refalign' to build a master-slave multiple sequence alignment. - """ - inFileName = "" - keepRefseq = False - outFileName = "" - verbose = 0 - try: - opts,args=getopt.getopt(sys.argv[1:],"hi:ro:v:") - except getopt.GetoptError, err: - print str(err); help(); sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-r": - keepRefseq = True - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - if inFileName == "": - print "ERROR: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if verbose > 0: - print "build a multiple alignment from '%s'..." % ( inFileName ) - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s.fa_aln" % ( inFileName ) - - csh = ChangeSequenceHeaders() - csh.setInputFile( inFileName ) - csh.setFormat( "fasta" ) - csh.setStep( 1 ) - csh.setPrefix( "seq" ) - csh.setLinkFile( inFileName+".shortHlink" ) - csh.setOutputFile( inFileName+".shortH" ) - csh.setVerbosityLevel( verbose - 1 ) - csh.run() - - bsDB = BioseqDB( inFileName+".shortH" ) - bsDB.upCase() - bsDB.save( inFileName+".shortHtmp" ) - del bsDB - os.rename( inFileName+".shortHtmp", inFileName+".shortH" ) - - pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" ) - if keepRefseq: - pL.launchRefalign( outFileName=inFileName+".shortH.fa_aln", refseqName="seq1", verbose=verbose ) - else: - pL.launchRefalign( outFileName=inFileName+".shortH.fa_aln", verbose=verbose ) - - csh.setInputFile( inFileName+".shortH.fa_aln" ) - csh.setFormat( "fasta" ) - csh.setStep( 2 ) - csh.setLinkFile( inFileName+".shortHlink" ) - csh.setOutputFile( outFileName ) - csh.setVerbosityLevel( verbose - 1 ) - csh.run() - - for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.fa_aln" ]: - os.remove( f ) - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchRepeatMasker.py --- a/commons/launcher/LaunchRepeatMasker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#! /usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.checker.CheckerUtils import CheckerUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess - -class LaunchRepeatMasker(object): - - def __init__(self,queryFileName="", libFileName ="",sensitivity="", engine="wu", cutOff=225, outputDir = ".",verbosity=0): - self._queryFileName = queryFileName - self._libFileName = libFileName - self._engine = engine - self._sensitivity = sensitivity - self._cutOff = cutOff - self._outputDir = outputDir - self._verbosity = verbosity - - def setAttributesFromCmdLine(self): - description = "LaunchRepeatMasker runs the RepeatMasker program ." - parser = RepetOptionParser(description = description) - parser.add_option("-q", "--query", dest="queryFileName", default = None, action="store", type="string", help="input query file [compulsory] [format: fasta]") - parser.add_option("-l", "--libFileName", dest="libFileName", default = None, action="store", type="string", help="custom library [optional]") - parser.add_option("-n", "--outputDir", dest="outputDir", default=".", action="store", type="string", help="outputDir (default : current directory) [optional] ") - parser.add_option("-c", "--cutOff", dest="cutOff", default=225, action="store", type="int", help="Sets cutoff score for masking repeats when using -lib (default 225) [optional] ") - parser.add_option("-e", "--engine", dest="engine", default = "wu", action="store", type="string", help="engine [optional] ") - parser.add_option("-u", "--sensitivity", dest="sensitivity", default = "", action="store", type="string", help="sensitivity can be s, q, qq[optional] ") - parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ") - - (options, args) = parser.parse_args() - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self._queryFileName = options.queryFileName - self._libFileName = options.libFileName - self._outputDir = options.outputDir - self._engine = options.engine - self._sensitivity = options.sensitivity - self._cutOff = options.cutOff - self._verbosity = options.verbosity - - def checkOptions(self): - if self._queryFileName != "": - if not FileUtils.isRessourceExists(self._queryFileName): - raise Exception("ERROR: Query file: %s does not exist!" % self._queryFileName) - else: - raise Exception("ERROR: No specified --query option!") - - def run(self): - if not CheckerUtils.isExecutableInUserPath("RepeatMasker") : - print "ERROR: RepeatMasker must be in your path" - else: - self.checkOptions() - - engine = "" - if self._engine == "wu": - engine = "-e wublast" - elif self._engine == "cm": - engine = "-e crossmatch" - sensitivity = "" - if self._sensitivity: - sensitivity = "-%s" % self._sensitivity - libFileName = "" - if self._libFileName != "": - libFileName = "-lib %s" % self._libFileName - - cmd = "RepeatMasker %s -dir %s -pa 1 -gccalc -no_is -nolow %s %s %s" % (self._queryFileName,self._outputDir,engine,sensitivity,libFileName) - cmd = cmd.split() - - if self._verbosity>0: - print("Running RepeatMasker with following commands : %s" %cmd) - - process = subprocess.Popen(cmd, stdout=subprocess.PIPE,stderr = subprocess.PIPE) -# process.wait() - output= process.communicate() - if self._verbosity>0: - print("".join(output)) - return process.returncode - -if __name__ == "__main__": - iLaunchRepeatMasker = LaunchRepeatMasker() - iLaunchRepeatMasker.setAttributesFromCmdLine() - iLaunchRepeatMasker.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchTRF.py --- a/commons/launcher/LaunchTRF.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,155 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.ConfigChecker import ConfigRules -from commons.core.checker.ConfigChecker import ConfigChecker -import subprocess -import glob -import os - -LOG_DEPTH = "repet.launchers" - -class LaunchTRF(object): - - def __init__(self, inFileName = "", outFileName = "", maxPeriod=15, doClean = False, verbosity = 0): - self.inFileName = inFileName - self.setOutFileName(outFileName) - self.maxPeriod=maxPeriod - self._doClean = doClean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "Launch TRF to detect micro-satellites in sequences." - epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0" - epilog += "\n\t" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-i", "--in", dest = "inFileName", action = "store", type = "string", help = "input file name [compulsory] [format: fasta]", default = "") - parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: .TRF.set]", default = "") - parser.add_option("-m", "--maxPeriod", dest = "maxPeriod", action = "store", type = "int", help = " maximum period size to report [default: 15]", default = 15) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setInFileName(options.inFileName) - self.setOutFileName(options.outFileName) - self.maxPeriod = options.maxPeriod - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def setInFileName(self, inFileName): - self.inFileName = inFileName - - def setOutFileName(self, outFileName): - if outFileName == "": - self._outFileName = "%s.TRF.set" % self.inFileName - else: - self._outFileName = outFileName - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self.inFileName == "": - self._logAndRaise("ERROR: Missing input file name") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - - def _launchTRF(self): - cmd = "trf %s 2 3 5 80 10 20 %d -h -d" % (self.inFileName, self.maxPeriod) - self._log.debug("Running : %s" % cmd) - process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE) - output = process.communicate() - self._log.debug("Output:\n%s" % output[0]) - - def _parseTRF(self): - self._log.debug("Parsing TRF output") - with open( "%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod),'r') as inFile: - with open(self._outFileName,'w') as outFile: - nbPatterns = 0 - nbInSeq = 0 - for line in inFile.readlines(): - if line == "": - break - data = line.split(" ") - if len(data) > 1 and "Sequence:" in data[0]: - nbInSeq += 1 - seqName = data[1][:-1] - if len(data) < 14: - continue - nbPatterns += 1 - consensus = data[13] - copyNb = int( float(data[3]) + 0.5 ) - start = data[0] - end = data[1] - outFile.write( "%i\t(%s)%i\t%s\t%s\t%s\n" % ( nbPatterns, consensus, copyNb, seqName, start, end ) ) - self._log.debug("Finished Parsing TRF output") - - def _clean(self): - try: - os.remove("%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod)) - except:pass - - - def run(self): - """ - Launch TRF to detect micro-satellites in sequences. - """ - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START Launch") - self._log.debug("Input file name: %s" % self.inFileName) - - self._launchTRF() - self._parseTRF() - - if self._doClean: - self._log.warning("Files will be cleaned") - self._clean() - self._log.info("END Launch") - -if __name__ == "__main__": - iLaunchTRF = LaunchTRF() - iLaunchTRF.setAttributesFromCmdLine() - iLaunchTRF.run() - diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/LaunchTallymer.py --- a/commons/launcher/LaunchTallymer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,328 +0,0 @@ -#!/usr/bin/env python - -""" -Launch Tallymer's sub programs, generate map file, and convert output to gff and wig, as well as visual (RPlot) data -""" - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import shutil -import subprocess -import time -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.LoggerFactory import LoggerFactory -from SMART.Java.Python.convertTranscriptFile import ConvertTranscriptFile -from commons.core.seq.BioseqUtils import BioseqUtils -from commons.core.seq.BioseqDB import BioseqDB -from Tallymer_pipe.PlotBenchMarkGFFFiles import PlotBenchMarkGFFFiles - -LOG_DEPTH = "repet.tools" - - -class LaunchTallymer(object): - """ - Launch Tallymer's sub programs, generate map file, and convert output to - gff and wig, as well as visual (RPlot) data - """ - - _lValidFormats = ["gff", "gff3", "wig", "bed", "map"] - - def __init__(self, inputFasta="", indexationFasta=None, merSize=20, minOccs=4, outputFormats="gff", nLargestScaffoldsToPlot=0, clean=False, verbosity=0): - self.inputFasta = inputFasta - self.indexationFasta = indexationFasta if indexationFasta != None else inputFasta - self.merSize = merSize - self.minOccs = minOccs - self.outputFormats = outputFormats - self.nLargestScaffoldsToPlot = nLargestScaffoldsToPlot - self.doClean = clean - self.verbosity = verbosity - - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity) - self._workdir = os.path.join(os.getcwd(), "launchTallymer_%s" % time.strftime("%Y%m%d%H%M%S")) - self._tmpSearchFileName = None - self._tmpMapFileName = None - self._tmpStatFileName = None - self._tmpPngFileName = None - self._plot_data = {} - self._plot_data2 = {} - - def setAttributesFromCmdLine(self): - description = "Generates stats from the results of the tallymer search ." - parser = RepetOptionParser(description=description) - parser.add_option("-i", "--inputFasta", dest="inputFasta", default = "", action="store", type="string", help="input fasta file [compulsory] [format: fasta]") - parser.add_option("-u", "--indexationFasta", dest="indexationFasta", default = "", action="store", type="string", help="input indexation fasta file used to generate kmer index (defaults to input fasta)[optional] [format: fasta]") - parser.add_option("-s", "--merSize", dest="merSize", default = 20, action="store", type="int", help="input merSize [optional][default:20]") - parser.add_option("-m", "--minOccs", dest="minOccs", default = 4, action="store", type="int", help="input minimal kmer occurence count [default:4]") - parser.add_option("-f", "--outputFormats", dest="outputFormats", default = "gff", action="store", type="string", help="comma separated list of output file formats (can be %s) [optional] [default:gff]" % ", ".join(self._lValidFormats)) - parser.add_option("-n", "--nLargestScaffoldsToPlot",default = 0, type="int", action="store", dest = "nLargestScaffoldsToPlot", help = "generate graph of Kmer repartition along the input sequence for the n biggest scaffolds") - parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true") - parser.add_option("-v", "--verbosity", dest="verbosity", default = 1, action="store", type="int", help="verbosity [optional] ") - options, args = parser.parse_args() - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.inputFasta = options.inputFasta - self.indexationFasta = options.indexationFasta if options.indexationFasta != "" else options.inputFasta - self.merSize = options.merSize - self.minOccs = options.minOccs - self.outputFormats = options.outputFormats - self.nLargestScaffoldsToPlot = options.nLargestScaffoldsToPlot - self.doClean = options.clean - self.verbosity = options.verbosity - - def _checkOptions(self): - if self.inputFasta == "": - self._logAndRaise("Error: missing input fasta file") - if self.merSize < 1: - self._logAndRaise("Error: invalid kmer size '%i'; must be a positive integer" % self.merSize) - - self.outputFormats = self.outputFormats.lower().split(',') - sOutFormats = set(self.outputFormats) - sValidFormats = set(self._lValidFormats) - lInvalidFormats = list(sOutFormats - sValidFormats) - self.outputFormats = list(sValidFormats.intersection(sOutFormats)) - if lInvalidFormats: - self._log.warning("Warning: ignoring invalid formats: <%s>" % " ".join(lInvalidFormats)) - if not self.outputFormats: - self._logAndRaise("Error: no valid output formats specified") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def clean(self): - try: - shutil.rmtree(self._workdir) - except Exception as inst: - self._log.error(inst) - - def run(self): - LoggerFactory.setLevel(self._log, self.verbosity) - self._checkOptions() - self._log.debug("Input fasta file: %s; K-mer size: %s; Output formats: %s; Cleaning: %s" % (self.inputFasta, self.merSize, str(self.outputFormats), self.doClean)) - try: - os.makedirs(self._workdir) - except:pass - - srcPath = os.path.abspath(self.inputFasta) - dstPath = os.path.join(self._workdir,os.path.basename(self.inputFasta)) - os.symlink(srcPath, dstPath) - - if (self.indexationFasta != self.inputFasta): - srcPath = os.path.abspath(self.indexationFasta) - dstPath = os.path.join(self._workdir,os.path.basename(self.indexationFasta)) - try: - os.symlink(srcPath, dstPath) - except OSError as inst: - pass - - os.chdir(self._workdir) - - if (self.indexationFasta != self.inputFasta): - self.indexationFasta = os.path.basename(self.indexationFasta) - else: - self.indexationFasta = os.path.basename(self.inputFasta) - self.inputFasta = os.path.basename(self.inputFasta) - - self._tmpSearchFileName = "%s.tallymer" % os.path.splitext(os.path.basename(self.inputFasta))[0] - self._tmpMapFileName = "%s_tmp.map" % self._tmpSearchFileName - self._tmpStatFileName = "%s.stat" % self._tmpSearchFileName - self._tmpPngFileName = "%s.png" % self._tmpSearchFileName - - - - - - self._runTallymerSearch() - self._convertTallymerToMap() - self._writeOutputFiles() - - if self.nLargestScaffoldsToPlot > 0: - self._doPlot() - shutil.copy2(self._tmpPngFileName, "../.") - - shutil.copy2(self._tmpStatFileName, "../.") - os.chdir("..") - - if self.doClean: - self.clean() - - def _runTallymerSearch(self): - self._log.info("Starting to run tallymer search of sequence %s " % (self.inputFasta)) - self._indexInputFastaFile() - self._countAndIndexKmersForGivenK() - self._searchKmersListInTallymerIndex() - self._log.info("Finished running tallymer scan of sequence %s " % (self.inputFasta)) - - def _convertTallymerToMap(self): - self._log.info("Starting to run tallymer search to map conversion") - totalNbOcc, dKmer2Occ, self._plot_data, self._plot_data2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(self.inputFasta, self._tmpSearchFileName, self._tmpMapFileName) - self._log.debug("totalNbOcc=%i" % totalNbOcc) - self._writeOccurencesNbAndFrequencyOfKmers(totalNbOcc, dKmer2Occ) - self._log.info("Finished tallymer search to map conversion") - - def _doPlot(self): - iBioseqDB = BioseqDB() - iBioseqDB.load(self.inputFasta) - largest_seqsDb = iBioseqDB.bestLength(self.nLargestScaffoldsToPlot) - - for seq in largest_seqsDb.db: - headerCleaned = seq.header.replace(" ", "_") - shortFastaName = "%s_%s" % (os.path.basename(self.inputFasta),headerCleaned) - data = self._plot_data2[seq.header] - gffPlotter = PlotBenchMarkGFFFiles(yLabel="Number of Kmer Occurences", maxLength=1, title="Kmer repartition along the input sequence: %s; MerSize: %i" % (shortFastaName, self.merSize) ) - gffPlotter.setOutFileName("%s_%s.png" % (self._tmpSearchFileName, headerCleaned)) - gffPlotter._title = "Mers along the input sequence: %s MerSize: %i" % (shortFastaName, self.merSize) - gffPlotter._xLabel = "Coordinates along the input sequence (%s)" % shortFastaName - gffPlotter._rawData = data - gffPlotter.run() - - def _indexInputFastaFile(self): - self._log.debug("index the input fasta file: get an enhanced suffix array.") - cmd = "gt suffixerator -dna -pl -tis -suf -lcp -v -db %s -indexname %s.reads" % (self.indexationFasta, self.indexationFasta) - process = subprocess.Popen(cmd.split(' '),stdout=subprocess.PIPE, stderr=subprocess.PIPE) - self._log.debug("Running suffixerator with following params %s" % cmd) - output = process.communicate() - self._log.debug("Suffixerator Output:\n%s" % output[0]) - if process.returncode != 0: - self._logAndRaise("Error in generating enhanced suffix array in %s" % self.indexationFasta) - - def _countAndIndexKmersForGivenK(self): - self._log.debug("Counting and indexing k-mers for k = %i " % self.merSize) - cmd = "gt tallymer mkindex -mersize %i -minocc %i -indexname %s.tyr-reads -counts -pl -esa %s.reads" % (self.merSize, self.minOccs, self.indexationFasta, self.indexationFasta) - process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE) - self._log.debug("Running tallymer mkindex with following params %s" % cmd) - output = process.communicate() - self._log.debug("Tallymer mkindex Output:\n%s" % output[0]) - if process.returncode != 0: - self._logAndRaise("Error in indexing kmers in %s.reads" % self.indexationFasta) - - def _searchKmersListInTallymerIndex(self): - self._log.debug("Searching list of kmers in tallymer-index ") - cmd = "gt tallymer search -output qseqnum qpos counts sequence -tyr %s.tyr-reads -q %s" % (self.indexationFasta, self.inputFasta) - process = subprocess.Popen(cmd.split(' '),stdout=subprocess.PIPE, stderr=subprocess.PIPE) - self._log.debug("Running tallymer search with following params %s" % cmd) - output = process.communicate() - self._log.debug("Tallymer search Output:\n%s" % output[0]) - if process.returncode != 0: - self._logAndRaise("Error in searching for kmers in %s.tyr-reads" % self.indexationFasta) - tmpOutputFile = open(self._tmpSearchFileName,'w') - tmpOutputFile.write(output[0]) - tmpOutputFile.close() - - def _writeOccurencesNbAndFrequencyOfKmers(self, totalNbOcc, dKmer2Occ): - with open(self._tmpStatFileName, "w") as statFile: - statFile.write("kmer\tocc\tfreq\n") - for kmer in dKmer2Occ.keys(): - statFile.write("%s\t%i\t%.10f\n" % (kmer, dKmer2Occ[kmer], dKmer2Occ[kmer] / float(totalNbOcc))) - - def _writeOutputFiles(self): - for format in self.outputFormats: - self._log.info("Generating %s file" % format) - outputFileName = "%s.tallymer.%s" % (os.path.splitext(self.inputFasta)[0], format) - try: - iConvertTranscriptFile = ConvertTranscriptFile(inputFileName=self._tmpMapFileName, name="Tallymer",\ - inputFormat="map", outputFileName=outputFileName, outputFormat=format,feature= "Match", featurePart="Match-part", verbosity=0) #self.verbosity - iConvertTranscriptFile.run() - except Exception as inst: - self._log.error("Error: %s - Failed to generate %s format ouput, skipping" % (inst, format)) - shutil.copy2(outputFileName, "../.") - - -class ConvertUtils(object): - - def convertTallymerFormatIntoMapFormatAndGenerateData(fastaFileName, searchFileName, mapFileName): - dIndex2NameLengthList = ConvertUtils._createDictOfNameLengthAccordingToSeqOrder(fastaFileName) - plotData = {} - plotData2 = {} - with open(searchFileName, "r") as talFile: - with open(mapFileName, "w") as mapFile: - totalNbOcc = 0 - dKmer2Occ = {} - line = talFile.readline() - while line: - data = line[:-1].split("\t") - name = "%s_%s" % (data[3], data[2]) - nbOccs = int(data[2]) - chrname = dIndex2NameLengthList[int(data[0])][0] - if data[1][0] == "+": - start = int(data[1][1:]) + 1 - end = start + len(data[3]) - elif data[1][0] == "-": - start_revcomp = int(data[1][1:]) - start = dIndex2NameLengthList[int(data[0])][1] - start_revcomp - 1 - end = end - len(data[3]) + 1 - mapLine = "%s\t%s\t%s\t%s\t%i\n" % (name, chrname, start, end, nbOccs) - mapFile.write(mapLine) - - if plotData2.get(chrname,None) is None: - plotData2[chrname] = {} - if plotData2[chrname].get(start, None) is None: - plotData2[chrname][start]=0 - plotData2[chrname][start] += nbOccs - - totalNbOcc += 1 - if dKmer2Occ.has_key(data[3]): - dKmer2Occ[data[3]] += 1 - else: - dKmer2Occ[data[3]] = 1 - plotData[start] = nbOccs - line = talFile.readline() - return totalNbOcc, dKmer2Occ, plotData, plotData2 - - convertTallymerFormatIntoMapFormatAndGenerateData = staticmethod(convertTallymerFormatIntoMapFormatAndGenerateData) - - def _createDictOfNameLengthAccordingToSeqOrder(fastaFileName): - with open(fastaFileName) as fastaFile: - line = fastaFile.readline() - i = 0 - length = 0 - dIndex2Name = {} - while line: - if line[0] == ">": - dIndex2Name[i] = [line[1:-1]] - if i > 0: - dIndex2Name[i - 1].append(length) - length = 0 - i += 1 - else: - length += len(line[:-1]) - line = fastaFile.readline() - dIndex2Name[i - 1].append(length) - return dIndex2Name - - _createDictOfNameLengthAccordingToSeqOrder = staticmethod(_createDictOfNameLengthAccordingToSeqOrder) - -if __name__ == "__main__": - iLaunchTallymer = LaunchTallymer() - iLaunchTallymer.setAttributesFromCmdLine() - iLaunchTallymer.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/MafftClusterLauncher.py --- a/commons/launcher/MafftClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch MafftProgramLauncher on several files in parallel on a cluster. - - -from pyRepet.launcher.AbstractClusterLauncher import * -from commons.launcher.MafftProgramLauncher import MafftProgramLauncher - - -class MafftClusterLauncher( AbstractClusterLauncher ): - """ - Launch Mafft on several files in parallel on a cluster. - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractClusterLauncher.__init__( self ) - AbstractClusterLauncher.setAcronym( self, "Mafft" ) - - self._cmdLineSpecificOptions = "p:" - - self._exeWrapper = "MafftProgramLauncher.py" - self._prgLauncher = None - self._prgLauncher = self.getProgramLauncherInstance() - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -p: parameters for 'mafft' (default='--auto')" - return string - - - def getProgramParameters( self ): - return self._prgLauncher.getProgramParameters() - - - def getProgramLauncherInstance( self ): - if self._prgLauncher == None: - self._prgLauncher = MafftProgramLauncher() - self._prgLauncher.setInputFile( GENERIC_IN_FILE ) - self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) ) - self._prgLauncher.setClean() - self._prgLauncher.setVerbosityLevel( 1 ) - self._prgLauncher.setListFilesToKeep() - self._prgLauncher.setListFilesToRemove() - return self._prgLauncher - - -if __name__ == "__main__": - i = MafftClusterLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/MafftProgramLauncher.py --- a/commons/launcher/MafftProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,188 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch Mafft (multiple alignment). -# -# options: -# -h: this help -# -i: name of the input file (format='fasta') -# -p: parameters for 'mafft' (default='--auto') -# -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln') -# -c: clean -# -v: verbosity level (default=0/1) - - -import os -import sys -import getopt -import exceptions - -from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher -from pyRepet.seq.fastaDB import * -from commons.core.seq.FastaUtils import FastaUtils -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -class MafftProgramLauncher( AbstractProgramLauncher ): - """ - Launch Mafft (multiple alignment). - """ - - - def __init__( self ): - """ - Constructor. - """ - AbstractProgramLauncher.__init__( self ) - self._prgName = "mafft" - self._formatInFile = "fasta" - self._prgParam = "--auto" - self._cmdLineSpecificOptions = "p:o:" - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -p: parameters for '%s' (default='--auto')" % ( self.getProgramName() ) - string += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')" - return string - - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - """ - Set a specific attribute from the command-line arguments. - """ - if o == "-p": - self.setProgramParameters( a ) - elif o == "-o": - self.setOutputFile( a ) - - - def checkSpecificAttributes( self ): - """ - Check the specific attributes before running the program. - """ - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - - - def setWrapperCommandLine( self ): - """ - Set the command-line of the wrapper. - Required for MafftClusterLauncher. - """ - self._wrpCmdLine = self.getWrapperName() - self._wrpCmdLine += " -i %s" % ( self.getInputFile() ) - self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() ) - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - self._wrpCmdLine += " -o %s" % ( self.getOutputFile() ) - if self.getClean(): - self._wrpCmdLine += " -c" - self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - - - def setProgramCommandLine( self ): - """ - Set the command-line of the program. - """ - self._prgCmdLine = self.getProgramName() - self._prgCmdLine += " %s" % ( self.getProgramParameters() ) - if self.getVerbosityLevel() == 0 and "--quiet" not in self._prgCmdLine: - self._prgCmdLine += " --quiet" - self._prgCmdLine += " %s.shortH" % ( self.getInputFile() ) - self._prgCmdLine += " > %s.shortH.fa_aln" % ( self.getInputFile() ) - if self._verbose < 2: - self._prgCmdLine += " 2> /dev/null" - - - def setListFilesToKeep( self ): - """ - Set the list of files to keep. - """ - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - self.appendFileToKeep( self.getOutputFile() ) - - - def setListFilesToRemove( self ): - """ - Set the list of files to remove. - """ - self.appendFileToRemove( "%s.shortH" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.shortH.fa_aln" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.shortHlink" % ( self.getInputFile() ) ) - - - def setSummary( self ): - self._summary = "input file: %s" % ( self.getInputFile() ) - self._summary += "\nparameters: %s" % ( self.getProgramParameters() ) - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - self._summary += "\noutput file: %s" % ( self.getOutputFile() ) - - - def run( self ): - """ - Run the program. - """ - self.start() - - lInitHeaders = FastaUtils.dbHeaders( self.getInputFile(), self.getVerbosityLevel()-1 ) - - csh = ChangeSequenceHeaders() - csh.setInputFile( self.getInputFile() ) - csh.setFormat( "fasta" ) - csh.setStep( 1 ) - csh.setPrefix( "seq" ) - csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) ) - csh.setOutputFile( "%s.shortH" % ( self.getInputFile() ) ) - csh.setVerbosityLevel( self.getVerbosityLevel() - 1 ) - csh.run() - - bsDB = BioseqDB( "%s.shortH" % ( self.getInputFile() ) ) - bsDB.upCase() - bsDB.save( "%s.shortHtmp" % ( self.getInputFile() ) ) - del bsDB - os.rename( "%s.shortHtmp" % ( self.getInputFile() ), - "%s.shortH" % ( self.getInputFile() ) ) - - self.setProgramCommandLine() - cmd = self.getProgramCommandLine() - if self.getVerbosityLevel() > 0: - print "LAUNCH: %s" % ( cmd ) - sys.stdout.flush() - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus ) - print string - sys.exit(1) - - csh.setInputFile( "%s.shortH.fa_aln" % ( self.getInputFile() ) ) - csh.setFormat( "fasta" ) - csh.setStep( 2 ) - csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) ) - csh.setOutputFile( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) ) - csh.setVerbosityLevel( self.getVerbosityLevel() - 1 ) - csh.run() - - absDB = AlignedBioseqDB( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) ) - outFileHandler = open( self.getOutputFile(), "w" ) - for header in lInitHeaders: - bs = absDB.fetch( header ) - bs.upCase() - bs.write( outFileHandler ) - outFileHandler.close() - os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) ) - - self.end() - - -if __name__ == "__main__": - i = MafftProgramLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/MapClusterLauncher.py --- a/commons/launcher/MapClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch MapProgramLauncher.py on several files in parallel on a cluster. - - -import os -import sys -import getopt -import exceptions - -from pyRepet.launcher.AbstractClusterLauncher import * -from commons.launcher.MapProgramLauncher import MapProgramLauncher - - -class MapClusterLauncher( AbstractClusterLauncher ): - """ - Launch Map on several files in parallel on a cluster. - """ - - - def __init__( self ): - """ - Constructor. - """ - AbstractClusterLauncher.__init__( self ) - AbstractClusterLauncher.setAcronym( self, "Map" ) - - self._cmdLineSpecificOptions = "s:m:O:e:" - - self._exeWrapper = "MapProgramLauncher.py" - self._prgLauncher = None - self._prgLauncher = self.getProgramLauncherInstance() - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() ) - string += "\n -m: penalty for a mismatch (default='%i')" % ( self.getMismatchPenalty() ) - string += "\n -O: penalty for a gap openning (default='%i')" % ( self.getGapOpenPenalty() ) - string += "\n -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() ) - return string - - - def getGapSize( self ): - return self._prgLauncher.getGapSize() - - - def getMismatchPenalty( self ): - return self._prgLauncher.getMismatchPenalty() - - - def getGapOpenPenalty( self ): - return self._prgLauncher.getGapOpenPenalty() - - - def getGapExtendPenalty( self ): - return self._prgLauncher.getGapExtendPenalty() - - - def getProgramLauncherInstance( self ): - if self._prgLauncher == None: - self._prgLauncher = MapProgramLauncher() - self._prgLauncher.setInputFile( GENERIC_IN_FILE ) - self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) ) - #TESt de SATannot verifier si clean est a vrai - #self._prgLauncher.setClean() - self._prgLauncher.setVerbosityLevel( 1 ) - self._prgLauncher.setListFilesToKeep() - self._prgLauncher.setListFilesToRemove() - return self._prgLauncher - - -if __name__ == "__main__": - i = MapClusterLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/MapProgramLauncher.py --- a/commons/launcher/MapProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,251 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch Map (multiple alignment). -# -# options: -# -h: this help -# -i: name of the input file (format='fasta') -# -s: size above which a gap is not penalized anymore (default='50') -# -m: penalty for a mismatch (default='-8') -# -O: penalty for a gap opening (default='16') -# -e: penalty for a gap extension (default='4') -# -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln') -# -c: clean -# -v: verbosity level (default=0/1) - - -import sys -import os - -from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher -from commons.core.seq.FastaUtils import FastaUtils -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -class MapProgramLauncher( AbstractProgramLauncher ): - """ - Launch Map (multiple alignment). - """ - - - def __init__( self ): - """ - Constructor. - """ - AbstractProgramLauncher.__init__( self ) - self._prgName = "rpt_map" - self._formatInFile = "fasta" - self._cmdLineSpecificOptions = "s:m:O:e:o:" - self._gapSize = 50 - self._mismatchPenalty = -8 - self._gapOpenPenalty = 16 - self._gapExtendPenalty = 4 - self._outFile = "" - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() ) - string += "\n -m: penalty for a mismatch (default='%i', match=10)" % ( self.getMismatchPenalty() ) - string += "\n -O: penalty for a gap opening (default='%i')" % ( self.getGapOpenPenalty() ) - string += "\n -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() ) - string += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')" - return string - - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - """ - Set a specific attribute from the command-line arguments. - """ - if o == "-s": - self.setGapSize( a ) - elif o == "-m": - self.setMismatchPenalty( a ) - elif o == "-O": - self.setGapOpenPenalty( a ) - elif o == "-e": - self.setGapExtendPenalty( a ) - elif o == "-o": - self.setOutputFile( a ) - - - def setGapSize( self, arg ): - self._gapSize = int(arg) - - - def setMismatchPenalty( self, arg ): - self._mismatchPenalty = int(arg) - - - def setGapOpenPenalty( self, arg ): - self._gapOpenPenalty = int(arg) - - - def setGapExtendPenalty( self, arg ): - self._gapExtendPenalty = int(arg) - - - def getGapSize( self ): - return self._gapSize - - - def getMismatchPenalty( self ): - return self._mismatchPenalty - - - def getGapOpenPenalty( self ): - return self._gapOpenPenalty - - - def getGapExtendPenalty( self ): - return self._gapExtendPenalty - - - def checkSpecificAttributes( self ): - """ - Check the specific attributes before running the program. - """ - if self.getGapSize() <= 0: - string = "ERROR: gap size should be > 0" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getMismatchPenalty() >= 0: - string = "ERROR: mismatch penalty should be < 0" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getGapOpenPenalty() < 0: - string = "ERROR: gap opening penalty should be >= 0" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getGapExtendPenalty() < 0: - string = "ERROR: gap extension penalty should be >= 0" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - - - def setWrapperCommandLine( self ): - """ - Set the command-line of the wrapper. - Required for MapClusterLauncher. - """ - self._wrpCmdLine = self.getWrapperName() - self._wrpCmdLine += " -i %s" % ( self.getInputFile() ) - self._wrpCmdLine += " -s %i" % ( self.getGapSize() ) - self._wrpCmdLine += " -m %i" % ( self.getMismatchPenalty() ) - self._wrpCmdLine += " -O %i" % ( self.getGapOpenPenalty() ) - self._wrpCmdLine += " -e %i" % ( self.getGapExtendPenalty() ) - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - self._wrpCmdLine += " -o %s" % ( self.getOutputFile() ) - if self.getClean(): - self._wrpCmdLine += " -c" - self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - - - def setProgramCommandLine( self ): - """ - Set the command-line of the program. - """ - self._prgCmdLine = self.getProgramName() - self._prgCmdLine += " %s.shortH" % ( self.getInputFile() ) - self._prgCmdLine += " %i" % ( self.getGapSize() ) - self._prgCmdLine += " %i" % ( self.getMismatchPenalty() ) - self._prgCmdLine += " %i" % ( self.getGapOpenPenalty() ) - self._prgCmdLine += " %i" % ( self.getGapExtendPenalty() ) - self._prgCmdLine += " > %s.shortH.fa_aln" % ( self.getInputFile() ) - - - def setListFilesToKeep( self ): - """ - Set the list of files to keep. - """ - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - self.appendFileToKeep( self.getOutputFile() ) - - - def setListFilesToRemove( self ): - """ - Set the list of files to remove. - """ - self.appendFileToRemove( "%s.shortH" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.shortH.fa_aln" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.shortHlink" % ( self.getInputFile() ) ) - - - def setSummary( self ): - self._summary = "input file: %s" % ( self.getInputFile() ) - self._summary += "\ngap size: %i" % ( self.getGapSize() ) - self._summary += "\nmismatch penalty: %i" % ( self.getMismatchPenalty() ) - self._summary += "\ngap openning penalty: %i" % ( self.getGapOpenPenalty() ) - self._summary += "\ngap extension penalty: %i" % ( self.getGapExtendPenalty() ) - if self.getOutputFile() == "": - self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) ) - self._summary += "\noutput file: %s" % ( self.getOutputFile() ) - - - def run( self ): - """ - Run the program. - """ - self.start() - - lInitHeaders = FastaUtils.dbHeaders( self.getInputFile(), self.getVerbosityLevel()-1 ) - - csh = ChangeSequenceHeaders() - csh.setInputFile( self.getInputFile() ) - csh.setFormat( "fasta" ) - csh.setStep( 1 ) - csh.setPrefix( "seq" ) - csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) ) - csh.setOutputFile( "%s.shortH" % ( self.getInputFile() ) ) - csh.setVerbosityLevel( self.getVerbosityLevel() - 1 ) - csh.run() - - self.setProgramCommandLine() - cmd = self.getProgramCommandLine() - if self.getVerbosityLevel() > 0: - print "LAUNCH: %s" % ( cmd ) - sys.stdout.flush() - returnStatus = os.system( cmd ) - if returnStatus != 0: - string = "ERROR: program '%s' returned status '%i'" % ( self.getProgramName(), returnStatus ) - print string - sys.exit(1) - - csh.setInputFile( "%s.shortH.fa_aln" % ( self.getInputFile() ) ) - csh.setFormat( "fasta" ) - csh.setStep( 2 ) - csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) ) - csh.setOutputFile( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) ) - csh.setVerbosityLevel( self.getVerbosityLevel() - 1 ) - csh.run() - - absDB = AlignedBioseqDB( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) ) - outFileHandler = open( self.getOutputFile(), "w" ) - for header in lInitHeaders: - bs = absDB.fetch( header ) - bs.upCase() - bs.write( outFileHandler ) - outFileHandler.close() - if self.getClean(): - os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) ) - - self.end() - - -if __name__ == "__main__": - i = MapProgramLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/NWalignProgramLauncher.py --- a/commons/launcher/NWalignProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,187 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch NWalign (pairwise alignment). -# -# options: -# -h: this help -# -i: name of the input file (queries, format='fasta') -# -s: name of the subject file (format='fasta') -# -p: parameters for 'NWalign' (default='-d 2') -# -o: name of the output file (format='align', default=inFile+'.align') -# -c: clean -# -v: verbosity level (default=0/1) - - -import os -import sys - -from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.core.coord.AlignUtils import AlignUtils - - -class NWalignProgramLauncher( AbstractProgramLauncher ): - """ - Launch NWalign (pairwise alignment). - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractProgramLauncher.__init__( self ) - self._prgName = "NWalign" - self._formatInFile = "fasta" - self._sbjFile = "" - self._prgParam = "" - self._cmdLineSpecificOptions = "s:p:o:" - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: name of the subject file (format='fasta')" - string += "\n -p: parameters for '%s'" % ( self.getProgramName() ) - string += "\n -o: name of the output file (format='align', default=inFile+'.align')" - return string - - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - """ - Set a specific attribute from the command-line arguments. - """ - if o =="-s": - self.setSubjectFile( a ) - elif o == "-p": - self.setProgramParameters( a ) - elif o == "-o": - self.setOutputFile( a ) - - - def setSubjectFile( self, arg ): - self._sbjFile = arg - - - def getSubjectFile( self ): - return self._sbjFile - - - def checkSpecificAttributes( self ): - """ - Check the specific attributes before running the program. - """ - if self._sbjFile == "": - string = "ERROR: missing subject file (-s)" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - - - def setWrapperCommandLine( self ): - """ - Set the command-line of the wrapper. - Required for NWalignClusterLauncher. - """ - self._wrpCmdLine = self.getWrapperName() - self._wrpCmdLine += " -i %s" % ( self.getInputFile() ) - self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() ) - if self.getProgramParameters() != "": - self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() ) - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self._wrpCmdLine += " -o %s" % ( self.getOutputFile() ) - if self.getClean(): - self._wrpCmdLine += " -c" - self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - - - def setProgramCommandLine( self ): - """ - Set the command-line of the program. - """ - self._prgCmdLine = self.getProgramName() - if self.getProgramParameters() != "": - self._prgCmdLine += " %s" % ( self.getProgramParameters() ) - self._prgCmdLine += " -o %s.afa" % ( self.getInputFile() ) - self._prgCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - self._prgCmdLine += " %s" % ( self.getSubjectFile() ) - self._prgCmdLine += " %s" % ( self.getInputFile() ) - - - def setListFilesToKeep( self ): - """ - Set the list of files to keep. - """ - if self.getOutputFile() == "": - self.setOutputFile( "%s.afa" % ( self.getInputFile() ) ) - self.appendFileToKeep( self.getOutputFile() ) - - - def postprocess( self ): - absDB = AlignedBioseqDB( "%s.afa" % ( self.getInputFile() ) ) - lHeaders = absDB.getHeaderList() - queryHeader = lHeaders[0] - subjectHeader = lHeaders[1] - queryLength = absDB.fetch( queryHeader ).getLength() - subjectLength = absDB.fetch( subjectHeader ).getLength() - lAligns = absDB.getAlignList( queryHeader, subjectHeader ) - for i in lAligns: - if "re-oriented" in i.getQueryName(): - i.setQueryName( queryHeader.replace(" re-oriented","") ) - start = i.getQueryStart() - end = i.getQueryEnd() - i.setQueryStart( queryLength - end + 1 ) - i.setQueryEnd( queryLength - start + 1 ) - if "re-oriented" in i.getSubjectName(): - i.setSubjectName( subjectHeader.replace(" re-oriented","") ) - start = i.getSubjectStart() - end = i.getSubjectEnd() - i.setSubjectEnd( subjectLength - end + 1 ) - i.setSubjectStart( subjectLength - start + 1 ) - if not i.isQueryOnDirectStrand(): - i.reverse() - AlignUtils.writeListInFile( lAligns, self.getOutputFile() ) - os.remove( "%s.afa" % ( self.getInputFile() ) ) - - - def setSummary( self ): - self._summary = "input file: %s" % ( self.getInputFile() ) - self._summary += "\nsubject file: %s" % ( self.getSubjectFile() ) - self._summary += "\nparameters: %s" % ( self.getProgramParameters() ) - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self._summary += "\noutput file: %s" % ( self.getOutputFile() ) - - - def run( self ): - """ - Run the program. - """ - self.start() - - self.setProgramCommandLine() - cmd = self.getProgramCommandLine() - if self.getVerbosityLevel() > 0: - print "LAUNCH: %s" % ( cmd ) - sys.stdout.flush() - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus ) - print string - sys.exit(1) - - self.postprocess() - - self.end() - - -if __name__ == "__main__": - i = NWalignProgramLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/RepeatMaskerClusterLauncher.py --- a/commons/launcher/RepeatMaskerClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch RepeatMaskerProgramLauncher on several files in parallel on a cluster. - - -import os -import sys -import getopt -import exceptions - -from pyRepet.launcher.AbstractClusterLauncher import * -from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher - - -class RepeatMaskerClusterLauncher( AbstractClusterLauncher ): - """ - Launch RepeatMasker on several files in parallel on a cluster. - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractClusterLauncher.__init__( self ) - AbstractClusterLauncher.setAcronym( self, "RM" ) - - self._cmdLineSpecificOptions = "s:n:gbl" - - self._exeWrapper = "RepeatMaskerProgramLauncher.py" - self._prgLauncher = RepeatMaskerProgramLauncher() - self._prgLauncher.setInputFile( GENERIC_IN_FILE ) - self._prgLauncher.setOutputFile( GENERIC_IN_FILE ) - self._prgLauncher.setClean() - self._prgLauncher.setVerbosityLevel( 1 ) - self._prgLauncher.setListFilesToKeep() - self._prgLauncher.setListFilesToRemove() - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: name of the subject file (repeats, format='fasta')" - string += "\n -n: nb of processors to use in parallel (default=1)" - string += "\n -g: calculate the GC content" - string += "\n -b: skip bacterial insertion element check" - string += "\n -l: mask low-complexity DNA or simple repeats" - return string - - - def getSubjectFile( self ): - return self._prgLauncher.getSubjectFile() - - - def getNbProcessors( self ): - return self._prgLauncher.getNbProcessors() - - - def getCalculateGCcontent( self ): - return self._prgLauncher.getCalculateGCcontent() - - - def getSkipBacterialIsCheck( self ): - return self._prgLauncher.getSkipBacterialIsCheck() - - - def getMaskSsr( self ): - return self._prgLauncher.getMaskSsr() - - -if __name__ == "__main__": - i = RepeatMaskerClusterLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/RepeatMaskerProgramLauncher.py --- a/commons/launcher/RepeatMaskerProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,286 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch RepeatMasker (pairwise alignment for repeat detection). - - -import os -import sys - -from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher - - -class RepeatMaskerProgramLauncher( AbstractProgramLauncher ): - """ - Launch RepeatMasker (pairwise alignment for repeat detection). - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractProgramLauncher.__init__( self ) - self._prgName = "RepeatMasker" - self._formatInFile = "fasta" - self._sbjFile = "" - self._nbProc = 1 - self._calcGc = False - self._skipIs = False - self._maskSsr = True - self._onlySsr = False - self._cmdLineSpecificOptions = "s:n:gblmo:" - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: name of the subject file (repeats, format='fasta')" - string += "\n -n: nb of processors to use in parallel (default='%i')" % ( self.getNbProcessors() ) - string += "\n -g: calculate the GC content" - string += "\n -b: skip bacterial insertion element check" - string += "\n -l: does not mask low-complexity DNA or simple repeats" - string += "\n -m: only masks low complex/simple repeats (no interspersed repeats)" - string += "\n -o: name of the output file" - string += "\n with -s: format='align', default=inFile+'.cat.align')" - string += "\n with -m: format='path', default=inFile+'.cat.path')" - return string - - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - """ - Set a specific attribute from the command-line arguments. - """ - if o =="-s": - self.setSubjectFile( a ) - elif o == "-n": - self.setNbProcessors( a ) - elif o == "-g": - self.setCalculateGCcontent() - elif o == "-b": - self.setSkipBacterialIsCheck() - elif o == "-l": - self.unsetMaskSsr() - elif o == "-m": - self.setOnlySsr() - elif o == "-o": - self.setOutputFile( a ) - - - def setSubjectFile( self, arg ): - self._sbjFile = arg - - - def setNbProcessors( self, arg ): - self._nbProc = int(arg) - - - def setCalculateGCcontent( self ): - self._calcGc = True - - - def setSkipBacterialIsCheck( self ): - self._skipIs = True - - - def unsetMaskSsr( self ): - self._maskSsr = False - - - def setOnlySsr( self ): - self._onlySsr = True - - - def getSubjectFile( self ): - return self._sbjFile - - - def getNbProcessors( self ): - return self._nbProc - - - def getCalculateGCcontent( self ): - return self._calcGc - - - def getSkipBacterialIsCheck( self ): - return self._skipIs - - - def getMaskSsr( self ): - return self._maskSsr - - - def getOnlySsr( self ): - return self._onlySsr - - - def checkSpecificAttributes( self ): - """ - Check the specific attributes before running the program. - """ - if ( self.getSubjectFile() == "" and not self.getOnlySsr() ) \ - or ( self.getSubjectFile() != "" and self.getOnlySsr() ): - string = "ERROR: need to specify -s or -m" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getOutputFile() == "": - if not self.getOnlySsr(): - self.setOutputFile( "%s.cat.align" % ( self.getInputFile() ) ) - else: - self.setOutputFile( "%s.cat.path" % ( self.getInputFile() ) ) - - - def setWrapperCommandLine( self ): - """ - Set the command-line of the wrapper. - Required for RepeatMaskerClusterLauncher. - """ - self._wrpCmdLine = self.getWrapperName() - self._wrpCmdLine += " -i %s" % ( self.getInputFile() ) - if self.getSubjectFile() != "": - self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() ) - self._wrpCmdLine += " -n %i" %( self.getNbProcessors() ) - if self.getCalculateGCcontent(): - self._wrpCmdLine += " -g" - if self.getSkipBacterialIsCheck(): - self._wrpCmdLine += " -b" - if not self.getMaskSsr(): - self._wrpCmdLine += " -l" - if self.getOnlySsr(): - self._wrpCmdLine += " -m" - if self.getOutputFile() != "": - self._wrpCmdLine += " -o %s" % ( self.getOutputFile() ) - if self.getClean(): - self._wrpCmdLine += " -c" - if self.getVerbosityLevel() != 0: - self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - - - def setProgramCommandLine( self ): - """ - Set the command-line of the program. - """ - self._prgCmdLine = self.getProgramName() - self._prgCmdLine += " -dir ." - self._prgCmdLine += " -pa %i" % ( self.getNbProcessors() ) - if self.getCalculateGCcontent(): - self._prgCmdLine += " -gccalc" - if self.getSkipBacterialIsCheck(): - self._prgCmdLine += " -no_is" - if self.getMaskSsr(): - self._prgCmdLine += " -nolow" - if self.getOnlySsr(): - self._prgCmdLine += " -int" - if self.getSubjectFile() != "": - self._prgCmdLine += " -lib %s" % ( self.getSubjectFile() ) - self._prgCmdLine += " %s" % ( self.getInputFile() ) - - - def setListFilesToKeep( self ): - """ - Set the list of files to keep. - """ - if self.getOutputFile() == "": - if not self.getOnlySsr(): - self.setOutputFile( "%s.cat.align" % ( self.getInputFile() ) ) - else: - self.setOutputFile( "%s.cat.path" % ( self.getInputFile() ) ) - self.appendFileToKeep( self.getOutputFile() ) - self.appendFileToKeep( "%s.cat" % ( self.getInputFile() ) ) - - - def setListFilesToRemove( self ): - """ - Set the list of files to remove. - """ - self.appendFileToRemove( "%s.stderr" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.tbl" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.ori.out" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.masked" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.out" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.log" % ( self.getInputFile() ) ) - self.appendFileToRemove( "%s.ref" % ( self.getInputFile() ) ) - - - def convertCatIntoAlign( self ): - """ - Convert a 'cat' file into the 'align' format. - """ - cmd = os.environ["REPET_PATH"] + "/bin/RMcat2align.py" - cmd += " -i %s.cat" % ( self.getInputFile() ) - cmd += " -o %s.cat.align" % ( self.getInputFile() ) - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR while converting 'cat' file into 'align' format" - print string - sys.exit(1) - - - def convertCatIntoPath( self ): - """ - Convert a 'cat' file into the 'path' format. - """ - cmd = os.environ["REPET_PATH"] + "/bin/RMcat2path.py" - cmd += " -i %s.cat" % ( self.getInputFile() ) - cmd += " -o %s.cat.path" % ( self.getInputFile() ) - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR while converting 'cat' file into 'path' format" - print string - sys.exit(1) - - - def setSummary( self ): - self._summary = "input file: %s" % ( self.getInputFile() ) - if self.getSubjectFile() != "": - self._summary += "\nsubject file: %s" % ( self.getSubjectFile() ) - self._summary += "\nnb processors: %i" % ( self.getNbProcessors() ) - if self.getCalculateGCcontent(): - self._summary += "\ncalculate the GC content" - if self.getSkipBacterialIsCheck(): - self._summary += "\nskip bacterial insertion element check" - if self.getMaskSsr(): - self._summary += "\nmask low-complexity DNA or simple repeats" - if self.getOnlySsr(): - self._summary = "\nonly masks low complex/simple repeats (no interspersed repeats)" - if self.getOutputFile() == "": - if not self.getMaskSsr(): - self.setOutputFile( "%s.cat.align" % ( self.getInputFile() ) ) - else: - self.setOutputFile( "%s.cat.path" % ( self.getInputFile() ) ) - self._summary += "\noutput file: %s" % ( self.getOutputFile() ) - - - def run( self ): - """ - Run the program. - """ - self.start() - - self.setProgramCommandLine() - cmd = self.getProgramCommandLine() - if self.getVerbosityLevel() > 0: - print "LAUNCH: %s" % ( cmd ) - sys.stdout.flush() - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus ) - print string - sys.exit(1) - - if not self.getOnlySsr(): - self.convertCatIntoAlign() - else: - self.convertCatIntoPath() - - self.end() - - -if __name__ == "__main__": - i = RepeatMaskerProgramLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/YassClusterLauncher.py --- a/commons/launcher/YassClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch YassProgramLauncher on several files in parallel on a cluster. - - -from pyRepet.launcher.AbstractClusterLauncher import * -from commons.core.coord.AlignUtils import AlignUtils -from commons.launcher.YassProgramLauncher import YassProgramLauncher -from commons.tools import srptBlasterMatcher - - -class YassClusterLauncher( AbstractClusterLauncher ): - """ - Launch Yass on several files in parallel on a cluster. - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractClusterLauncher.__init__( self ) - AbstractClusterLauncher.setAcronym( self, "Yass" ) - - self._cmdLineSpecificOptions = "s:p:A" - - self._exeWrapper = "YassProgramLauncher.py" - self._prgLauncher = None - self._prgLauncher = self.getProgramLauncherInstance() - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: name of the subject file (format='fasta')" - string += "\n -p: parameters for 'yass'" - string += "\n -Z: concatenate output files" - string += "\n -A: same sequences (all-by-all)" - return string - - - def getSubjectFile( self ): - return self._prgLauncher.getSubjectFile() - - - def getProgramParameters( self ): - return self._prgLauncher.getProgramParameters() - - - def getProgramLauncherInstance( self ): - if self._prgLauncher == None: - self._prgLauncher = YassProgramLauncher() - self._prgLauncher.setInputFile( GENERIC_IN_FILE ) - self._prgLauncher.setClean() - self._prgLauncher.setVerbosityLevel( 1 ) - self._prgLauncher.setListFilesToKeep() - self._prgLauncher.setListFilesToRemove() - return self._prgLauncher - - - def processOutputFile( self, tmpFile, outFile ): - sortFile = "%s.sort" % ( tmpFile ) - AlignUtils.sortAlignFile( tmpFile, sortFile ) - if self._prgLauncher.getAllByAll(): - srptBlasterMatcher.filterRedundantMatches( sortFile, - outFile ) - os.remove( sortFile ) - else: - os.rename( sortFile, outFile ) - - -if __name__ == "__main__": - i = YassClusterLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/YassProgramLauncher.py --- a/commons/launcher/YassProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,195 +0,0 @@ -#!/usr/bin/env python - -##@file -# Launch Yass (pairwise alignment). -# -# options: -# -h: this help -# -i: name of the input file (queries, format='fasta') -# -s: name of the subject file (format='fasta') -# -p: parameters for 'yass' (default='-d 2') -# -o: name of the output file (format='align', default=inFile+'.align') -# -c: clean -# -v: verbosity level (default=0/1) - - -import os -import sys - -from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher - - -class YassProgramLauncher( AbstractProgramLauncher ): - """ - Launch Yass (pairwise alignment). - """ - - def __init__( self ): - """ - Constructor. - """ - AbstractProgramLauncher.__init__( self ) - self._prgName = "yass" - self._formatInFile = "fasta" - self._sbjFile = "" - self._prgParam = "" - self._allByAll = False - self._cmdLineSpecificOptions = "s:p:Ao:" - - - def getSpecificHelpAsString( self ): - """ - Return the specific help as a string. - """ - string = "" - string += "\nspecific options:" - string += "\n -s: name of the subject file (format='fasta')" - string += "\n -p: parameters for '%s'" % ( self.getProgramName() ) - string += "\n -A: same sequences (all-by-all)" - string += "\n -o: name of the output file (format='align', default=inFile+'.align')" - return string - - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - """ - Set a specific attribute from the command-line arguments. - """ - if o =="-s": - self.setSubjectFile( a ) - elif o == "-p": - self.setProgramParameters( a ) - elif o == "-A": - self.setAllByAll() - elif o == "-o": - self.setOutputFile( a ) - - - def setSubjectFile( self, arg ): - self._sbjFile = arg - - - def getSubjectFile( self ): - return self._sbjFile - - - def setAllByAll( self ): - self._allByAll = True - - - def getAllByAll( self ): - return self._allByAll - - - def checkSpecificAttributes( self ): - """ - Check the specific attributes before running the program. - """ - if self._sbjFile == "": - string = "ERROR: missing subject file (-s)" - print string - print self.getHelpAsString() - sys.exit(1) - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - - - def setWrapperCommandLine( self ): - """ - Set the command-line of the wrapper. - Required for YassClusterLauncher. - """ - self._wrpCmdLine = self.getWrapperName() - self._wrpCmdLine += " -i %s" % ( self.getInputFile() ) - self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() ) - if self.getProgramParameters() != "": - self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() ) - if self.getAllByAll(): - self._wrpCmdLine += " -A" - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self._wrpCmdLine += " -o %s" % ( self.getOutputFile() ) - if self.getClean(): - self._wrpCmdLine += " -c" - self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() ) - - - def setProgramCommandLine( self ): - """ - Set the command-line of the program. - """ - self._prgCmdLine = self.getProgramName() - self._prgCmdLine += " -d 2" - if self.getProgramParameters() != "": - self._prgCmdLine += " %s" % ( self.getProgramParameters() ) - self._prgCmdLine += " -o %s.blast" % ( self.getInputFile() ) - self._prgCmdLine += " %s" % ( self.getInputFile() ) - self._prgCmdLine += " %s" % ( self.getSubjectFile() ) - - - def setListFilesToKeep( self ): - """ - Set the list of files to keep. - """ - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self.appendFileToKeep( self.getOutputFile() ) - - - def setListFilesToRemove( self ): - """ - Set the list of files to remove. - """ - pass - - - def convertBlastIntoAlign( self ): - """ - Convert a 'blast' file into the 'align' format. - """ - cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py" - cmd += " -i %s.blast" % ( self.getInputFile() ) - cmd += " -o %s" % ( self.getOutputFile() ) - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR while converting 'blast' file into 'align' format" - print string - sys.exit(1) - - - def setSummary( self ): - self._summary = "input file: %s" % ( self.getInputFile() ) - self._summary += "\nsubject file: %s" % ( self.getSubjectFile() ) - self._summary += "\nparameters: %s" % ( self.getProgramParameters() ) - if self.getAllByAll(): - self._summary += "\nall-by-all" - if self.getOutputFile() == "": - self.setOutputFile( "%s.align" % ( self.getInputFile() ) ) - self._summary += "\noutput file: %s" % ( self.getOutputFile() ) - - - def run( self ): - """ - Run the program. - """ - self.start() - - self.setProgramCommandLine() - cmd = self.getProgramCommandLine() - if self.getVerbosityLevel() > 0: - print "LAUNCH: %s" % ( cmd ) - sys.stdout.flush() - exitStatus = os.system( cmd ) - if exitStatus != 0: - string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus ) - print string - sys.exit(1) - - self.convertBlastIntoAlign() - - self.end() - - -if __name__ == "__main__": - i = YassProgramLauncher() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchBlasterMatcherPerQuery.py --- a/commons/launcher/launchBlasterMatcherPerQuery.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,196 +0,0 @@ -#!/usr/bin/env python - -""" -This program splits the input fasta file in a given number of files, launch Blaster and/or Matcher on them in parallel and collect the results afterwards. -""" - -import os -import sys -import getopt -import exceptions -import logging -import ConfigParser - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -import pyRepet.launcher.programLauncher -import pyRepet.seq.fastaDB - -#----------------------------------------------------------------------------- - -def help(): - - """ - Give the list of the command-line options. - """ - - print - print "usage:",sys.argv[0]," [ options ]" - print "options:" - print " -h: this help" - print " -q: fasta filename of the queries" - print " -s: fasta filename of the subjects (same as queries if not specified)" - print " -Q: queue name on the cluster" - print " -d: absolute path to the temporary directory" - print " -C: configuration file" - print " -n: max. number of jobs (default=10,given a min. of 1 query per job)" - print " -m: mix of Blaster and/or Matcher" - print " 1: launch Blaster only" - print " 2: launch Matcher only (on '*.align' query files)" - print " 3: launch Blaster+Matcher in the same job (default)" - print " -B: parameters for Blaster (e.g. \"-a -n tblastx\")" - print " -M: parameters for Matcher (e.g. \"-j\")" - print " -Z: collect all the results into a single file (format 'align', 'path' or 'tab')" - print " -c: clean" - print " -v: verbose (default=0/1/2)" - print - -#----------------------------------------------------------------------------- - -def main(): - - """ - This program splits the input fasta file in a given number of files, launch Blaster and/or Matcher on them in parallel and collect the results afterwards. - """ - - qryFileName = "" - sbjFileName = "" - queue = "" - tmpDir = "" - configFileName = "" - maxNbJobs = 10 - minQryPerJob = 1 - mix = "3" - paramBlaster = "" - paramMatcher = "" - collectFormat = "" - clean = False - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hq:s:Q:d:C:n:m:B:M:Z:cv:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-q": - qryFileName = a - elif o == "-s": - sbjFileName = a - elif o == "-Q": - queue = a - elif o == "-d": - tmpDir = a - elif o == "-C": - configFileName = a - elif o == "-n": - maxNbJobs = int(a) - elif o == "-m": - mix = a - elif o == "-B": - paramBlaster = a - elif o == "-M": - paramMatcher = a - elif o == "-Z": - collectFormat = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - - if qryFileName == "" or configFileName == "" or collectFormat == "": - print "*** Error: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "\nbeginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if not os.path.exists( qryFileName ): - print "*** Error: query file '%s' doesn't exist" % ( qryFileName ) - sys.exit(1) - if sbjFileName != "": - if not os.path.exists( sbjFileName ): - print "*** Error: subject file '%s' doesn't exist" % ( sbjFileName ) - sys.exit(1) - else: - sbjFileName = qryFileName - - pL = pyRepet.launcher.programLauncher.programLauncher() - - nbSeqQry = pyRepet.seq.fastaDB.dbSize( qryFileName ) - qryPerJob = nbSeqQry / float(maxNbJobs) - - # split the input query file in single files into a new directory - prg = os.environ["REPET_PATH"] + "/bin/dbSplit.py" - cmd = prg - cmd += " -i %s" % ( qryFileName ) - if qryPerJob <= 1.0: - cmd += " -n %i" % ( minQryPerJob ) - else: - cmd += " -n %i" % ( qryPerJob + 1 ) - cmd += " -d" - pL.launch( prg, cmd ) - - # prepare the subject databank - if sbjFileName != qryFileName: - prg = "blaster" - cmd = prg - cmd += " -q %s" % ( sbjFileName ) - cmd += " -P" - pL.launch( prg, cmd ) - - # launch Blaster+Matcher in parallel - prg = "srptBlasterMatcher.py" - cmd = prg - cmd += " -g %s_vs_%s" % ( qryFileName, sbjFileName ) - cmd += " -q %s/batches" % ( os.getcwd() ) - cmd += " -s %s/%s" % ( os.getcwd(), sbjFileName ) - cmd += " -Q '%s'" % ( queue ) - if tmpDir != "": - cmd += " -d %s" % ( tmpDir ) - cmd += " -m %s" % ( mix ) - if paramBlaster != "": - cmd += " -B \"%s\"" % ( paramBlaster ) - if paramMatcher != "": - cmd += " -M \"%s\"" % ( paramMatcher ) - cmd += " -Z %s" % ( collectFormat ) - cmd += " -C %s" % ( configFileName ) - if clean == True: - cmd += " -c" - cmd += " -v %i" % ( verbose - 1 ) - pL.launch( prg, cmd ) - - suffix = "" - if mix in ["2","3"]: - if "-a" in paramMatcher: - suffix = "match.%s" % ( collectFormat ) - else: - suffix = "clean_match.%s" % ( collectFormat ) - os.system( "mv %s_vs_%s.%s %s_vs_%s.align.%s" % ( qryFileName, sbjFileName, collectFormat, qryFileName, sbjFileName, suffix ) ) - - # clean - if clean == True: - prg = "rm" - cmd = prg - cmd += " -rf batches formatdb.log %s_cut* %s.Nstretch.map" % ( sbjFileName, sbjFileName ) - pL.launch( prg, cmd ) - - if verbose > 0: - print "%s finished successfully\n" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#---------------------------------------------------------------------------- - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchMafft.py --- a/commons/launcher/launchMafft.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,104 +0,0 @@ -#!/usr/bin/env python - -# DEPRECATED - -import user, os, sys, getopt, exceptions - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -import pyRepet.launcher.programLauncher -import pyRepet.seq.fastaDB -from pyRepet.seq.BioseqDB import * - -#------------------------------------------------------------------------------ - -def help(): - - print - print "DEPRECATED" - print - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='fasta')" - print " -o: name of the output file (default=inFileName+'.fa_aln')" - print " -v: verbose (default=0/1)" - print - -#------------------------------------------------------------------------------ - -def main(): - - """ - This program launches MAFFT to build a multiple sequence alignment. - """ - - inFileName = "" - outFileName = "" - verbose = 0 - - try: - opts,args=getopt.getopt(sys.argv[1:],"hi:o:v:") - except getopt.GetoptError: - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "*** Error: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "beginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if verbose > 0: - print "build a multiple alignment from '%s'..." % ( inFileName ) - sys.stdout.flush() - - pyRepet.seq.fastaDB.shortenSeqHeaders( inFileName ) - - bsDB = BioseqDB( inFileName+".shortH" ) - bsDB.upCase() - bsDB.save( inFileName+".shortHtmp" ) - del bsDB - os.rename( inFileName+".shortHtmp", inFileName+".shortH" ) - - pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" ) - pL.launchMafft( outFileName=inFileName+".shortH.fa_aln", verbose=verbose ) - - pyRepet.seq.fastaDB.retrieveInitSeqHeaders( inFileName+".shortH.fa_aln", - inFileName+".shortHlink", - inFileName+".shortH.fa_aln.initH", - verbose-1 ) - - if outFileName == "": - outFileName = "%s.fa_aln" % ( inFileName ) - os.system( "mv %s.shortH.fa_aln.initH %s" % ( inFileName, outFileName ) ) - - for f in [inFileName+".shortH",inFileName+".shortH.fa_aln",inFileName+".shortHlink"]: - os.remove( f ) - - if verbose > 0: - print "%s finished successfully" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#------------------------------------------------------------------------------ - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchMreps.py --- a/commons/launcher/launchMreps.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -#!/usr/bin/env python - -from commons.core.seq.BioseqDB import BioseqDB -from commons.core.parsing.MrepsToSet import MrepsToSet -import subprocess -import os -import sys -import getopt - -def help(): - """ - Give the list of the command-line options. - """ - print - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='fasta')" - print " -o: name of the output file (default=inFileName+'.Mreps.set')" - print " -f: error filter (default=1.0)" - print " -c: clean" - print " -v: verbosity level (default=0/1)" - print - -def main(): - """ - Launch Mreps. - """ - inFileName = "" - outFileName = "" - errorFilter = 1.0 - clean = False - verbose = 0 - - try: - opts=getopt.getopt(sys.argv[1:],"hi:o:f:cv:")[0] - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - elif o == "-f": - errorFilter = float(a) - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "beginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - # Mreps 2.5 doesn't fully support IUPAC nomenclature - if verbose > 0: - print "* check IUPAC symbols"; sys.stdout.flush() - tmpInFileName = "%s.tmp%i" % ( inFileName, os.getpid() ) - if os.path.exists( tmpInFileName ): - os.system( "rm -f %s" % ( tmpInFileName ) ) - bsDB = BioseqDB( inFileName ) - for bs in bsDB.db: - if verbose > 0: - print bs.header; sys.stdout.flush() - bs.partialIUPAC() - onlyN = True - for nt in ["A","T","G","C"]: - if nt in bs.sequence: - onlyN = False - if onlyN == True: - if verbose > 0: - print "** Warning: only Ns"; sys.stdout.flush() - else: - bsDB.save( tmpInFileName ) - - if not os.path.exists( tmpInFileName ): - sys.exit(0) - - if verbose > 0: - print "* remove N stretches"; sys.stdout.flush() - prg = os.environ["REPET_PATH"] + "/bin/cutterDB" - cmd = prg - cmd += " -l 200000" - cmd += " -o 0" - cmd += " -w 11" - cmd += " %s" % ( tmpInFileName ) - if verbose > 0: - print cmd; sys.stdout.flush() - log = os.system( cmd ) - if log != 0: - print "ERROR: %s returned %i" % ( prg, log ) - sys.exit(1) - - # launch Mreps on the input file - MrepsOutFileName = "%s.Mreps.xml" % ( tmpInFileName ) - prg = "mreps" - cmd = prg - cmd += " -res 3" - cmd += " -exp 3.0" - cmd += " -maxsize 50" - cmd += " -xmloutput %s" % MrepsOutFileName - cmd += " -fasta %s_cut" % tmpInFileName - process = subprocess.Popen(cmd, shell = True) - process.communicate() - if process.returncode != 0: - raise Exception("ERROR when launching '%s'" % cmd) - - if outFileName == "": - outFileName = inFileName + ".Mreps.set" - - # parse Mreps results in xml format - iMrepsToSet = MrepsToSet(inFileName, MrepsOutFileName, outFileName, errorFilter) - iMrepsToSet.run() - if clean: - iMrepsToSet.clean() - - # remove temporary input filename - os.remove(tmpInFileName) - os.remove("%s_cut" % tmpInFileName) - os.remove("%s.Nstretch.map" % tmpInFileName) - - if verbose > 0: - print "%s finished successfully\n" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchPhyML.py --- a/commons/launcher/launchPhyML.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt - -from pyRepet.launcher.programLauncher import programLauncher -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -def help(): - print - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (aligned fasta)" - print " -c: clean" - print " -v: verbose (default=0)" - print - - -def main(): - - inFileName = "" - clean = False - verbose = 0 - try: - opts,args=getopt.getopt(sys.argv[1:],"hi:cv:") - except getopt.GetoptError, err: - print str(err) - help(); sys.exit(1) - for o,a in opts: - if o == "-h": - help(); sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - if inFileName == "": - print "ERROR: missing compulsory options" - help(); sys.exit(1) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - csh = ChangeSequenceHeaders() - csh.setInputFile( inFileName ) - csh.setFormat( "fasta" ) - csh.setStep( 1 ) - csh.setPrefix( "seq" ) - csh.setLinkFile( inFileName+".shortHlink" ) - csh.setOutputFile( inFileName+".shortH" ) - csh.run() - - pL = programLauncher( inFileName+".shortH" ) - - pL.launchSreformat( outFormat="phylip", outFileName=inFileName+".shortH.phylip", verbose=verbose ) - - pL.reset( inFileName+".shortH.phylip" ) - - pL.launchPhyML( verbose=verbose ) - - csh.setInputFile( inFileName+".shortH.phylip_phyml_tree.txt" ) - csh.setFormat( "newick" ) - csh.setStep( 2 ) - csh.setLinkFile( inFileName+".shortHlink" ) - csh.setOutputFile( inFileName+"_phyml.newick" ) - csh.run() - - if clean: - for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.phylip", - inFileName+".shortH.phylip_phyml_lk.txt", inFileName+".shortH.phylip_phyml_tree.txt" ]: - os.remove( f ) - os.system( "mv %s.shortH.phylip_phyml_stat.txt %s_phyml.txt" % ( inFileName, inFileName ) ) - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchPrank.py --- a/commons/launcher/launchPrank.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt - -from pyRepet.launcher.programLauncher import programLauncher - - -def help(): - print - print "usage: launchPrank.py [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format=fasta)" - print " -o: name of the output file (format=aligned fasta, default='inFileName'+fa_aln)" - print " -P: Prank's parameters" - print " -c: clean" - print " -v: verbose (default=0/1)" - print - - -def main(): - """ - Launch PRANK. - """ - inFileName = "" - outFileName = "" - parameters = "" - clean = False - verbose = 0 - - try: - opts, args = getopt.getopt( sys.argv[1:], "hi:o:P:cv:" ) - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - elif o == "-P": - parameters = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing input file (-i)" - help() - sys.exit(1) - - if not os.path.exists( inFileName ): - print "ERROR: can't find file '%s'" % ( inFileName ) - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s.fa_aln" % ( inFileName ) - - pL = programLauncher( inFileName ) - returnStatus = pL.launchPrank( outFileName, parameters, "yes", verbose ) - if returnStatus != 0: - print "ERROR: launchPrank() returned '%i'" % ( returnStatus ) - sys.exit(1) - - if verbose > 0: - print "END %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchTCoffee.py --- a/commons/launcher/launchTCoffee.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -import exceptions - -if not os.environ.has_key( "REPET_PATH" ): - print "ERROR: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -from pyRepet.launcher.programLauncher import programLauncher - - -def help(): - print - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='fasta')" - print " -P: parameters" - print " -o: name of the output file (format='aligned fasta', default='inFileName'+fa_aln)" - print " -c: clean" - print " -v: verbosity level (default=0/1)" - print - - -def main(): - - inFileName = "" - parameters = "" - outFileName = "" - clean = False - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:P:o:cv:") - except getopt.GetoptError, err: - print str(err); help(); sys.exit(1) - for o,a in opts: - if o == "-h": - help(); sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-P": - parameters = a - elif o == "-o": - outFileName = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = "yes" - - if inFileName == "" and parameters == "": - print "ERROR: missing compulsory options" - help() - sys.exit(1) - - if outFileName == "": - outFileName = "%s.fa_aln" % ( inFileName ) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - pL = programLauncher( inFileName ) - pL.launchTcoffee( outFileName, parameters ) - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/launchTEclass.py --- a/commons/launcher/launchTEclass.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -import glob -import shutil - - -def help(): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " -i: name of the input file (format='fasta')" - print " -o: name of the output file (format='map', default=inFileName+'.map')" - print " -c: clean" - print " -v: verbosity level (default=0/1)" - print - -def parseFastaFileFromTEclass( inFile, outFile, verbose=0 ): - tmpHandler = open( inFile, "r" ) - outHandler = open( outFile, "w" ) - dClassif2Count = {} - header = "" - classif = "" - while True: - line = tmpHandler.readline() - if line == "": - break - if line[0] == ">": - header = line[1:].split("|")[0] - classif = line[1:-1].split(": ")[1].split("|")[0] - if not dClassif2Count.has_key( classif ): - dClassif2Count[ classif ] = 0 - dClassif2Count[ classif ] += 1 - else: - seqLength = len(line[:-1]) - outHandler.write( "%s\t%s\t%i\t%i\n" % ( classif, header, 1, seqLength ) ) - tmpHandler.close() - outHandler.close() - if verbose > 0: - for classif in dClassif2Count.keys(): - print "%s: %i sequences" % ( classif, dClassif2Count[ classif ] ) - sys.stdout.flush() - - -def main(): - """ - Launch TEclass to classify TE sequences. - """ - inFileName = "" - outFileName = "" - clean = False - verbose = 0 - - try: - opts, args = getopt.getopt( sys.argv[1:], "hi:o:cv:" ) - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing input file (-i)" - help() - sys.exit(1) - if not os.path.exists( inFileName ): - print "ERROR: can't find input file '%s'" % ( inFileName ) - help() - sys.exit(1) - if outFileName == "": - outFileName = "%s.TEclass.map" % ( inFileName ) - - if verbose > 0: - print "START %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - if verbose > 0: - print "launch TEclass..." - sys.stdout.flush() - prg = "test_consensi_2.1.pl" - cmd = prg - cmd += " %s" % ( inFileName ) - returnValue = os.system( cmd ) - if returnValue != 0: - print "ERROR: '%s' returned %i" % ( prg, returnValue ) - sys.exit(1) - - lOut1 = glob.glob( "%s_*" % ( inFileName ) ) - outDir = "" - for i in lOut1: - if os.path.isdir( i ): - lOut2 = glob.glob( "%s/*" % ( i ) ) - if len(lOut2) == 4 and "%s/%s.lib" % ( i, inFileName ) in lOut2: - outDir = i - break - if outDir == "": - print "ERROR: can't find output directory" - sys.exit(1) - os.chdir( outDir ) - - if verbose > 0: - print "parse the results..." - sys.stdout.flush() - parseFastaFileFromTEclass( "%s.lib" % ( inFileName ), - outFileName, - verbose ) - os.system( "mv %s .." % ( outFileName ) ) - os.chdir( ".." ) - - if clean: - if verbose > 0: - print "clean the temporary files..." - sys.stdout.flush() - shutil.rmtree( outDir ) - - if verbose > 0: - print "END %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/MockDataBankForBlat.py --- a/commons/launcher/tests/MockDataBankForBlat.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,299 +0,0 @@ -class MockDataBankForBlat(object): - - def write(self, inFileName): - f = open(inFileName, 'w') - f.write('>Vein_ctg_2286\n') - f.write('AGCAAAAaCGTATTTTCTAAGCTAAAATTTAGCGTAGAAGCTTGGACTCGCTtATTTTTT\n') - f.write('ATCCTAGGAATTAGTAGAATCTCTCTATAAATATTTATTTTTTATCCGCGCAAAGCTAGG\n') - f.write('AAACTATAGAATCTTATATATTAGTATATTCTAGCGATTATCTAGAGATTGTaGGGGGGG\n') - f.write('ggAAAGGTAGTAATAGGCGTGTAAGAGAGATAAAGAGTTtATCTTAGAATCTCCCTACGC\n') - f.write('CAAGCGAGATTCCTAAGGTAAGAATCCTAAGGTAAAGAATCTAAGCGAGAATTTAGAATC\n') - f.write('ACGTGCTCGCTTCCTACTACCGTAATTTTACGGTTATAGAGTACGACAGTTCCTATATAT\n') - f.write('AACCTATACTTATAACAACGAATATAaTATAAGACGTTAATTTGATTTTTTACCGTGTTA\n') - f.write('CTTATAATAAGGTGTCCCAAAGTTGTTCGAATTTTTTTTGTCCAAGATTGAATACGGTGT\n') - f.write('TGGTCATGTGATAGTATTTTCACGGTATTTAAACGGAAATTTTACCTACGGCCCCCcGCC\n') - f.write('TATGTACATCATGAGGATGCACGATGGAGATGAAATGCTTCGTTTCATACTGAGTGGCCG\n') - f.write('ATTGATGGACGCGTGAACGTCAAAGTAACTTCCATTTGTTTCCTGTCGTTGTCCGGTAGC\n') - f.write('CTGGCAAATAGTGACATGTTTGATGTCTTTGGAACAGGGTGGAAACTTTTTTTGGGTtGC\n') - f.write('AAATCGTCAAGAGTCACGTGTCCACACAGTGGCGCAAGTGGGGGCTTAAAATGGTGGACT\n') - f.write('TGCGCGAGGGCGATTTCTTTTCTTCCCCAACCACAATCTATCGTGATCAAAGAAGCACCC\n') - f.write('ATCCGGTTGTTGAGGTATGCCAGCCAGCATCCAATGATGCGCTCAAACAACAACTAACTC\n') - f.write('TCATACAGATCGCCATGCAGATTTTCGTGAAGACCCTCACGGGCAAGACTATCACCCTcG\n') - f.write('AGGTGGAGTCCTCCGACACCATTGACAATGTCAAGACCAAGATTCAGGGTACGTGGCCTC\n') - f.write('GCGCAAGCATTTGTAACCATCTTCTAACCCTCTGCCGTAGACAAGGAAGgAATCCCCCCA\n') - f.write('GACCAGCAGCGCTTGATCTTCGCCGGCAAGCAGCTCGAAGATGGACGCACCCTATCGGAC\n') - f.write('TACAACATCCAGAAGGAGTCGACCCTCCACCTCGTCCTCCGACTCCGTGGTGGTATGGCC\n') - f.write('AAGAaGCGCAAGAAGAAGGTCTACACCACCCcAAAGAaGATCAAGCACAAGCGCAAGAaG\n') - f.write('ACCAAGTTGGCTGTCcTCAAGTACTACAAGGTGGATGGCGATGGAAAgaTCGAGcGCcTC\n') - f.write('CGACGAGAGTGCCcAGCTGACGAGTGTGGTgCCGGTgTCTTCATGGCTGCCATGCACAAC\n') - f.write('CGtcAATACTGCGGAAAGTGCCACCTCACCtACGTTTTCGACGAGAGCAAGTAGACGGTT\n') - f.write('CTGGAAAGCATACAATGACAACCATGATTATGCTGTGGGATGATGGATGCTGAACAAAGG\n') - f.write('GAGGGAATAGCGACGGACACCGCGTTCTGTAGCTACACAATCAAGCAAAACCTTCACCTC\n') - f.write('GATAGCGGGCCTCGATCCATGTACTATCTTATGATATGTGACATTGAATGTGCGAGTGTT\n') - f.write('CATTATTCTTTCGCCGTAGCTTCGTTCTCTCTGTGTTCACCCAACCTCCAAGAATCCCGA\n') - f.write('CAGTTTCTGGCGATGTTCAAGAATGATATTGCCAGAAATTTATCGGTACCGAACCCTAGA\n') - f.write('TAAAAGGATGGGTTCGGAGTTAACGTAATTTCGAAGGGCAGATGCCATGTGCTTGGGTGC\n') - f.write('CGCGTTACGAGAATTACTATGATGGTGCTGTGTATCTTCACAATGGCAACATGGCAGAAC\n') - f.write('AACGCCAAGAAGTTTCTCCAATGTCAACCCAAGGTCTCCGGACGAATCTAGATGCACCCT\n') - f.write('GACTGCATCGTTATCGGTCATGCAAAAGCACGCCTAATGTGCAGCGTGATGACAAGGTGG\n') - f.write('AAAaGGAGGCAAATGCTGGTCTAGTGTCTTGTGGCAGAAGTCAGAGTCACGATGAGCAAG\n') - f.write('CATGGCGCATGAGGGTTGCCTCCGCAAGCATCCGACAGAGTAGAGACAGAGAAAACACCA\n') - f.write('CAGCAAAAGATGTCACGGCACTCTCGATTCGCTTGTGACGGCCAAGTCTAGGTCCAGGTC\n') - f.write('CAGGTCCAGGATACGGATACAAGGCGAATGTGGACACCCCAGCCTCCCGATTAGGGAACT\n') - f.write('ATACAGCGGGCTGGGTTTATGAATAATGAATCCAATTGCAGCATGAGATCATAGCGTTTG\n') - f.write('TCTAAGAGGCTTTTTGCTACTGTACATGGCGATTGGCGAGTGTTGGGGGTTAGGTGAGAC\n') - f.write('GGTCTTGGCTGGCAACCCTGTGAGCGCAAAGATGGAGAAGGGAATGGCAGGCGATCAGGA\n') - f.write('CGATTGTTTCATGGATGAGCAATGGGCATCTCAAaGAAACACGGATCGTTTCTGATGGAC\n') - f.write('AGACGGGCCAAGACTGACCAAGCATTTGTGAAATTGGGACAGGAGAAGGGATGGTGGCTT\n') - f.write('CGACGTGCTGCAGCTGCATACTGTGTAGCTGCGTGTTGATAGCTGCACAACTGCATTGGC\n') - f.write('TCGACCAGACACATTCCCGGAGCGTTATGCATCCAGCGCCTGATTCGCTTGGGACTTGGG\n') - f.write('TCGCGACTCGCGAGAGAATTGGTACTCGTAGTCGGTACCTAAGCTGCACCTTGTCCCCGA\n') - f.write('AGTAGACTGTCGAGACTGTATAGtAGAGGTCGAGGTATATTCTATGCTATACTGTACATT\n') - f.write('ATTGAAGTGCTCCCATCATATCACCAACCCTCCCGCCTCGTCTTCCATGTCcGTTTCCGC\n') - f.write('CTTCACATTTCAAAAAGTCGTTGAGTGGTCCTAGTGCTCAATTAAATTGCTTACCAGAGC\n') - f.write('GTCAGAGCTCTCCTGGAGTCCTGGCAAAAGCCAaaGCTCAACGACCAATTGCCCCATCCT\n') - f.write('CTCTCCTACCGAGTACTCCGTACCGCTCATCTCGTCAACCACCACCGCAGACAACAATCG\n') - f.write('CACCACTTCTCCAGCGCGTCCACTGAACTCAGGTCTCGCTGTGGTTGCGCAGTATTGCCT\n') - f.write('GTCGGACCCATCTCGCGCGCGCTACTGTCATTCCAACTCCCGGATCTTTCGGCCACAAAT\n') - f.write('TGGTCCGTGGCCTGCTCGTCACTCTCCGTCACCATCAAAACTCAACAGGCCGCCTTCACC\n') - f.write('TCACCAAAGTCACCCTTCCTACCACCACCGCGACCACCGCGACCACCACCACCACCTACA\n') - f.write('ATGTCGCCCACGCTGCCCTCGTTCGACTTCGCCACTACCAGAGGGAAGCGGTCGCGGATG\n') - f.write('CCTTCGTTCGCGCCGGCCCTTCCGGACGGACTTTCACACCTACCAAACATGCGATACATC\n') - f.write('ATTCCTCGCCAGGTGAGAAGGAGATGGAGAGCAACAAAGGGCAGACTACGTGTTGGACAG\n') - f.write('TCACCTGCTTCGAATGTCTTTAGACTGCAGACTTCTTGGTCGCCCACCGACACAATAGCT\n') - f.write('GCAcTGCGCACGCATCAGTGGTCATTGTATGACTTTCAGTACTTGGGACTGGCAATTCTG\n') - f.write('GGCATTTTCTGCTTGAGCATTATGGAgACTCcAGGTCCTATGGTTAAGACGTTCGGCGCT\n') - f.write('ACCGCACTCTTGCTATCTCTTTGTTTtCCCGTTACAAGTCAATTCTGGCTCCCAACGTTA\n') - f.write('CCCGTTGTAGGCTGGATCATTCTGTTCTTCTCCTGCAGGTACGTACACCCTTGCTTAATT\n') - f.write('TCTAATCGACCATTTCCAACTCGATACTAACACGCGTTTCTTTGTAGATTCATCGATGGC\n') - f.write('GCATATCGTCCTTCCATCCACGTCCGCGTTCTCCCTGCCCTAGAAAACATATTTTACGGC\n') - f.write('GCCAATCTCAGCAACATCCTATCTAGCCaCAAAAaTTCCTTCCTCGAtGTCCTCGCATGG\n') - f.write('CTACCATATGGCATCACCCACTTTGGAGCGCCCTTCGTCGTTTCAATCATCATGTTCATC\n') - f.write('TGGGGACCTCCAGGGATCGTCCCGACCTTTGCCCGCGCTTTTGGTTACaTGAACATTGCA\n') - f.write('GGTGTTCTCATCCAaCTGCTGTTTCCATGCTCTCCACCGTGGTATGAAAATCTATACGGT\n') - f.write('TTGGTGCCTGCAAACTACAGCATCCCGGGCTCACCGGCGGGTTTGGCGGCTGTGGACAAG\n') - f.write('CTCTTTGGGGTCGACATGTACACTACAGCGTTCACCGGCTCTCCCCAGGTTTTCGGCGCC\n') - f.write('TTCCCATCTTTACACTCCGCCAACGCCACCGTCGAGGCTCTCTTCATGAGCTTTGTTTTC\n') - f.write('CCAAAGCTTGCACCCCTATTCATTGCTTACACGCTTTGGCTTTGGTGGGCAACTATGTAC\n') - f.write('CTGTCGCACCACTACGCTGTAGATCTCGTTGGCGGAAGTCTTCTCGCTGGCATTGCTTTT\n') - f.write('TATATTGCTAAAGCAAAGTTCCTCCCACGCATGCAACCCGACAAGGAATTTCGATGGGAT\n') - f.write('TACGACTACCTTGAGATTGGCGAATCTCAGGACAATTATTCAGCCAAGGATGGCACTGGG\n') - f.write('TTTTACGAAGAGTTTCAGACCGGCGTATCTGATGACGAATGGACCGTTGGCTCAAGTTCC\n') - f.write('AGCATCTCGTCCAGAAGTAGAAGCCCTTCCAACACCAACAGATCCTCTAGCGAAACATCA\n') - f.write('ATGTGGGAAGGTGAAACCCTGGCCTCGACTtCCGACACCGAACAACGAAGCAGGTAGTAC\n') - f.write('CAGCAAaTTAAtctCAACATCCTCGCcTtCCCcGCGACCCAAGCTACATTCTCAaCcAAC\n') - f.write('CTGGTTCcTCGATTTTtCGTATCGGTACCCTTGTTGTTCACACGGGACACAATCACGTCA\n') - f.write('ACATTGGGCGGAGTTTTGCATCTCTGCATTTGCATGTCACATCTGCAGttagg\n') - f.write('>Vein_ctg_2288\n') - f.write('GCTGACTTGATATGGAGACAATAACGCAAGGCTGACCGACTGACtGTTTGATtATGTGCA\n') - f.write('GGAaTAAAAATACAAAATTGGAATTCGCAAGAGGACAAACAAAACTCTTTTGAACAGCTG\n') - f.write('TAGAGATCCACAAAAGATTACAGACCGACCCGGTAATCTGAGACGCTCAGCCTGCAACAC\n') - f.write('TTCACCCGTACGAAACAATGGAAACCTGGGCAGACGAATGAGAGGAAGTGGATATTCGCG\n') - f.write('GAGTAATTTACATCGAGAAACATTCAGCCACCAGATCCATGATCGTGAAACGCCAAAGGT\n') - f.write('CGAAATGGGTTAGCTGGAAGAGGGCGTTTTTGTGGAGAGTCGTCGACGACAACAATGGAT\n') - f.write('CCACAGCTTTCTATCAATTCAGTAATCCAACAGTAGCAGCTGACCTAAACATGGCCAGCT\n') - f.write('ATAGATCGATCAATATATCCAAGCTTCAGATACCTCCCGAcTCCGCCGGACGATATGGAG\n') - f.write('AGCGCACGTCGTGCAAGCTACGCACTTGATGCCCGAGAACGAGAAGGAAAGGAACCGACA\n') - f.write('ATGTAAACACCGAACGGATTACACTCAACTACATTAGTaTAAAAAATCGCCAGAGCGACG\n') - f.write('TCGTAAACCCCTCAATATGCCATAACAACGCGCCCCGACCTGGTATAAAACTGCCAAATT\n') - f.write('TCCCATAAACACCACCCCATCGCACGAATGTCCTCCTGCGCAACAGGATAAAAGAGGCCT\n') - f.write('TACCGAGCATCCACGTACCTCTCCCCCTTGTCCACACCCCcAACCTCCCTCTTCTCCTTC\n') - f.write('CTCGCCCCcACAAGCGCAAGCCCCGCCAACACCAACCCAACAACATCCGTCAAGAAAATA\n') - f.write('GGAATCAACATCCACCTCCAAGCCTCCATATTCCGAACCTTGTTCCTAAACGTCTTCTTC\n') - f.write('AAGCTCTCCTCGATGGGAAGCTTGAGGACGGCTTTGTACCATGTTTCTGGCGTCCAGCGA\n') - f.write('TGGTCTGGGTAGGGTTCTCCTGCGCGAAGGAGGGAGGGCGTGATTtGTTTGTGCTTGGTT\n') - f.write('TGGGAGGTTACGGTGAAGGTGAAGATGAGGGCGGAGAGTGTGAAGAGCGTTGCTAGTGTA\n') - f.write('AGGAGGATTGTCAGGACCAGGACGAGGGTCGGTGTACTCTATTCACAAACACATATTAGC\n') - f.write('CTGATATCGGAAGAACATTCGATACAGGAAGCGAGGGAGCGATACATAcTTTtCCCTTTT\n') - f.write('tGTATCGGAAGGCAATGAACATGCCCAGGAGACCTAGGAAAAACCCATAACCGGCCACGC\n') - f.write('CGTTAGATGTGTGGCCTTGATCGAGCCAGATGTGGGCTGGGAGTGCTTTCATCTGGATGC\n') - f.write('TCTCGCTTGACGACACTTGAACGGAATAACCAGGCCCGTATTTTTGGACGTGCAGGAAAC\n') - f.write('CGACCATGGAACTTATGAGGCCTAGATTCGTGATGGAGAGTGCACTCAGCACGAATTGCG\n') - f.write('AGACGAAAAGGGGGAGgAGTAACATGATTCCTGGTGTGATTGCTAGGTGTGTAGTGTACT\n') - f.write('CTGAGGAATAAAAGAGTATGTAATAGCCAAATTCCAAAATATTAGGGCGTTTGGAATGGA\n') - f.write('CGTGGAACGAGGAACGATGAaCAAAGAGAAGAATAAGCGTCCCGTCGAGATCACAAACAT\n') - f.write('CCCGCGCCGCCTTGTTTCTCTATCTATACGAACACACACACACATACATACCTCAGCCGC\n') - f.write('AAGGGAACCGCATTGGCAAAGCTTGTGCAAAATATGCATGGTTGCCGGTAGGTATGTAAG\n') - f.write('ACGCGCAGCAGCGGCACACAAGAGTCAAGACACATCTTGTCCAAAAGCCCCGGCCACATG\n') - f.write('GAATGCAGATTCGTTGGCACCCTCTCAGCACGGATATGTGTATCCATTACCGTTATCGGT\n') - f.write('TTTCGGGTTAGTGCTGACTGATGCGATTTTTTACATGCTGAGAGTGTGGGTATTAGGAAG\n') - f.write('CAGTATGTATGTAATCATGCTGCGGTCTACGGTCTGCGGGTCGGTCAGGCTGAGGCTGAG\n') - f.write('ACATTCACCGCTTGGTATCTTGATCATGATAATGTTTGTTGCTGCGCAGAGGATAGCGAT\n') - f.write('TGACCAGTGTTTGTATGTATTAACCATGATTGAAGCTTTTTTTTTCATTGCCAATTTTCT\n') - f.write('GGTTGTCGAGTTCGGCCCAAGCTTTtGTCTTGTGGATGGAACGTTTTCAGCTCCTGTTCA\n') - f.write('GATCGGGCAAAGGCCGGGTTTTGAATGTTGGGGTGTGGCATTTCGCTATTTGGTGGGGTT\n') - f.write('GTGCAGACTGCATAAAGAGTGATTACTACAACTGTTTGCATGTGGAGCTGTGTGACCAGT\n') - f.write('TTGTATGCACAGAATCTTTCAAAATGGCATAATCACTGCCATAGGAGGTTCGATTCGATG\n') - f.write('GAACCTTTGCAGGGACAGTCTTCCTTCTCGAATATCGAGTTCAGTATTTGGGGCGTCTTT\n') - f.write('GCTCATCTTCGTTGGCATCGTCTTTGCAAATTGTGATCAGTTGCCTTTGCACCTGCGTGC\n') - f.write('CTTACAAGTCCCCGTTGCTGGTTCGAATTATTTCATGTCTGATAGGATCCTTGACATTGA\n') - f.write('TGTGTTCGGGCAATAGCTTGGAGTAAGCACAGAATGCTGGAACGTCTACAGGGTAATTAT\n') - f.write('GAATACGCAAAGTGGAACGAGGCATGTCACAAACCAGCTGGTGCGACAGTAGGATGGACA\n') - f.write('ATTCCATCGAAACTCACGGGGAAAGGCCAAAAGGGACGGCATCACGGTGTCACACATCGG\n') - f.write('GGAGCGGCATCTCCAGGAGAATATGCCAGCAGCATTCCTGCTTTGCCATGCTCTGCTCAT\n') - f.write('GCCTCATGCATAGCGGCATGAATTGGTCTGTTCAGTCTGGgTAAATTGTATTCGGTTTGA\n') - f.write('CTACAGTTTACACCATCCTCAGCCACCACGCTGAAAGAGCCCCGGTTTGGGAAGCCCTAA\n') - f.write('TGCCATATCCTtCCTTTTGTCATGATTCTTGGTATAATGCGTGTGTATCTAACCGACCAA\n') - f.write('TTGGACGACTCCACCGGCGTCCTTAAtCTTTTtCTCGGCCTCTGCGGAGAAGtATCGGGC\n') - f.write('GCGAACGACGAGTGGGATTTctGGGAGACGACCCTTTCCGAGGACCTTGGAGTAACCGAA\n') - f.write('GGAGAGCTTTtCAAAGATTAGCGATTGCGATGGAATCGGCGCGTAGAGATACGTACGAGG\n') - f.write('TCGAGGACTGGAGCGGTGTCGGACTTCTTGTTTGAGAGGTACTTCTCACGCTGCTCGAGA\n') - f.write('GGAACGAGGGACCAAAGCTGTACTGGTTAGTAGCGGTACAATTTGAATTGGACTGCAGAA\n') - f.write('CTGACCTTGTCCAAGTTGATGGTTGGCTTCCAGAAGTGGTTGCCTTGCTTGTGGAAGTAT\n') - f.write('CGCATACCGACCTTTCCGAAGTAACCTGGATGGTATTTATCCATGTTGGTTCTGTGGTGG\n') - f.write('TGCTGACCACCAGCGAGACCACGACCACCGGGATGCTTGCGGCTATGCGACTGTTAGCCA\n') - f.write('ATGCCCTCTGATTCAATTAAGCCCAGTCCTGTAGGCGCTCTTCTTTCAAGTAGCAGTGAG\n') - f.write('TGTGGGCGAGAGCATTCGCAAAGCTGAAGAATTCCTCCCACACTGACTGCAATCGCGAAA\n') - f.write('TTTCGAAGATCCATTCGACATCGAGGAGAGGGTTATTGCTGAGGGCGTAACATACTGCTT\n') - f.write('GCCGACACGACCGTGACCGGCAGAGACGTGACCGCGGTGCTTGCGGGTGTTCGATAATCT\n') - f.write('GGTAGGCATCTTGGATGTGAAGGTGCTTGTCGTTGCTTCGGGATGGGAGATAGCGCGAAG\n') - f.write('TTTCGATATTCTCGTCTCTGTGTAGCGAGATTTTCCCGACGCCAATATAATAGTGACGCT\n') - f.write('AGCCGCGTCGGGAACTCTGATCATGTGACCACATCGGACTACCAaGAAGTTGGAAATGAT\n') - f.write('TGATTTGATTCATCTTGGTTCAAATTTACTTTGAAGCAAGATCTAATGATTCTAATCCCT\n') - f.write('CTTCTTACAAATGGAAGTGCCCAATATCAACGCTCATTTTCCACCACGGAATGTCGAGCC\n') - f.write('CCAGAGTCCAACCGAAGCCAGACAGAGACCACAATCTTCCAGTTCAAGATCAAACCAaCG\n') - f.write('CAGTTCAATCTCTCCGCGCACAAACAATACcATAAACCCGAATAAAGGGTGTACCAATTG\n') - f.write('ACTAACCAATCGCAGCCCGCTCAAATCCAATCGGCCCTCTCTCCCCACATCTCCAGCCTC\n') - f.write('GGTATCATGGCAAAGaTATCACCGTCGGCCTAAGAACcTtGAAATGCCGGGGAATAaaCC\n') - f.write('ACCGCCGCATAAGCATTCCAACTCTTAAGAACTGCATTTGTGAAAACCaTATCCATCTAT\n') - f.write('CTCATTCCCCGCTCCAGCACTCTCACAGTCCTTTAAaTACTTCTGCGCGCGCAAGTCTCT\n') - f.write('GTCTTCTAAGCTCATCCCCTCCACCTTACCTCGTACTTCTACCGAAGCAATCCACAATGT\n') - f.write('CAAAACAACTCTCCACAAAGGAAGTCGCAGAACACAAGTCCGTCGAAGAGGGTCTCTGGA\n') - f.write('TCATAATCGACAACGAAGTCTACGACGTCACAAAATTCATCGACGAACACCCCGGCGGTG\n') - f.write('TCAAGATCCTAAAGCGCGTCGCTGGAAAGGATGCCAGCAAGCAATTCTGGAAGGTGAGAG\n') - f.write('ATAATCCTCTTTCCCCCCAGACGTTCTGTAGTTGTAACTAACCCcGCTCGTGTTCATAGT\n') - f.write('ACCACAGCGACAACGTCCTAAAAAAGTACAAGCCAAAACTCAAAATCGGAAaCGTAAAGG\n') - f.write('AAGACGCCAAaCTATAAAACCCCCGCGCACACACAAGGAGAAACATTGAAGAGTGGAGGA\n') - f.write('TATGACACGAGTACAAGGCAGGCAGGCAGGCAGGCGGgCGGGCGGTCAGGCAGGCACGAG\n') - f.write('GCCGTCCAGCGTTATACCGGCATGATGAGAGAACGGCATTGCATATACACCCACCAGTAA\n') - f.write('TCTTGTCTACCTTGGGGGGgTTATATAGACGCATGCATAGATGAGCGGAGCGTACTAGTT\n') - f.write('TTACTTGCAGCAGACACTGCTGAACATCATCATTTTGGATACTTCACTTTCAATTCGTTG\n') - f.write('GTTTGGGCTACTTTACTCCTTTGCGGAAAGGAAGTGATTGGTCAATGTAGAATCAAGGAG\n') - f.write('CCATTCCAAATTTCCGTTGTTCCAATCCTGATGCTTTCATGAATGGCAATCGGCTGAAGT\n') - f.write('TTTCAGGGCGAAGAGTATTGATTCGTGGGATAGACAACCCCAACTTCACCACAAAGGAAA\n') - f.write('GGAGAAACAGAACCAATGGACAAAAACAACGGGGAGAGTGGTCATAAAAAGCACAATGGT\n') - f.write('ATCAATTACTAAAAGCAATAGtGACGAtCGAATTtCCCTCCCAAACTCATATtCTGAGTT\n') - f.write('CCCACAGCCGTGATCCCAAACGCCACGACATTGAGAAaTGAAAAGTCAGACAAGCAACGC\n') - f.write('CATCGGGGTgTCCGAATCAATAAGAAGAAAaTAAAGGAATAAAGCAACGCAACGCGACAT\n') - f.write('TCCATCGTATTGGTTCAACCATTCTCACAATGCCCAGTACCATGTCCGCTAATCACCGAG\n') - f.write('ATGGATGTTTCCCCAAACTCGCATCCAGCCGTGCTGGCCTCGACATAAATgCTTGATAGG\n') - f.write('ATCGCATAGTTGCGGCAGTCTCACTTTTGTGCTCTTGGGTCGTCGTCCGAGGTCGCAGTT\n') - f.write('GTTTTGTATCTGAAAACCCCGCAGGGAGGGCCCTCAAAAGCTGTCGATTCGGACAGCCCA\n') - f.write('TGGGATTTGTACCACCAAGATCATTCGCGCCACTCTGAGCAGACCTCTCATTGTCATTTG\n') - f.write('AAGATTTGGGACCAGACTGGCAGGAAATCACAGCACTTGTAAGCTGAGTGGgCGAGTGGA\n') - f.write('GAGAATTGACACCATTTGCAGGCTGAGTAGGCGCACCATTGACCACCAGGCCTTGTTGGG\n') - f.write('ATTGTCCGCCTCTCTGTATATGATCCGTtACCCGCTTGCAGCGCCCATCGTCCATCGTCT\n') - f.write('GAAGTTGGAGCTTGATATTTGCTGGCATGGTCGCAAGAACATGACTAGGTAGGTGgCTTG\n') - f.write('CAACGACATCCGCACTTCTCAAaaCTGGTTTGGGCTTACTGCCGAATCCATCAGGGCGCT\n') - f.write('TTTGAGCAATGCTTTGATTGCCATCTGAAGAGTCGAAACCAGAACTGCGCAAAACATGAA\n') - f.write('TGAGCAACGATAATTCTAACGAGACGTAGAGCTTTGTGGGCTGTTTTTTTAGTAGATGGT\n') - f.write('GAGATGGAAATGATATTTGGCTGATGAACCGAAACGCCCCAAAATTGTGGGTCTCCGCAT\n') - f.write('GGAGACTTACGACTTGAGGAGTTGGGCGTCCAACCTCTTCAAATCGCT\n') - f.write('>Vein_ctg_5197\n') - f.write('AAACCATTTGTACAGTCCTAGCCTCCTCTTCAAGAACCAGACGCTAAACAAGCCGACGAA\n') - f.write('GAGTACTAAAGCACCACGCGTCATCTGGTAGATAGACGCGGCCACAAACAACAAGCCCAC\n') - f.write('ATTCATAAGCGTAGTGCCTATGATATCGCAGATCGCTGGCAGAGCTAGATAtGTCACTTT\n') - f.write('CCAGCCTCCCAAAGTCGCTCTTCCATCGTGTGTAAGtGTGAGAGAGgTCGCTAGCGGATC\n') - f.write('GTCCGAGTATGCATCAtcGTCATCGTCTTCGGGCTCTTCATTGTTAACGAGTAAAGGATC\n') - f.write('GGGGGCGGAGGAAGGGATGGAGAAGTAGCCGGCCTGCTTCCCTCGTCGTTCCTGGATACG\n') - f.write('TCTGTAGAGAGAGTGTGCTCCGACAACGAGCCAGCAGCCcATCTcGCCCATGAACaTTTG\n') - f.write('CAGCGTTTGTATGACtGGTTGTTCGAAGTGTcTCCTGTtCTTTGGGTTGGTAGCTTTGCA\n') - f.write('GTTGCCAGTACaTTGCATGtCCTTTCGCGATCCAGTCAGTTAAGGCCTCATATCAGCTAG\n') - f.write('CAGGAGACAACCATACCTGGTACTTCGTGAGCAGAGTATTACACACTCCCGTCGTCAACA\n') - f.write('TCATAGCCaCCAAAAACGGAATCACCGCCTTCACGGCcATGGCTGCGTGCGAGGCCGGAG\n') - f.write('CTCAACGAGCTCAAGGCAGGGGATGGGAGAGCTTCGggCAGGCCTATAAGACGCAAGCTG\n') - f.write('ATGAATAGTTGTCAGTGATATTGGAGGTACTTTAGCTGGAGGAGAGCTGTTGGGTATTTT\n') - f.write('CAGTGTTTGAAGGTAGGCACTATAGAAGCTCGTCGCGTGATGGTGATTCAGACAGGGTCT\n') - f.write('GTGATAAGTAACGACCTCGGGAGGTCCGTTCACAAGCTACGATAGTACCGATTTACCAGT\n') - f.write('GCTTGGCACTGTTGGCAGACATCGCGGTCGCGAAAGACGAACGCATGAGGCATCTGATTA\n') - f.write('CAGCGAGCACGCTAGGAAAGATATGAGTGTGGGATTCTCCACACAAAAAGTGGCACAGTA\n') - f.write('TCAGTCATAACACATCGCTTCTATTGTTTGTTTGAACTCGCAGAAGTGAAATCTAGAGTC\n') - f.write('CCCAGGAGCAGACTCCTTCGCATAACCGTTCCTTCGTGAGCCGCATTAACACATGGAAAG\n') - f.write('AAGTTGACCGGCTATTTTtGCATACTTTGACGAACGTCGAACCATGCCCCATGAGAAAAA\n') - f.write('AAAaaCaGATGCAGTGGATATATTGAAGACCTGAGAATGCAAaGAtAACTTTGCGGgAGA\n') - f.write('GGTTCCTACCCGACGTTTCCATCAGAAAACCCATTCCGCTAATCACCCTCATCGAACTAT\n') - f.write('GGGTCGTGGAGCATCTACTTCTTGGCACCAGCCTtGACGGCAGCCTTGGTAACCTTACCG\n') - f.write('GCTTTGTCGACCTTGACGACGCTCTTGATGACACCGACAGCGACAGTCTGTCTCATGTCA\n') - f.write('CGGACAGCGAAACGTCCGAGTGGTGGGTAGTCAgTGAAAGCCTCAACaCACATtGgCTTG\n') - f.write('GAaGgAAtcATCTTGACAaTGGCGGCGTCACCAGACTtGATGAACTTGGGGCTGGTTTCG\n') - f.write('GTGGCTTtACCAGTACGGCGATCGATCTtCTCCAAAAGCTCAGCAAACTTGCAAGCAATG\n') - f.write('TGGGCAGTGTGGCAATCcAAGACTGGAGCGTAACCAGCACcGACCTGACCTGGGTGGTTG\n') - f.write('AGGACGATGACCTGGGCGTTGAAGGACTCGGCACCCTTTGGAGGGTCGTTCTTGGAGTCA\n') - f.write('CCGGCGACGTtACCACGACGAATTTCCTTGACGGAAACGTTCTTGACGTTGAATCCGACG\n') - f.write('TTGTCACCTGGGAGACCCTCAACGAGCTGCTCGTGGTGCATCTCGACGGACTTGACTTCA\n') - f.write('GTGGTGACACCAGCTGGGGCGAaGGTAACGACCATACcGGCCTTGATGACACCGGTCTCG\n') - f.write('ACACGACCGACTGGCACTGTTCCAATACCACCGATCTTGTAGACATCCTGGAGAGGAAGA\n') - f.write('CGgAGGGgCTTGTCGGATGgACGGGATGGTGGgTCGATGGCATCAATGGCCTCGAGGAGG\n') - f.write('GtCTTTCCGGTGACCTTGGACTtGGTCTCCTTCTCCCAACCCTTGTACCATGGGCAGTTG\n') - f.write('CTGGAGTTGTCGATCATGTTGTCACCGTTGAAACCGGAGATTGGCACGAATGGGACGTGC\n') - f.write('TTTGGGTTGTAACCAACCTTCTTGATGAAGGAGGATGTCTCCTTGATGATTTCGTTGAAT\n') - f.write('CGCTCCTCGGACCACTTGGTGGTGTCCATCTTGTTGATGGCGACGATGAGCTGCTTGACA\n') - f.write('CCcAAGGTGTAGGCGAGCAGGGCGTGCTCACGAGTCTGACCATCCTTGGAGATACCAGCC\n') - f.write('TCGAACTCACCAGTACCAGCGGCAAtGATGAGAATGGCGCAATCAGCCTGGGAGGTACCA\n') - f.write('GTGATCATGTTCTTGATGAAATCaCGGTgACCgtGGGgCGTCAATGACGGTGAC\n') - f.write('>Vein_ctg_10638\n') - f.write('AGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCA\n') - f.write('GAGCACTGGGCAGAAATCACATTGCGTCAACACCACTTTCTGGCCATCGCAATGCTATGT\n') - f.write('TTTAATTAGACAGTCAGATTCCCCTTGTCCGTACCAGTTCTAAGTTGGTTGTTAAGCGTA\n') - f.write('GACTGGGTTCCCTTGGTTGTAGACCAAGAAGATGAAAGAACAGAGTTGCCCCCATTCTCT\n') - f.write('CTTCCTCAAGGTCAATACCAAGGGTCCATTTCTACCCAACCCTTAGAGCCAATCCTTATT\n') - f.write('CCGAAGTTACGGATCTATTTTGCCGACTTCCCTTATCTACATTGTTCTATCAACTAGAGG\n') - f.write('CTTTTCACCTTGGAGACCTGCTGCGGTTATGAGTACGACTAGGCGAGAAAATTATTCTTT\n') - f.write('CCCTTGGATTTTCAAGGATCGTTATGAATGCACCGGACACAGCAAAAaGTACTGTGCTCT\n') - f.write('ACCAGCAGATAAACCTTTTCTCCTGCTAAACAGATTTCAAGGTTTATACTAACTGTCAAA\n') - f.write('AAGAAAAGATAACTCTTCCCGGGACCCATACTGATGTCTCCAAGTTCAATCGCGTTGCCG\n') - f.write('CAAAAAATCCTCGTCCTAGTACCGGAATATTAACCGGTTTCCCTTTCGATAGGCGGCCCA\n') - f.write('AAAATTGGGCGCTTTGAAAAAACGGAACTTCCCTATCTCTTAGGATCGACTAACCCTGGA\n') - f.write('CCAACTGATGTTCTCCAGGAACCTTTCTCCACTTCAGTCTTCAAAGTTCTCATTTGAATA\n') - f.write('TTTGCTACTACCACCAAGATCTGCACTAGAGGCTGTTTCACTCCGGTTCACACCAAGAGC\n') - f.write('TTCTTAACAGTTTATAAAAACCTCCACGCCTGCCTACTCGTTATTGCTTCGCTTTTACAA\n') - f.write('TAACGGCAGAGTATGGGTAACACGCTTAAGCGCCATCCATTTTCAGGGctAGTTCATTCG\n') - f.write('GCAGGTGAGTTGTTACACACTCCTTAGCGGATTCCGACTTCCATGGCCACCGTCCTGCTG\n') - f.write('TCTAGATGAACTAACACCTTTTGTGGTGTCTGATGAGCGTGTATTCCGGCACCTTAACTC\n') - f.write('TGCGTTCGGTTCATCCCGCATCGCCAGTTCTGCTTACCAAAAaTGGCCCACTAGAAACTC\n') - f.write('TGCATTCAATGACCTGCTTCAATTAAGCAAACAGGTCGTCTTACATATTTAAAGTTTGAG\n') - f.write('AGTGGTTGAAGGGCGTTTAGCCCCCCGAGACCCCAATCATTCGCTTTACCACATAAAACT\n') - f.write('GCGTATAAGTTTCTGCTATCCTGAGGGAAACTTCGGCAGGAACCAGCTACTAGATGGTTC\n') - f.write('GATTAGtCTTTcGCCCCTATaCCCAAATTTGACGATCGATTTGCACGTCAGAATCGCTAC\n') - f.write('GAGCCTCCACCAGAGTTTCCTCTGGCTTCACCCTATTCAGGCATAGTTCACCATCTTTCG\n') - f.write('GGTCCCATCATTAGTGCTTTGTCTCGGTCAATTCAGTATAAAACGTCAGCGCCGGACGAT\n') - f.write('ACTGCCTCCTTAATGGATTCGTATCAATCAGTTTCCTTACGCATATGGGTTTGGCACCCA\n') - f.write('AATACTCGCACTAATGGTGGACTCCTTGGTCCGTGTTTCAAGACGGGTCATTTAGAGTCA\n') - f.write('TTAAGCCAACAACCTAAGCGAATAGAAGTATAACCAAAAAGATCAACCTTGATACCGTAG\n') - f.write('TACCTCAGAAAACCTTCCTGGAAAACTCGCCAATAAGCATTCGCTGCGTTCCTCAATCCA\n') - f.write('ACCCAAGGTATTTTCTAAGGGACTATAACACCCACAAGTGGGCCACATTTCCCCTAGTTT\n') - f.write('TTTCCCTCAAGTCAAATTGTCGTTGGCAGGCATAGCCTGCAAGTGCATCCAGGCCGAAGC\n') - f.write('CTAGATTGATTACAGACAAGCCAGTCTGGCTCCAAACGGTTCCCTTTTAACAATTTCACA\n') - f.write('TACTGTTTAACTCTCTTTTCAAAGTTCTTTTCATCTTTCCCTCACGGTACTTGTTCGCTA\n') - f.write('TCGGTTTCTCGCCAATATTTAGCTTTAGGTGAGATTTACCACCCAATTTAGGCTGCATTC\n') - f.write('CCAAACAACCTGACTCTTTGAAAGCGTATCACAAAAGGCAAATGCTCAAGCCAAAGACGG\n') - f.write('GATTCTCACCCTCTATGATGCCCTGTTCCAAAGGACTTATTTACTCGGCTTGCCTGGAAA\n') - f.write('ACACTTCTACAGTCTACAATCCGGTTTAGCTAGGCCAAACAGGTTCCAACTTTGAGCTCT\n') - f.write('TTCCTCTTCACTCGCCGTTACTAGGGAAATCATTGTTATTTTCTTTTCCTCCGCTTATTG\n') - f.write('ATATGCTTAAGTTCAGCGGGTAATCCCACCTGACTTCAGATCATAGTTTGAAAGTTACTG\n') - f.write('GATTATACTCTTGTACTTTACTTCCTGGGCGAACCAAAAAAAAaGATCCTGAGACCAGCG\n') - f.write('TAATATTCCTGCCTAGCAAGCCAGACAGAAAATCACACACATTTTAGGTGCTCACTGTAA\n') - f.write('TAAAACAGCGATGCGACCCATCACCACATAAACAAATGTTATGTGTGGGTTTGTGATGAT\n') - f.write('ACTGAAGCAGGCGTACTCTATAGAAAAACCAT\n') - f.write('>Vein_ctg_10639\n') - f.write('ACAAACAGACAAACAGACAAACAGACAAACAGACAAACAGACAAACAGAGAGGCAGACAA\n') - f.write('ACAGAGAGGCAGACAAGCAGACAAACTTAACATAATGCTTGCATACAAGTATCCTTGAAG\n') - f.write('ATCAGAAGCCAAGTGTCAAACTGCTAAAACTGAATTACATAAGTGAATCTAGATAAAGAA\n') - f.write('TCACATGTGGGGGAAGAACATTAAACTAATACTGTTTACATAAAAAAAAaGCAAAAAAAA\n') - f.write('ATAATATTTAATTTGTATAGCTGAAAGTGTTCCCGTAAGGAACAAATTCAATGACAAGGG\n') - f.write('CTTAATCTCAGTACATCGTAGCAACAAAGGCTACTCTAGTACTTACAATACCCCGTCCAT\n') - f.write('TTCATGTCGTCTGCATGCGATTTATCACTTTGATCATTTGCATTATCATCACAGGGTAGT\n') - f.write('GAATCACAGCATTTCCGCTGCAAAGCCTATCCCGCAAGTAAGGTTTTCAAGCCGAAGCTT\n') - f.write('TATTTGTACACAACTAGTACAATCAAAGCACAGTAGTATCGCTTCCAGCATGGATTCTGA\n') - f.write('CTTAGAGGCGTTCAGCCATTATCCAGCAGATGGTAGCTTCGCGGCATTGGCCTTTCAACC\n') - f.write('AGCCGCAAATACCAATTATCTGAATGAAGGGTTCCTCTCGTACTAACTTCAATTACTGTT\n') - f.write('GCGATACCAATACCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGC\n') - f.write('TCACGTTCCCTATTAGTGGGTGAACAATCCAACACTTAATGAATTCTGCTTCATTATGAT\n') - f.write('AGGAAGAGCCGACATCGAAGAATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACA\n') - f.write('AGCCAGTTATCCCTGTGGTAACTTTTCTGGCACCTCTAGCCTCAAATCTTGAGATTCTAA\n') - f.write('AGGATCGATAGGCCACACTTTCATGGTTTGTATTCACACTGAAAATCAAAATCAAGGGGA\n') - f.write('CTTTTACCCTTTTATTCTACAGGAGATTTCTGTTCTCCTTGAGTCCCCCTTAGGACACCT\n') - f.write('GCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACTTGACAATGTCAATAA\n') - f.write('CATGGGTCGCACCCTAATGGATGCTTAAAGCTAGAAGGTGAGTCTTGCGACTCAATCCCA\n') - f.write('CTTAATTATTTAAGTAAAAAAaCAATAGA\n') - f.close() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/MockESTBankForBlat.py --- a/commons/launcher/tests/MockESTBankForBlat.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5996 +0,0 @@ -class MockESTBankForBlat(object): - - def write(self, inFileName): - f = open(inFileName, 'w') - f.write(">gi|226792376|gb|GO546081.1|GO546081 Mdas9010M17_e784.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_850886.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("GTTTCACGCTCTTCCTCAGCTTCATCAACCTCCGAACCCTAAATTCCCAAATGGCCTCCTCGCCGGACCA\n") - f.write("CCACATCAACGGCGACACCAAAACCCACATCTCCAAAAAACCTAAACTTTCCCCAAATTTCATCACTGCC\n") - f.write("GCCGAAATCGCCGCCGAATTCTCCCACCACGACCCGAACGTCGCCCGGATCAACAACGGCAGCTTCGGCT\n") - f.write("CCTGCCCCGCCTCCTTGATCGAAGCCCAGCGGCGGTGGCAGCTCAAAAACCTCGCCCAGCCCGACCATTT\n") - f.write("CTACGTCAACGAGCTCAAGAAGGGAATCCACCGTTCCAGAACCATTATCAAGGAGCTCATCAATGCGGAC\n") - f.write("CATGTCAACGAGGTCTCACTCGTCGACAACGCCACCACCGCCGCCGCCATCGTGCTTCAGCAGACGGC\n") - f.write("\n") - f.write(">gi|226792375|gb|GO546080.1|GO546080 Mdas9010J22_e767.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTCCCATTAAAGAATTATAAAAGATCAATACATAGAGAAATAAGAGAGGGACATATATATTGTCA\n") - f.write("CATATACTGGCTAGATATATATATATCTAGCTAGCTACTTGACAGTTATTTGTACGTAATTACTTGACAA\n") - f.write("TTAAAAGAAGAAGAAGCAAAGAAAAGTGAACAAGACAAAGATGGAAGTAAGACCATGAGGGTGGAAGTGC\n") - f.write("ATTCTCAAATGAACCGATTTAGAAAAATAAGGTGGCGGGGGACTGTAAGGATTTACAGGATAAAGGCTTG\n") - f.write("GTGGTACTATAGAGGGCGCAAATGGA\n") - f.write("\n") - f.write(">gi|226792374|gb|GO546079.1|GO546079 Mdas9010L17_e779.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAG35782.1|AF280060_1 tonneau 1 [Oryza sativa], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTCAGTTACTAATTTATATTTCAAGAAATCAATCAAAAAGCACTCCAACAAAGCACTA\n") - f.write("AATCAAATCAAAATAGGGTATAATCTTACATAACATGCCTATCATTTGCGGGTGAAATACACAAAATCAA\n") - f.write("ATACCGTGCAGTTATACAAAGGTTGTCATCGTGCAGCTACATCTGGTCAGCCCTGCCGTCATCCTCACTA\n") - f.write("ATTCCATCTCCTGCGTGCCGCCAAAATGTTGTTAAATTGCGAGCTTTTCTATCCAACTGGAGGTTTTCCA\n") - f.write("TCGCACTTGAAGCTCGAATGACATCCTCTGGACTTTCATCACTGTCGTATCTATAGCTGTAGTCATCTTT\n") - f.write("CCTGTAGCCAGACATGGAGGACCCACCTCTTCGATCAAATGACTGGGAAGATGCACCAGGCCTTCCTAGT\n") - f.write("GGAGGTAGCCCACCAGCAACAGATGATGAAGAAGGTCTTCTCATATTGCGAGAATCTAAATTGGACAGGG\n") - f.write("ATTCTGTTTCTGAAGTCGTTAGCCTCCTTCCGGTACCCCTTGATTGAGATAGATTCTCAAATTTCAAAAA\n") - f.write("TCCTTCAAGCACATCCAAAAGCAAAGGACCACTATCTCCATTTCGGTTAAGATCATATCCATTCTTGCTA\n") - f.write("CTAAAGTCCTTCAACTCAGCTTTCCAAGAATCCTTTT\n") - f.write("\n") - f.write(">gi|226792373|gb|GO546078.1|GO546078 Mdas9010H22_e754.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n") - f.write("AAAAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCATTTGCTGGCCAGACTGCTTTGAA\n") - f.write("GCAGTCCAATGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCCGCTTCTCCATGCGGCGCACCGTC\n") - f.write("AAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTACTTGGGACCATTCTCCGAGCAAA\n") - f.write("CTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGACACTGCTGGACTATCTGCAGACCC\n") - f.write("CGAGACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGATGGGCCATGCTTGGTGCACTGGGA\n") - f.write("TGCGTCTTCACAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGAGGCTGTCTGGTTCAAGGCTGGAT\n") - f.write("CGCAAATCTTCTCTGAGGGCGGCCTTGACTACCTTGGGCACCCAAACCTTATCCATGCTCAGAGCATCTT\n") - f.write("GGCAATCTGGGCTGTCCAGGTCGTGCTCATGGGATTCATTGAGGGATACAGAGTTGGAGGAGGAACCACT\n") - f.write("CGGTGAAGGACTAGACCCACTTTACCCAGGAGGGGCCTTTGACCCCCTTGGACTTGCTGATGATCCCGAA\n") - f.write("GCTTTTGCTGAACTGAAGGT\n") - f.write("\n") - f.write(">gi|226792372|gb|GO546077.1|GO546077 Mdas9010K23_e774.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187130.1| ribose 5-phosphate isomerase -related [Arabidopsis thaliana] gb|AAF04905.1|AC011437_20 putative ribose 5-phosphate isomerase [Arabidopsis thaliana] gb|AAG51427.1|AC009465_27 putative ribose 5-phosphate isomerase; 91580-90750 [Arabi, mRNA sequence\n") - f.write("TTTTTTTGAAGCACGAAGGTAATTCATTTCACATTATTTCACAATTCACAATTCCATCATTCTTTAGTAT\n") - f.write("CATTAGTATACCACTGAGTCGAAACCGCAATGCTCAACAAACAATAAGACTATCGAATGCAGAATTTTCG\n") - f.write("ACAAATTTCCCATTTCGCCAATCTAAAATTACACCAAAGCAGCTAAATTTCACCAGTAAATACTGAACAA\n") - f.write("CAAGCAGCAAGTACCAAAACCCCCCAAAAATATGGAAAAAAACAGAGTACTAATGGAGATTCCAAATACT\n") - f.write("CACCACCACCGGAGAACCCGAAAAAAGCCAATCACTTGGTCTTCACATCCACTCCATCCGTGCCCGCAAT\n") - f.write("GATCACCGCCGTCGCCATGTCCAAGAACAACCCATGTTCCACAACCCCTTCAAATTTCAAAATCTCCTTC\n") - f.write("CCTGCCGCCGGCCCGTCTTTAATCGGAGTCTGGAAGTACAAATCCACAATGTAATTGAAGTTATCAGCCA\n") - f.write("CATACGGCTTCCCGTCGCCGTCGATCC\n") - f.write("\n") - f.write(">gi|226792371|gb|GO546076.1|GO546076 Mdas9010F21_e739.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) (PS I subunit 5) pir|A60695 photosystem I chain II precursor - cucumber prf|1710320A photosystem I 20kD protein, mRNA sequence\n") - f.write("TCACTGAAGTTGCATTTTAATGAAATCAAATTACAAGAAGCACAAATTATACTCACATAGTCATCATCAT\n") - f.write("GATCTTAAATACATTGCAAATTACACAAATCAATATCATGATCATATGTCATAAACTTGCTTGCCGGTGA\n") - f.write("ACTTGACCTCAATTGGGTTGACATTCTTCCCAATCGACCTAAAGTTCTGGCCAACCCCTTGGCGCCCAGG\n") - f.write("GTTCACCTTCTCAGGGTACACACCATCCTTGGGGTGCAAGTATTGGACCTCCCCGTTAGGGAAAACCCTG\n") - f.write("TAAAACTGGTACTTAATCTTGTACTTTGACCTCAGCCTTGTCCCAAGAACCAAGCACTGCTCTTTCCTAA\n") - f.write("CCAGTTTCAACAAGTTAGGACCCTCCCTCATGATGGCTGCTCCGCCGGTCGGCATCTCAAAAATCTGCTC\n") - f.write("CTTTGGTGACTCCCATGTGATCACGTAAAACTCTTCCTCCTGCGCTTTCCTCAACAGCCCGCCGGTGCTG\n") - f.write("CCGCCAAAGATCGGCGAGGGAGTTGGTGGGTCCAGCTCGGG\n") - f.write("\n") - f.write(">gi|226792370|gb|GO545820.1|GO545820 Mdas9004G01_e277.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192425.1| 4-coumarate:CoA ligase (4-coumaroyl-CoA synthase) family [Arabidopsis thaliana] pir|H85064 4-coumarate-CoA ligase-like protein [imported] - Arabidopsis thaliana emb|CAB81058.1| 4-coumarate--CoA ligase-like protein [Arabidopsis tha, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTACTGTAGAAGAAGACTGTATACTCCATATGGTAAAATGATATACCTCTGC\n") - f.write("CCTTTTCGGGCAAGAATGCTAGATCCACCGAAAAGTACGTATACTCGTTATGGTGAAATGAAAAATATAA\n") - f.write("ATAATTTGCATTAAAAGCAACGTACTGAGGTTGTTGCTATTTTTCTTTTTGGGTATAGGAGTTTCTATAT\n") - f.write("GGACATAATGAAACTGCTCTTCTTTATTTAAATCCAAAAACTTACTGCTCAGATTGTTGAAGAGAATCGT\n") - f.write("AGAGAGTTGGTACTAAGAGCTACGTCCTGCTCTTCTTCCCTATAAAGAATGGCAGCACAGCTGAATATCG\n") - f.write("TAACATACCTGCAACTTTAAAACAAGCGTACGGAACTTGTAGTGTTCCTACAAGCCTTCCCGATAAAGCA\n") - f.write("AACATCGCATCAATGAGGAGCCATGATACAATTTCATATTTTCGACCGCACTTTCTCGATGAGCTCTCTT\n") - f.write("CTGAGGATTTTGCCCGATGCTGACTTGGGGACACTGTTTATGAATGATACTCTTCGTAGTCGTTTGAAAG\n") - f.write("ATGCAACTTGACTAGCAATAAAGCTCTTGACATCTTCTTCAGTTAGAGAACTATTTGGCGTACGTACACA\n") - f.write("ATATGCAGCGGGGACCTCACCAGCTTCAGCATCAGGG\n") - f.write("\n") - f.write(">gi|226792369|gb|GO545819.1|GO545819 Mdas9003M23_e232.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTGTGAAGAATTTCTAGTTTTGAGGATTCTAGAAAACTGAATGTAG\n") - f.write("AATTTATAGCCCAACAGTTACATCAACAAGTATTCTGTGGCTTTTATATCTCAGTTCAATGTTTCCAGCT\n") - f.write("ATAGATTGGCTAGCTCATGCTGGTTGAGATGGTGTTGTCTCTTTCTCTTATGAATAAAATAATTCTTTGT\n") - f.write("GCCGATGTGTTGCCTCAACCACAGCACGTACGGCATCGAAGTCAACATTGGGGCCGACATCGGTGGCCTT\n") - f.write("GAGCACTCGAATGCTCAAATTCTGATTAACCTTGCCGATGATTTCAGCAGCATGACCAACCGTCAGATGT\n") - f.write("GCTTCAGGATTAAATTGTAGCGTTACAGCACCATCGCTGTCCAA\n") - f.write("\n") - f.write(">gi|226792368|gb|GO545818.1|GO545818 Mdas9003L19_e221.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T02087 gag/pol polyprotein - maize retrotransposon Hopscotch gb|AAA57005.1| copia-like retrotransposon Hopscotch polyprotein, mRNA sequence\n") - f.write("TCGAGAAACAAATATTTTTCCAATTTGGAGATCATAAAGACGATGCCATTTTTGCCTATAAAGGTATCCA\n") - f.write("AGGAATATGCATTGGGAGGCACATGCATCAAATTTGGTGAGTCGTTTATCATCTGTGGAGCTTATGGTGG\n") - f.write("ATGGTGAACGGGTATGTTTAGCTAAAGGGCAAACTGAACAATAATTAATTTCAGAAAACTGAATGTCTTT\n") - f.write("TACATATGCTTGCATTAATCGGAAATGTTTATCGGAAAGGTGCCCAAGGCGTTCATGCCAAAGGCAGGAA\n") - f.write("ATAGCGGACTTGCTGACAAAATTGCAGATAGCCTCCATAGTAACAATGTTGAGATAGTAGAGTCATCCCC\n") - f.write("TTTCAGTTCTCGTCCCAATCATCATCCCCAAGCATTGGTCCTGTAACACAAATAGGTTTTTAGCAAAAAA\n") - f.write("GGCAATGTAGTCCGAGTGTTGGACAAGTTTAGCGACGGATATTAGATTCAATTGGAATGAAGGAACACAT\n") - f.write("AAGACATTACGAATGGTCAAATTGGGAGAGAATTTGACACTCCCTACGTGTGTAACAGTAGCACTCATGC\n") - f.write("CATTTGGTAATTGTATGGTTCGATTTTGTATTAATGAGCACGTAATAAGTAGGGCAGGAGAGTACACTAT\n") - f.write("ATGATCAGTTGCTCCTGTGTCCAAGATCCAAGCTACGTCTTTCCAAAGAGCGAAGCCACGAAAAGATTTA\n") - f.write("CCTGAGAGACTA\n") - f.write("\n") - f.write(">gi|226792367|gb|GO545817.1|GO545817 Mdas9004B15_e260.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O24059|MT3_MALDO Metallothionein-like protein type 3 pir|T17015 metallothionein-like protein AMT2 - apple tree gb|AAC23698.1| metallothionein-like protein [Malus x domestica], mRNA sequence\n") - f.write("CAAAATACCATTCAAGCGAAAACCCTAATTTAAACACATCTTCAGCTCCAAGTTCTTAAGTTTATCTTCA\n") - f.write("ACATGTCGGGCAAGTGCGGCAACTGCGATTGTGCTGACAGCTCCCAGTGCGTGAAGAAGGGAAACGGCTA\n") - f.write("CGACTTGGTGATCGTGGAGACTGAGAACCGCTCCATGGACACCGTCGTCGTGGACGCTCCTGCAGCCGAG\n") - f.write("AACGACGGAAAGTGCAAGTGTGGCACAACCTGCCCATGTGTGAACTGCACCTGTGGTCAGTAAGCCCAGA\n") - f.write("TAACCAAATTAAAGATGTGATTAATAAAAGTGTCATATTAATTAAGGGATTATAGACCCTTAATTAATGA\n") - f.write("AAAGTGTTTGTGGGATAAAATAACGTTGTGGCTTTGTCTCTTGTTTGCTTATAGTATTTGAGTCTGTCGA\n") - f.write("GTGACATGTTGTACGTCTGTGAAAACATGTCACTCATATGTTTGTGTTTCTGTGATTGTGTCATGTAATG\n") - f.write("GCCATGTTCATGGCCCTTTGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792366|gb|GO545816.1|GO545816 Mdas9004B22_e262.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA10129.1| hypothetical protein [Cicer arietinum], mRNA sequence\n") - f.write("AATTAGGGTTTCTAGCTCCTCCTCCTTATCTCTCGATTTACCAGACGGCATGGGAGGAGGCAACGGTCAG\n") - f.write("AAGGCCAAGATGGCCCGCGAGAAGAACTTGGAGAAGCAGAAAGCTGTCGGCAAGGGAAGTCAGCTTAAAA\n") - f.write("CAAACGAGAAAGCCATGTCAATCCAGTGTAAGGTGTGTATGCAAGCATTTATGTGCACCACATCGGAAGT\n") - f.write("GAAATGCAGGGAGCATGCTGAGGCAAAGCATCCCAAGTCTGATGTCTACGCTTGTTTCCCTCATCTCAAG\n") - f.write("AAATGAAAGAACATTTGGTAAGAAGTCACAGGGACAAATTGTGAACGTCGTGGCCCTTTATATTAAAGCC\n") - f.write("TGGAATGAATTTACCGAGTTCTTCTAGAGCGATAGCTATTTAATACTGCTTGTGGAGTTGTTTTTGTGTG\n") - f.write("TATGTGGTGTGTGTGAGTGAGGGAGAAAGAAAGAGATGTATCTCCTTGTTGAACCGAAACTCGGTCTTAA\n") - f.write("ATGATTGTGAATGTTGTTGGTGTAACTCTTGAAAAGAGTTTGTTTCATGGAACCTTGGTTCACTGCGTTG\n") - f.write("TGTCGTCTGTACGGGTTGAGTGTCGAGTTTGTGGAACTGCTGTTTGTCTGGCAACTCCGAGGCAAATTCA\n") - f.write("CACCAAACCTTGCCTCTTTGGTAATTAATTTGTGTGTCGAAGGTTCTGTTAAAA\n") - f.write("\n") - f.write(">gi|226792365|gb|GO545815.1|GO545815 Mdas9004A17_e252.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33652.1| carbonic anhydrase prf|1710354A carbonic anhydrase, mRNA sequence\n") - f.write("GAAGGAACCAACCTGGATCTCCGTTTATTATTTTTTCGCAAACGATTACAATCTCAAGGAAATTATACGA\n") - f.write("TTACATTTGCAACGACGCTGCAGATGAAATTAAGAAGGAAATTACAAACAGGAAGCAATTGAGTTGCATG\n") - f.write("GGAATGTGATTGCGATCATACGGAGAAGATGGGGTTGAGGCTGAAATCAACATCCCAGAGCTCGAAACGT\n") - f.write("CCGTTGACAAAGTCATAGTATCCTCCCTTGATTGCTAGGGTTTTCTTCAGCAAACCCTCTCTCACAAACG\n") - f.write("GATAGCTCAGCAGGTTTCCGATCGATACATTCACCGCCTCCTTTTCACAGTGGCCGCAGAGATCAGCGAA\n") - f.write("AGGAGCATCGGCACCATGATCTGCCTTCACCTTCTTCCCTGCCGGCGATGCGATACCAATCCAGTCTTCT\n") - f.write("ATGAAGTCAGTGCCAAGGGTAGACCCATCTTCTGGAATCGACAAGAGCGCCTTGATTCCTCCACAGGCGC\n") - f.write("TGTGCCCAATCACCACTATGTATGAAACCTTGAGATGCAAGACAGCATACTCAACGGCCGCCCCAGTTCC\n") - f.write("AGCGTATTTAGTC\n") - f.write("\n") - f.write(">gi|226792355|gb|GO546075.1|GO546075 Mdas9010C10_e729.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCTAGTTTTTTTTTTTTTTTTTTCTTGGAAAGCAGTCACCATATCGGAAAAATACTGCTGCTTGTGTGAT\n") - f.write("CATATAAATGTTATTAAATAATCAAGTGA\n") - f.write("\n") - f.write(">gi|226792354|gb|GO546074.1|GO546074 Mdas9010K17_e772.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GTAAGTAAATATAAAATACCACTTGAAAATTTCCCCAGTTGACTTACAAATAACATCCCACTTGATTTTC\n") - f.write("ATTGCTACCAAAAATCACAGAATTTTGCCTTATAGGGCAAACTTGCCATTAGTTATAACCAAATTGAATA\n") - f.write("AAACAAAAAAAACAACTTGCTAACCCTGTTTTGAAAAAAAAAAATGGAAATAGGGATGGAAACCCAAGCA\n") - f.write("CCTAAAAAAATGAAA\n") - f.write("\n") - f.write(">gi|226792353|gb|GO546073.1|GO546073 Mdas9010D09_e734.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCAC\n") - f.write("AATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAG\n") - f.write("CGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTA\n") - f.write("GGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTC\n") - f.write("CACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCT\n") - f.write("CCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTC\n") - f.write("GGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCACACCTGCATG\n") - f.write("CATTGCACTCTTCCTCCATTGCTTGCAATAGAGGTAATGTCATTGCTTTTTCTGGTGACAGGGAAAGCTG\n") - f.write("AGGAGGACTTGAGGCCGGTGAATGGAGCAACCATTCTGGCTTGAGCGGGGGCGGAAACTGTAGCCACGGC\n") - f.write("ACCGGAGGAAATCATGGAGGAAGCCATTGCTCTCTCTCTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792352|gb|GO546072.1|GO546072 Mdas9010N19_e792.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL18930.1|AF429389_1 hydroxymethylglutaryl coenzyme A synthase [Hevea brasiliensis], mRNA sequence\n") - f.write("ATTTTTTACGCTGACAATACTTAGCTGCCAATCAAACTATTGGCTTTTAACATACAAACTTAGGGAGGCC\n") - f.write("AGCATGTTCTGTTTTACGAGTTAGAACTGGCATCTAGCTACATAAATCTCAACTTAACCATGTGACCGGC\n") - f.write("TTGAATTACGTCCATCAGTGACCGTTGGCAACCACACCGTTGGCATTGGTGGTGGCGGCCGCATCCTTCT\n") - f.write("TGGCATAGAATCTACGGTACTTAGAGTCGACTTCGGTAAGATAGTATGTGCCTGGAAGTAGAAGGCTAAT\n") - f.write("GTCCTGGTTGGTCACAAAGTCTTTGCCTCCATACCTGTGCTCCATGATCTTCATCACTTCAACAAACTTC\n") - f.write("TCGGGAGGGAACTCATGTCTTGCCTTCAACTTCTCTCCAACATTCATCATGGCTGCGATGTTCTCCAAGC\n") - f.write("TAAAGGGCTGTTGACCAGCATTGAGACGCAATGAGAACATGGTTGCAGTTGAGCCACTTCCATAAGAGAA\n") - f.write("CAGTATCACCCGCTTGCCATCCAAGGAGCTGTGCTTGTTGTGGAGGAGGGATACAAATGCCGCATAAAGA\n") - f.write("GATGCAGTGTACATGTTTCCCACTTGCTTTGGTACCAAAGTTGTTGGTACAACCCTTAC\n") - f.write("\n") - f.write(">gi|226792351|gb|GO546071.1|GO546071 Mdas9010O08_e797.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S14305 chlorophyll a/b-binding protein (cab-11) - tomato, mRNA sequence\n") - f.write("TTTTCTTGACTTAATTCAGGTGGGGAAAACAATGGCAACAGTCACAACTCAGGCCTCGGCCGCCGTTTTC\n") - f.write("CGGCCATGCGTCAACTCGAAATCGAGGTTCCTTTCGGGTTCTTCTAGTAAGTTAAATAGGGAAGTGGCTT\n") - f.write("TTAGGCCTATGGCTTCTCCTCCTGCTTCTTCTTTTAAAGTTGAGGCTAAGAAGGGTGAGTGGTTACCTGG\n") - f.write("CTTGCCTTCACCAGACTACCTCACCGGCAGCCTTCCTGGTGACAATGGATTTGATCCTCTGGCACTTGCT\n") - f.write("GAGGACCCAGAGAACTTAAGGTGGTATATCCAAGCTGATCTTGTCAATGGCAGATGGGCAATGTTGGGCG\n") - f.write("TTGTTGGGATGCTATTGCCTGATGTGTTCACCATCATTGGGATCCTTATCTTTTCCTTTTGTCATG\n") - f.write("\n") - f.write(">gi|226792350|gb|GO546070.1|GO546070 Mdas9010L11_e778.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTACATTAACTACGATTACAATATCCTCCAACTACACAAACGGCCAACATATTTGACAAACGTTGAAAAC\n") - f.write("AATTGAG\n") - f.write("\n") - f.write(">gi|226792349|gb|GO546069.1|GO546069 Mdas9010J21_e766.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTAATGAAAAATCAGAGTTGTATCATATATAACCAGATTGTTGTACAG\n") - f.write("CACAGACCATCAACGAAGCTGCAGAGTTGTCAACACATCTTTTATTCTCGACATTTCATCTCCTGTCACG\n") - f.write("ATAGCACACCATCCGCGGTTGCAATTTTATCTGAGGATACAAATTTCTTCATATGTTTTGTCTTGATTCT\n") - f.write("GTGCTACCCATAAAAATTTCTCCTTGTCATGGGTTGCGAAATCTGGTGGTGCACATGAATATAGAACATG\n") - f.write("ATTAACATTCAATCCATGACCAACATTCTTATTTAGTCCAGAACATCGAACGAGGCCATACAAACAAGCT\n") - f.write("CTTTGAAATTCCAAGAGGAATCGAGAGTGACCTCCAAATATAGAAATAAAGGGAAAGGCTACCCAATAAC\n") - f.write("TAATTTGACCACAGTAAAGAAAATAACTAACAGACTTATTCCCTTGAAACAAAAAACAAGCAGCCTTGTC\n") - f.write("AGCCAACGAATCATAACCCAAAGTCTGTAGAGTACTGATGGAAAATCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792348|gb|GO546068.1|GO546068 Mdas9010I09_e759.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA10284.1| chlorophyll a/b binding protein [Cicer arietinum], mRNA sequence\n") - f.write("TTTTTTTTTTTCAGACACATATTGTAGCACATAGTTCAAATTATTGTTGTCCAATACTTGGTACCAAATT\n") - f.write("TACATCACCGACAACAATACAAACGAAAGTACAAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGT\n") - f.write("TTGTGGCGTAGTTCCAGGCATTGTTGGCGACTGGGTCAGCGAGGTGGTCGGCAAGGTTCTCCAATGGTCC\n") - f.write("CTTTCCGGTGACGATGGCCTGGACAAAGAATCCGAACATGGAGAACATGCCAACCTTCCATTCTTGAGCT\n") - f.write("CCTTCACCTTGAGCTCGGCAAAGGCTTCTGGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTCCGCCGGG\n") - f.write("GTAAAGGGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAAC\n") - f.write("ACAACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAGGTAGTCGA\n") - f.write("GACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCACACAGCCTCGCCGAACTTGACACCGTTGCG\n") - f.write("GGACAAGAGCTCGGGGAAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGC\n") - f.write("TCACGGTTCTTGGCGAAGGTCTCTG\n") - f.write("\n") - f.write(">gi|226792347|gb|GO545814.1|GO545814 Mdas9003N22_e235.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB01236.1| gene_id:MDJ14.23 unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTTGTCTATCAAAGTGATCATAAATCTACAAGCATTTAGAACATATTTAGTCGACTAATTAT\n") - f.write("TGATAATTACAATTATTTACAGATTGAATGGGGAATTGCCCCAAAGATGACTGGGAGATTTGAACTGAAT\n") - f.write("TTACAGCTATCTATTTTAGCAGAGAATTCCTATGCCTTTAGTTGCTGATATCAAAGTATTTCGGATCGGA\n") - f.write("AGGAAAGTGATATTCCACATGTAACTTGCCCTCATCAGCATCCGTCTGGCGTTGAGGGAACACGACCCTC\n") - f.write("AAATCATTATACAAGTAGAAGCGCCTCCCCCCTTCGACATCGATACTGTTTGTCGCTTGTCCAGATGATG\n") - f.write("GATCTAACTTGCATCTCTGGACTGACCTCGAACATTTCTTAGGAAATAGGCATGAGAAACGAAGGTGAAG\n") - f.write("AGCATAACGCAGAACGCCAGCACCAGCAGTTTTCTTGCTCGTCTTTAAAGGGCTACGCACCCTACTTTCA\n") - f.write("CTAATCTCACTGGTCTTTTCAGACGTACAAAGGCTACAATCACTGGGTTCACTGTGATAACAGGCCTTTG\n") - f.write("TGCGTTCTCCCTCTCTTTGGTACTGATTAACTACATCCTTAAACTCGTTTGAGTCCGCATCATTGTC\n") - f.write("\n") - f.write(">gi|226792346|gb|GO545813.1|GO545813 Mdas9003P22_e248.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTGCTACTATAATAGCTCTCCAATTGCAATATATATATTCAAATTATCCTCACAACTGTAACATGCTCTA\n") - f.write("TTTACTAACTGGACATATTCCCTCTATG\n") - f.write("\n") - f.write(">gi|226792345|gb|GO545812.1|GO545812 Mdas9004H08_e282.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198322.1| GDSL-motif lipase/hydrolase protein [Arabidopsis thaliana] gb|AAM64916.1| putative GDSL-motif lipase/acylhydrolase [Arabidopsis thaliana] gb|AAO42146.1| unknown protein [Arabidopsis thaliana] gb|AAO50514.1| unknown protein [Arabid, mRNA sequence\n") - f.write("TTTCACGACACAAGGAAAATTATAATAAATGGGCAATACTAACGAAGACACATTGAGAAACTGAAGAAAG\n") - f.write("TCTTATGATAGAAAAACAAACACACCCCTTGTAGTTCTAGAACTAGTTCTAGGTCTTAGAGTCCAAGGCC\n") - f.write("AAAATAGTGCTGAGGTTCATTGGATTCATGTACTTGTTGGACCCAGTAAGGATTTGCTGCGCAATAATTC\n") - f.write("TGCTTGCCTTCTCAGAAGGATGGAATGCATCCCAAAACGCGTACAAATCTCTATTTGGGCACAAGTTGGA\n") - f.write("GGCAATTGTGCAGAGTCCGATCCCATTGTAGGGTCCTTGGCCACAGCAAGCTATCTTTGAAGTCACAAAT\n") - f.write("CCATAAGCTTGAGGATTGGAGATAAAATCCATGTGCATTTGAAATGCATTTGCAGCAACAAATACATCTG\n") - f.write("AGCCAATTTGGCCATTCAGGCTGTTGATCATATCGACTAGCTGTGGGTTAAATAAAGAAGCAGCTCGCTG\n") - f.write("CAGCTCCACCGCACATTCGCCTCTTCTGCTGCGCTGAGCCAACTCTGCTGGAGCACACCCTAGTGGCCCT\n") - f.write("GTGCCTGTCACCAAAACCTTACGAGCTCCTAATTCATACAGCCTGCTAGAACTTTGCGATACTCGGAGAT\n") - f.write("GAGGTAGACGACATAGTCCGGGAGAGAGAATTG\n") - f.write("\n") - f.write(">gi|226792344|gb|GO545811.1|GO545811 Mdas9003P14_e245.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T12041 cysteine proteinase (EC 3.4.22.-) 3 precursor - kidney bean emb|CAB17076.1| cysteine proteinase precursor [Phaseolus vulgaris], mRNA sequence\n") - f.write("AAACATGCGGCCGTACCGATCATCGCCGGTCGTGGCGATCCTCCTCCTCCTCACGATCTTCACCGTCTCA\n") - f.write("TCGGCCCTCGACATGTCGATCATCTCCTACGACAGCAACAACCACGTCGGAGACAGCAAGTCGTCGGGCA\n") - f.write("GCTGGAGGACAGACGATGAGGTGATGTCGATATACGAGGGGTGGCTGGCGGAGCACGGAAAGGCATACAA\n") - f.write("CGCTTTGGGAGAGAAGGAGAGAAGGTTCCAGATCTTCAAGGACAACCTTAGGTACATCGACGAACAAAAC\n") - f.write("TCCAAGAACCTCAGCTACAAGCTCGGTCTGAACAGGTTCGCCGATCTGTCGAACGAGGAGTACCGGAACA\n") - f.write("CTTACCTCGGCGCCAAGACTCGCGCGCAGATGAAGCGGGTGTCCAACAGGAACACCAAGAGCGACCGGTA\n") - f.write("CGCGCCACGTGTCGGCGATTCGTTGCCCGACTCCGTTGATTGGAGGAAGGAGGGCGCGGTGAGTCCAGTC\n") - f.write("AAAGACCAAGGCAGCTGCGGGAGTTGCTGGGCATTCTCAACTATCTCCGCCGTGGAAGGTATCAATAAGC\n") - f.write("TAGTCACCGGAGATCTCATCTCCCTATCTGAGCAGGAGCTGGTAGACTGCGATAGAACGTACAATGAA\n") - f.write("\n") - f.write(">gi|226792343|gb|GO545810.1|GO545810 Mdas9004J05_e291.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187574.1| 60S ribosomal protein L4/L1 (RPL4A) [Arabidopsis thaliana] sp|Q9SF40|RL4B_ARATH 60S ribosomal protein L4-2 (L1) gb|AAF23293.1|AC016661_18 putative 60S ribosomal protein L1 [Arabidopsis thaliana] gb|AAL09727.1| AT3g09630/F11F8_22 [, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTGTCACGAACGAAACTAGATTGATAAACTAAGCTACAAATATGA\n") - f.write("ATCCAGTGCCCGTTATACAAAATCTCCAACCAGATCGAACGGAGGAAAAACACCTTGAAACTTGCTTGTT\n") - f.write("AAACTCATTTCCCTGCAACTTATCATTCATAACTCAAAAGTAAACAAAAGACACAGATAAACACCACAAC\n") - f.write("AAAATAAACTAACAAAGGCAATGTCTTGTAAAATTTTAAAGCAATAAACTAAATCACTGGGCTACACCGA\n") - f.write("GCCACTTTGTGAAGTTGTCGAATTCTGTGTAATCGCTGTCAGAAATCATAGTTTTGTACCAAGCCTTTCC\n") - f.write("AGCTGCCTTGATGGCGGTAGCTTCCTCCTTAGTAATGGGCTTTCTCTTCTTGTCAAGCTTCTCCTTCTTG\n") - f.write("GCCTTCACGCGCTGCTCCTCAGCCAAAAGTGACATTCTCCTCGCTGTCTTAACATAGGGGTTCAACTTGA\n") - f.write("GCAGTGTGTTGAGATTTTTGAGAGGGTTTTTCTTCATTGGAGCTCTCTTGGCATCCTTCTTGATTGGCCT\n") - f.write("GACAACAGATTGAACTTCATCAGAGTTGATGATCCTCGCCAAGTCAGCATTGACCATCTTCGACCTCGGC\n") - f.write("AGCACATATCCCTTCTTCTTCTCCGAGGGCTTGTCAAACGACCCGTAAATTGAG\n") - f.write("\n") - f.write(">gi|226792342|gb|GO545809.1|GO545809 Mdas9004B06_e256.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TTTTCAAGATAAAGTTAAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAG\n") - f.write("CTTAAAGATCATCTATTGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGG\n") - f.write("CCCAGGCATTGTTGGTAACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGAC\n") - f.write("AATGGCCTGCACAAAGAAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTA\n") - f.write("AGCTCTGCAAATGCCTCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGT\n") - f.write("CAGTGATCTCACCAAGGGGTCCTCCGGCGATGCGGTAACCCTCAACCGCACCCATGAGGACCACCTGGGT\n") - f.write("TGCCCAGATTGCTAGAATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCG\n") - f.write("CTGAAGATTTGAGCTCCGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCT\n") - f.write("CCGGGAAAACACAGCCCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTC\n") - f.write("\n") - f.write(">gi|226792333|gb|GO546067.1|GO546067 Mdas9010O09_e798.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK38744.1| carotenoid 9,10-9',10' cleavage dioxygenase [Phaseolus vulgaris], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTAATCAACATAATTAAGATGGTATAGGTATTGCTATGTGACCCAC\n") - f.write("TGATTCTTTTTGTTCAAAGTAATTAAAACACCATCCGGTAGTTTAAACACAGAGGTGTATACATTATTTA\n") - f.write("TTGGTGTACATGTGGAGTAGACCGCCTACACGACAACAGGTTCAGTTTACGCTGGCGTGCCTTCCCCTTG\n") - f.write("TACGTTCTAACAATGATGAATAATTTTAGAGCTTTGCTTGTTCTTGCAGTTGCTCCTCTGTCACGAAGAA\n") - f.write("GGCATGGAAACCATATGGAACTCTGTGTGGCAATTCCACGACTGCAACGGGCTCTGATGACATTGTCTTT\n") - f.write("GCATCAACTACATGAACTGCTGATTTTCCAGTGTTCTCGTCATGAACAAAGAGTATTAAGTAGCCATCAT\n") - f.write("CTTCTTCAGAAGTAACGCCAGGAATACGAGGGACAAAAATAGCTTCAGAACCAAATCTGCCAGGTCCCAG\n") - f.write("GTCATAGAGGCCTTGGACATTTCCTCCAACCTCAATTTTTGTTTTTCCGACCTCTGGTTCAGCATGCAAA\n") - f.write("TCAAACTTGGCTACCCCTGTAACCTTG\n") - f.write("\n") - f.write(">gi|226792332|gb|GO546066.1|GO546066 Mdas9010M20_e786.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD31838.1| putative quinone oxidoreductase [Cicer arietinum], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTTCAGTAATAAAAACTGTTTATTCAATAATAAAACTTGTTACAACAATT\n") - f.write("AAATTTGACAAAGCAAATTATCCTTTACAAAAACACGAAATTGCAAATTGAAAACTGGACTGAAAATCAA\n") - f.write("GAACAAAAAAAATGAAAGTATGGAACACTCAACAGCGATCGTATAATTGATCATCATAATTAGGCAAATC\n") - f.write("CCTTAAGCTTCTTTGCGATGCCAGCAAAGTACTTTCCCTGGTGGCTAGCTGTTTCTAGTTCTAAATCAAA\n") - f.write("AGGTTGTCTTGTGCCATCCCCAGCATAAGTTCCCGCACCATAGGGGCTTCCACCCTTGACCTGCTCCATC\n") - f.write("TCGAACATGCCAGCTCCACTCGTGTATCCGATAGGCACAAAAAGCATTCCGTGGTGAACAAGCTGAGTAA\n") - f.write("TGGTCGTCAAGGGGGTAGTCTCTTGTCCACCACCTTGAGATCCAGTGCTGTAAAAAATTCCAGCGGGCTT\n") - f.write("GCCAGCAAGTGCTTGAGTTCTCCATAAGCCTCCAGTTGAATCGAAAAATGCTTTAAACTGTGCAGCCATC\n") - f.write("ATTCCAAATCTGGTAGGGAAACCGAAAATTATCCCATCAGCCTCCACAAGTTCCTCAGGTGAAATTACAG\n") - f.write("GCACTTCACTCTTTGGTGGTGCACCCATTTTTCCAAGAACTTCTGCTGGCAGCGTTTCTGGTACC\n") - f.write("\n") - f.write(">gi|226792331|gb|GO546065.1|GO546065 Mdas9011C01_e819.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191781.1| serine/threonine protein kinase, putative [Arabidopsis thaliana] pir|T48014 serine/threonine protein kinase-like protein - Arabidopsis thaliana emb|CAB71882.1| serine/threonine protein kinase-like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTAAAACATGAAATACCACCTTGCATTATGAACAAATCAAATACACCGCAAATAATGAAGCAATATA\n") - f.write("GTACATCTCTTTCAAAAAGAGGAAAAAAAGAAGAAAACGAAGCATATAGAACATTGTGCAAACAATATAC\n") - f.write("CACCAGACCACCCTCAGAACTCTATCCCCTTTTGTTACAATAATTGCATGCTGAATTACTTATACATGCA\n") - f.write("CACATGCCACACCTTCAGAGGCAAAGGGAGAGACAGAGGGAGATTGAGAGATTCACAAGTTTGGTGATTC\n") - f.write("ACCAGCAGGTCCATGACGAGCATTTAACAGGGGTTGGAGGGCTTTAACAACAATGCTCATGTTTGGGCGG\n") - f.write("AAATCAGCCTCATATTGCACGCACAAGGCAGCAACTGCAGCCATCTTTGCAACCGCCTTTGGTGGGTACT\n") - f.write("CTCCTCCAAGTCTTGAATCAATACACTGCCTAACTTTGTCTTCACTAAGCTTTGGTGTAGCCCATGTTAC\n") - f.write("TAGACTCTGCTGTCCCCGTGGTAATGTATGATCAACAGGTTTTCGTCCAGTCAAAAGCTCAAGCAGGACA\n") - f.write("ACACCAAAACTGTAAACATCACTCTTGGCATTCAACTGTCCTGTCATTGCATATTCAGGGGCATGATAGC\n") - f.write("CAAAAGTTCCTAGCACACGAGTGGAGTGAAGACGTGCTGC\n") - f.write("\n") - f.write(">gi|226792330|gb|GO546064.1|GO546064 Mdas9011C14_e822.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC32136.1| YGL010w-like protein [Picea mariana], mRNA sequence\n") - f.write("CTAATTTTCTCGGAAAATTCTCAAATGGGGAAGACCGGACTGTTTGATCTCGAAAAGCACTTTGCTTTCT\n") - f.write("ATGGAGCTTACCACAGCAACCCGGTCAACATAGCGATTCATATGCTCTTCGTCTGGCCTATCCTCTTCAC\n") - f.write("CGCTCTGCTCATCCTTTACTTCACGCCCTCGCTGCTCAGTTTTGGGGTTTCGGTGTTTGGTAACGACGTC\n") - f.write("GCTCTGCCTTTCAACGTCGGCCTGCTGTTGACTATAATCTATTCGGCGTTTTACATCTGTTTGGACGCAA\n") - f.write("AAGCTGGCTCCTTGGGTGCTCTGCTCTGCGTAATTTGCTGGGTTGGTAGCTGTTTCCTTGGAACCCTACT\n") - f.write("CGGATTTTCCATCTCTTGGAAGGTTGTTCTGGTGGCTCAGATAGTGTGTTGGACTGGACAATTTATCGGC\n") - f.write("CATGGAGTCTTTGAGAAAAGGGCACCAGCTTTGTTGGACAATCTTGCACAAGCCTTTATCATGGCTCCCT\n") - f.write("TCTTTGTTCTGTTAGAGGCTCTGCAGATCTTCTTCGGGTACGAACCGTACCCCGGGTTTCAAGCAATTGT\n") - f.write("TCAAGCAAAGATTGATGCTGAAATCAGTGAATGGCAAGAGAATAAGAAGAAACTGATCTCCTAATCTGTA\n") - f.write("ACTGGATTTACTTTTACTGTAATATCTGGGGTGTGGTTAAAAGCAATACCAAAGCTTTTATCTGTAAACA\n") - f.write("TGT\n") - f.write("\n") - f.write(">gi|226792329|gb|GO546063.1|GO546063 Mdas9010N01_e787.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568147.1| coatomer delta subunit (delta-coat protein) (delta-COP) [Arabidopsis thaliana] gb|AAK96656.1| coatomer delta subunit (delta-coat protein) (delta-COP) [Arabidopsis thaliana] gb|AAM47945.1| coatomer delta subunit (delta-coat protein), mRNA sequence\n") - f.write("ACGAATAGGCATCCACTTTTATTATTAACATTCCTTGGGGGGGAAGGGGATAGTATCAAATAACATGAAA\n") - f.write("GAATGCACATCTATAGCATCCAAATTCTGGCAGGCTTCCCTTCATCTCAAATTTAATGGGAATTAAAACA\n") - f.write("CCACAAAATGAAAACTCCTGGTTTTCGAATTCAATCCATATCCAAAAAGGTTGCAGATCCACACACCCCA\n") - f.write("AACCAATCACACCACTTGGTAATTCTCCGTCACCAACTGCGTTCTTTGAGAAAACTTGGGAGCGGCTCCA\n") - f.write("CCTTGCAGAGGTATAATGTTCAAAACCTTCAGGTCACTGAATGTCTCAGTGGCAGCGAAGCGCACAGAAA\n") - f.write("TGGGGAAAAATACAGATGGGTCTGCTGGGGGAACAACAAACTCCATTGATCCACTGCGGTTCGAGTTATC\n") - f.write("TACGAGAAGTATGGACCACTCCAACATTGAATTCCTAGCATCGTATCTCCATTCACCTTCAATCTGGTTT\n") - f.write("ACACGTGGAGCCTCTCTCGCAGCTGGGAGAGGTACAGAGATAACAACATTTCTCAGATCAAACATCTCTG\n") - f.write("AAGCCTCATACTCAATGTTGACATAAGTTTCATTCCCGGAAACAGTGGGCCAACAGTTGATTGTCAGGGG\n") - f.write("CACCATTGACTCATCTGAAGTCTGCATTCTCCATCTCAAAAGACCAACAC\n") - f.write("\n") - f.write(">gi|226792328|gb|GO546062.1|GO546062 Mdas9010O18_e800.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P54260|GCST_SOLTU Aminomethyltransferase, mitochondrial precursor (Glycine cleavage system T protein) (GCVT) pir|S59948 aminomethyltransferase (EC 2.1.2.10) precursor - potato emb|CAA81081.1| T-protein [Solanum tuberosum], mRNA sequence\n") - f.write("TCGAGTTGCTTGAGTATTACCTCAGCGCCAAGAAAGCCGCCCTCTGCCCTTCTTCTCTTCCCTATGGCCC\n") - f.write("ATGTGAGTCCAGCCTCCACAGGTGTTGTGTGTTGCTCCATGTCATTGCCATATAAACACAACCCAGCTTC\n") - f.write("CAGTCGGAGACTGTCACGAGCACCCAGACCTGTCAGCCTCACCTTCCCCTCGGATTTCTCCAAGATTGCC\n") - f.write("TTGGCAAGATCCACTGCATTCTCATCAGGAACCGAGATTTCAAATCCACAAACAATGTAGCATACACGAC\n") - f.write("ATGAGTGATTACAGTTCGATAAAAAGAAGCAAGTCTACTTGAAGAAGTAAGGAAGGTTAACAACATAGAG\n") - f.write("GAGGAAGTAGGCCCAAGTGACACCCGAAATGCCTCCGAAGAAGAAGCCGCCGGTGAATTTAGACCATCCC\n") - f.write("TCCGCGGTTTGAAGCTGGTCGGGCTCCTTCTTCCTGCCAGTCAATGTCAAAGCGGGCGCGGAGGACGGCT\n") - f.write("CTCCTTCCTTGAAGGAGGAAATTCCATAGATTGTCAAGCACAGGGTTTAGGATGACCACAAGACCAGCAG\n") - f.write("CAGCCAAGGAGCCAGCTCCCCAGCATAAAGGGGTGTTCCTCAATGGGCCAGTCTTGACAAACGGGCCTAC\n") - f.write("CAGAAAGAAAACCGTGGGCCAGGCCCACCTCAAATACCCCTGAGAAGTGGGCTGAC\n") - f.write("\n") - f.write(">gi|226792327|gb|GO545808.1|GO545808 Mdas9004B24_e263.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO85557.1| photosystem I subunit XI [Nicotiana attenuata], mRNA sequence\n") - f.write("TTGGAGACTCCAGTGACATCAAGCCCTTTGATTGCCTGGTACTTGTCCAACCTCCCAGCCTACAGGACAG\n") - f.write("CAGTCAGCCCACTTCTCAAGGGTATTGAGGTGGGCCTGGCCCACGGTTTCCTTCTGGTAGGCCCGTTTGT\n") - f.write("CAAGACTGGCCCATTGAGGAACACCCCCTATGCTGGGGGAGCTGGCTCCTTGGCTGCTGCTGGTCTTGTG\n") - f.write("GTCATCCTAACCCTGTGCTTGACAATCTATGGAATTTCCTCCTTCAAGGAAGGAGAGCCGTCCTCCGCGC\n") - f.write("CCGCTTTGACATTGACTGGCAGGAAGAAGGAGCCCGACCAGCTTCAAACCGCGGAGGGATGGTCTAAATT\n") - f.write("CACCGGCGGCTTCTTCTTCGGAGGCATTTCGGGTGTCACTTGTGCCTACTTCCTCCTCTATGTTGTTAAC\n") - f.write("CTTCCTTACTTCTTCAAGTAGACTTGCTTCTTTTTATCGAACTGTAATCACTCATGTCGTGTATGCTACA\n") - f.write("TTGTTTGTGCCTCGCGCCGAA\n") - f.write("\n") - f.write(">gi|226792326|gb|GO545807.1|GO545807 Mdas9003M08_e227.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T07086 acid phosphatase (EC 3.1.3.-) - soybean emb|CAA11075.1| acid phosphatase [Glycine max], mRNA sequence\n") - f.write("AGGAGTATTACTCTTCCTTCTTGCCATATTTTTCTCAACAACTCAAGCTTATGAGCCACTTATAAACCAC\n") - f.write("CATATCCATCTCCTCAGGCCGAAATCCGGGGCGGGTGGCAGCAGCGTTCCCGGCGTGTCTTGCCTGAGTT\n") - f.write("GGCGTTTGGGGGTGGAAGTTAGGAACATTATCAACTGGAAGACTGTTCCGGCACAGTGTGAAAGCTACGT\n") - f.write("TGGGCACTACATGCTTGGGCACCAGTACAGGAAGGACTCAAAAGCGGTCACTGATGTGGCTTGGCTCTAT\n") - f.write("GCTAAGAGCCTCAATCTTACAAAGGATGGCAAGAACGTTTGGGTCTTTGATATCGATGAAACTACACTCT\n") - f.write("CTAATCTACCGTATTATGCTCGTCATGGATTCGGGACCGAGGTATACAATTCCACTTCATTCAATGAATG\n") - f.write("GGTGTTGGAAGGCACAGCCCCAGCTTTGCCCGAGAGTCTTCAGCTGTACAAGAAATTGTTGAAACTTGGA\n") - f.write("GTCAAGGTCGTGTTCATAACAGGTAGAGGAGAAGATCAGAGAAGTGTCACAATCGCCAATCTCAAAAATG\n") - f.write("TCGGATATCACACCTGGGAGAAGCTTGTCTTAAAGGGATCAGCTTATTCTGGGAAGACATCGTACGAGTA\n") - f.write("\n") - f.write(">gi|226792325|gb|GO545806.1|GO545806 Mdas9004D04_e268.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P50694|TLP_PRUAV Thaumatin-like protein precursor gb|AAB38064.1| thaumatin-like protein precursor, mRNA sequence\n") - f.write("GGGAATGCAAGAGTATTATTCTTTATTTATTTCATTGAAATTATTACAAATTCATGACAATACTAAGCGT\n") - f.write("CAAAATTCATAAAGTTTATTTCTCCTTTAGTATGATATAAAGGGATATTACATAATATCCTTTCTAGTTC\n") - f.write("TATTTTTAGGGTGATGGACAGAATGTAATAACGTAGTTTGGTCCACCGCTGCATGTAAAGGTGCTGTTGA\n") - f.write("CATCATCATAAGCGTAGCTATAAGCCTGAGGGCACTGGTCCTCAAAGATCTTAGAGTAGTCTGTGGGTGG\n") - f.write("ACATGTAGCTGGTGTGTCATTAGGAGGAGTGCAGCAGTATTGTGGTTGATTAAATTGTGTACACGCACTC\n") - f.write("TTGCATGCAATTACGCTCCCATCGGACCCCTTCACTTGCAGCTCAGCTGGGCAAACAGCGTTGACGTTGG\n") - f.write("CGGGGCAAGAAGAGGTCTGGCAGTCGCCCGTGCCGCCTTGTGGGGCAACAGACACGGGCAAGTTGAAGCC\n") - f.write("ATCAACAAGACTTACGTCGTAGAAATCTTGGCCTCCGTTTGCGACAATATTTATTTCGACTAGGCTTGCT\n") - f.write("GGTGGAACTGCTCCGTTACCGTTGCATGTGACTTGGCCAGAGCTACACTCTGCTGTGGCACAACTGAACT\n") - f.write("TTCCTGAAGCGTCAGTGGAGCATCCGGTTCGGCCCCAGAAGCGGCCTTTCCATGGGACTGGAGTG\n") - f.write("\n") - f.write(">gi|226792324|gb|GO545805.1|GO545805 Mdas9004F09_e274.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179752.1| 40S ribosomal protein S25 (RPS25B) [Arabidopsis thaliana] sp|Q9SIK2|R25A_ARATH 40S ribosomal protein S25-1 pir|H84602 40S ribosomal protein S25 [imported] - Arabidopsis thaliana gb|AAD23647.1| 40S ribosomal protein S25 [Arabidops, mRNA sequence\n") - f.write("TAAAATTGTAGATTAAACAAAATCGACGCTAAATAGTCTGAAACGACATATAACGATACCCGAAACGACA\n") - f.write("ATTAAACACGAAAGAGCAAAGAGACCTAGGTGTTGGTAGCCCTGGTGTAGATCTGCTGGCTGGCGTGGGC\n") - f.write("AGAGACCATCCTAATCGAGCCTCTAGCCATCAACTCCCTGATGGCCTTCCTGGCCAGGGAACCGTTGATC\n") - f.write("CTGAGACGGTCGGAGAGAATGGATGGTGTGATGAGCTTGTACTTGGGGGCCTCAGTGAGGAGCTTGTCGT\n") - f.write("AGGTGCCCTGGTCGAAGAGCACCATGTTGTTCACCTTCTCCTTCTGCTTTCCCTTGCTCCACTTCTTCTT\n") - f.write("CTTCTGCTTGCCTCCTCCGGACTTCGCCGGCTTCGACGACGGCGGCGGTGCCTTGTCCTTCTTCGGCGCC\n") - f.write("ATGATCGGATTACAGCGACAGGGAAGGGAGGAGAGAGGAGGAGAGAGGGAGGGATCGGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792323|gb|GO545804.1|GO545804 Mdas9003O06_e237.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO85557.1| photosystem I subunit XI [Nicotiana attenuata], mRNA sequence\n") - f.write("CAACTGTGTCTGTGTATCTTCTGCAGTTGGTGCAAAAGTGATGGCCTCAGCTTCTCCAATGGCCAGCCAG\n") - f.write("CTTAAATCCAACTTCACCTCTCCGATCACCACCAGACCTGCCTTGTTTTCTCCCAAAGGCCTCTCTGCCT\n") - f.write("CCCCACTCAGGCTCTTCCCTTCCAAGAGACTCTCTTCCTTCTCCATCAAGGCTGTCCAATCTGACAAGCA\n") - f.write("AAATTTCCAAGTGATTCAACCCATCAACGGAGATCCTTTCATTGGAAGCTTGGAGACTCCAGTGACATCA\n") - f.write("AGCCCTTTGATTGCCTGGTACTTGTCCAACCTCCCAGCCTACAGGACAGCGGTCAGCCCACTTCTCAGGG\n") - f.write("GTATTGAGGTGGGCCTGGCCCACGGTTTCCTTCTGGTAGGCCCGTTTGTCAAGACTGGCCCATTGAGGAA\n") - f.write("CACCCCCTATGCTGGGGGAGCTGGCTCCTTGGCTGCTGCTGGTCTTGTGGTCATCCTAACCTTGTGCTTG\n") - f.write("ACAATCTATGGAATTTCCTCCTTCAAGGAAGGAGAGCCGTCCTCCGCGCCTGCTTTGACATTAACTGGTC\n") - f.write("GGAAGAAGGAGC\n") - f.write("\n") - f.write(">gi|226792322|gb|GO545803.1|GO545803 Mdas9004J23_e295.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P27608|AROF_TOBAC Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (Phospho-2-keto-3-deoxyheptonate aldolase 1) (DAHP synthetase 1) (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 1) gb|AAA34068.1| 3-deoxy-D-arabino-hept, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGTCAAAATCATACGCATTATTCAATTTATTTTTGCTTCCCTTCAA\n") - f.write("AGTTCAAAGTCTCCAACCATCACTTCCAGTATATACGTACAACACACAACATAAATTATCACTAAACACC\n") - f.write("AGTGACGTATTAACACAGTGCAGTTTTGAAAAGATGAATAAAATAACTTCCAGGGTTCTTAACCCTTGAG\n") - f.write("ACCATTCTACAGACCTAAAGCGGCAAGCGGGTTCTGTGACTTGATCCTTCTTTTCCTGAGGCGCTCGGCA\n") - f.write("ATGATAAAGGCGAGCTCAAGAGATTGTGAGGCGTTGAGCCTTGGGTCGCAGTGAGTGTGGTAGCGTGAGC\n") - f.write("TAAGGTCGTCGAATGTCACAGTGCGTGAACCTCCAATGCATTCCGTCACATTCTGGCCTGTCATCTCTAG\n") - f.write("ATGAACACCACCTGGGTGGCTTCCTTCTTGCTCGTGTACATCAAAGAACGCTCTCACCTCCGCCCTTATG\n") - f.write("GCATCAAAAGGACGTGTTTTGAGGCCGCAGGGAGCCTTAATGGTGTTTCCATGCATTGGGTCACTGACCC\n") - f.write("ATGTGACAATCTGTCCAGCCCTGCGG\n") - f.write("\n") - f.write(">gi|226792314|gb|GO546061.1|GO546061 Mdas9010N21_e794.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P36491|PSBA_POPDE Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) pir|S42492 photosystem II protein D1 precursor - cottonwood emb|CAA55040.1| D1 protein [Populus deltoides], mRNA sequence\n") - f.write("GAGAATTCGTGTGCTTGGGAGTCCCTGATGATTAATTATTAAATAAACCAAGATTTTACCATGACTGCAA\n") - f.write("TTTTAGAGAGACGCGAAAGCGAAAGCCTATGGGGTCGCTTTTGTAACTGGATAACCAGCACTGAAAACCG\n") - f.write("TCTTTACATTGGATGGTTTGGTGTTTTGATGATCCCTACTTTATTGACCGCAACTTCTGTATTTATTATT\n") - f.write("GCTTTCATTGCTGCACCTCCGGTAGATATTGATGGTATTCGTGAACCTGTTTCTGGATCTTTACTTTATG\n") - f.write("GAAACAATATTATTTCTGGTGCCATTATTCCTACTTCTGCAGCTATAGGTTTGCACTTTTACCCTATATG\n") - f.write("GGAAGCGGCTTCCGTTGATGAATGGTTATACAATGGTGGTCCTTATGAGCTAATTGTTCTACACTTCTTA\n") - f.write("CTTGGTGTAGCTTGCTACATGGGTCGTGAGTGGGAACTTAGTTTCCGTCTGGGTATGCGCC\n") - f.write("\n") - f.write(">gi|226792313|gb|GO546060.1|GO546060 Mdas9010O06_e796.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAN62336.1|AF506028_3 CTV.2 [Poncirus trifoliata], mRNA sequence\n") - f.write("TGCAAATCTCAGACTGCGGTGTCGTATTAATCCTTCTGCTTATCTTCCTGCTAATGTTAGCCCTCCGCTT\n") - f.write("CCCCTTTGCAACAGTTCTAACGTACAGCCCCTTGTTATTGCGGCGCATCCACAAGAAGCAAATCAGTTTG\n") - f.write("CATTAGGACTATCGGATGGTGCTGTTCACGTCTTTGAGCCCCTTGAATCTGAAGGCAAATGGGGTGTGGC\n") - f.write("TCCACCTGTTGAAAATGGTTCAGCAAGCAGTGCGCCGGCTACTCAAGTTGGAACTTCAGGTTCAGATCAA\n") - f.write("GCTCAGAGATGATCAAGAGGCTGGCAGAGCACAAGTTCTTTTACATGCTTTGCTTGCTGGCCTATTCCAA\n") - f.write("ATACAGTTTGTGTTCTTCATGCAGTGTAATTTAATCAAGGAAGGATGTGCAGATATGTATATTTAACAAG\n") - f.write("TTGGTTCAGAATCTCAAGTAAGGTA\n") - f.write("\n") - f.write(">gi|226792312|gb|GO546059.1|GO546059 Mdas9010C05_e728.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTGAAACTTTGAAAGCATATATATTTATGAATGTTTAATGGTACATGCTCATACACCTCACATTTAACA\n") - f.write("TTTGAAAATAATTACAAACTAAGCAAAACAAGTAATTAGTTTTTGCATCAAAAAGTGTCAAGTATGTTTG\n") - f.write("ATGCATTGTGTAAGATAAAGCCGAACACAGCTGACAAATATGTCAATATAGCTCAGCTTTATCCACACAT\n") - f.write("TATTTTAAGAAATACTATGGTAAAAACCATAAGCATCTGAAAGAGTAATGGCAGTGGACTCGCTCCGCCG\n") - f.write("GCTTGTGTCCTTCACTTTGTTGAAGTTTTTCGAGCCATTGCCGCCTTCAGTTTCTCCTCCCTTCTCACCC\n") - f.write("CCGCGCTGTTGCTTGAGAAAGATTTTGGAATCCAGTCCTGAGATTAAAAGAATGGATGACTGGAATATGC\n") - f.write("TCAACCGCCTGACGATCTTCACCATCCCTTTGAAGCTTGGCAATGAGTACAGTGGGCATGTCATGGAGAA\n") - f.write("ACAGTTCCTCGAGTTCCCGTAGACCCTCCATGCCGAGTGGAGGTAAATTCAAACTCTTACAATTGGACAG\n") - f.write("GGTTACCTTCTTAAGATTANGCATTGCTCCAGACTCAACTTTCATGGTATGTAGTTGATCAAATTGTTTG\n") - f.write("ATACTTAATATCTTTAGCTTCATGAACGTTTTAGCCTCAGATTCTAACACTTGTCCGGTATAATAGCAAA\n") - f.write("CCAAATGAAGCTCCATCATATTCGGCAATGCTT\n") - f.write("\n") - f.write(">gi|226792311|gb|GO546058.1|GO546058 Mdas9010C19_e731.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P93111|HMA1_CUCSA Glutamyl-tRNA reductase 1, chloroplast precursor (GluTR) pir|T10186 glutamyl-tRNA reductase (EC 1.2.1.-) - cucumber dbj|BAA08910.1| glutamyl-tRNA reductase [Cucumis sativus], mRNA sequence\n") - f.write("TTTAATTACTTTTTTTGAGAGTATTACTGATATCTCATATTTTCCATATGTTGCCGAACAGCCACTTACG\n") - f.write("AACATGTGGTGGTAGACATATAAATCACTCCCACAGAAAAATCATGTTACTGTGTCTTTCACCAGTGAAT\n") - f.write("GAATTGCAAGATCCCCCAGCCGGGACCACCACAATTTGTCTATCGAGTTGAAGATTACACCAGACTGAAC\n") - f.write("ACCAAAATGACAATGTGAGGATGTTTTCCCCTTATTCGAGTATGAGGAACTCCAGGTGTCATGAGAGATA\n") - f.write("TTTGACATTGTACCTTTAGTTCTGGGTTTGTTCCACCTTACCTCGAATTTTCTGTTCCCATACGGATCTC\n") - f.write("TCCGTCTCGAGGCTGAACATTCTGTTAATAGCGTGCATGTTCTCAATGGTCTCACTCAGAGTTCGACTAT\n") - f.write("CTCTCCCATCACATCTTAGATGATG\n") - f.write("\n") - f.write(">gi|226792310|gb|GO546057.1|GO546057 Mdas9010I08_e758.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTCATTTCGAATGGAACGTTTAATATAAATTGCTTGTTTACCAAAAA\n") - f.write("AGACATCAAGGATTTGATCCTTGTATTAGTGAATATACAAGAAAAATCCTACGAGTAACCAGGGAGGGCG\n") - f.write("TTAAAGCGCTGTACAACCGGTAAAGATTAGCAACGAGGCAGTTAGGAGTTGAGAGGGCGGCCTACTTAAT\n") - f.write("GTTTTAGCCGCTGGCGTTTATCCTGATGCCTGGAAAATGTTGGACTGCAAATTAAGTCAGGAGAAACAGA\n") - f.write("AAATTGATTTGGGCAACATGTCCATAAAGAATCTCCCCTAATTGCACTGGCACTACAACCGACTCAATAA\n") - f.write("TTCAAGAAACTCCACTGGTTCTTCATTTTCTTTAACAATCTTAATGATTGTGTCCTTTGGCAGACCCATT\n") - f.write("TGAACAAGAACATGAAAACCAACTTGATCCCAGTCACTCTCTTCTACATCAGTTCTCTCTCTTCCACTAT\n") - f.write("CTAGTTGAATGGAAAACTTATCACTGTTGAAAAATCTCCCCACCCAGAGGTACAAAACCCGGTCTTTACT\n") - f.write("TTTTCCAAAATCTGTATTTGGTGAGAAAATAGTGTAAGCAGCTTTAGAATCTAGTTCCCTCACACCAAAT\n") - f.write("GTCGCAATCTTCTCTAAACTGGGCCAACGGCACACAAAAGGTTGGATAAAATTGCATTGCGCTGGACAAC\n") - f.write("TT\n") - f.write("\n") - f.write(">gi|226792309|gb|GO546056.1|GO546056 Mdas9010P01_e803.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_177574.1| dolichyl-phosphate mannosyltransferase polypeptide 2 -related [Arabidopsis thaliana] pir|A96772 hypothetical protein F1M20.2 [imported] - Arabidopsis thaliana gb|AAG52357.1|AC011765_9 putative dolichyl-phosphate mannosyltransferas, mRNA sequence\n") - f.write("TTTTTTTAACAAGGTAATCAGTATCTGATCATTTCAGACACACTTGGATTCGGCTCCAAGGAAATGAAAA\n") - f.write("GAAACTAAAAGTGGGGGAAATACTGTCATCAAGCTTTCTTCTTTTTGGATTTTAACATGACAAATCCAAT\n") - f.write("GAAAATGCATAAAAAGCAGAGAAGCACCATGCCAGCAAACACAGGTATTAGTATGGCGTACTCTTGTGGG\n") - f.write("AGGAAATACCGGTGGATGAAGTGATCGTTGTTTACAAACGGCAGGATAATCACCCAAAATGTGTAATAAG\n") - f.write("TGAATATTGACAAACTGATGTAGGATAACAGAAATCCAACGGCCTTGTCCGCCAATTCCATTGTCGTGAT\n") - f.write("GTTTGTGGCTTCTGGTACCTGTAAATGGGGGAGAGGGACGATATGGCTACTGAGATGGTCTGCCTCGTGC\n") - f.write("CGAA\n") - f.write("\n") - f.write(">gi|226792308|gb|GO545802.1|GO545802 Mdas9004F21_e276.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_175036.1| histidine decarboxylase -related [Arabidopsis thaliana] pir|E96500 probable histidine decarboxylase [imported] - Arabidopsis thaliana gb|AAF63121.1|AC009526_6 Putative histidine decarboxylase [Arabidopsis thaliana] gb|AAK25943.1|, mRNA sequence\n") - f.write("TGCAGCTCGGCCACCTCTCGACCGTTCGATCTTTCAACATTACAAATTTCATGGATCACGAGAACGGAGC\n") - f.write("TGTGGCGGTGGAGATGCTATCCGATGATTTCGATCCCACGGCTGTGGTTGCGGAGCCTTTGCCTCCGGTT\n") - f.write("GTAACCAGCACCGACGACTGCGATCTCCTCGGAAAATTGGCCGAAGACCGCAAAGGTAGCCGGGAGAAAC\n") - f.write("AGATGGTTCTCGGCCGGAACGTGCACACCACGTGCCTCGCCGTGACGGAGCCCGAATCCAACGACGATTT\n") - f.write("CACCGGCGATAAGGAGGCGTACATGGCCAGCGTCCTCGCCCGCTACCGCAAAACCCTCATCGAGAGGACC\n") - f.write("AAGCACCATCTGGGTTATCCTTACAATTTGGACTTCGACTATGGTGCTCTGACGCAGCTTCAGCATTTCT\n") - f.write("CCATCAACAATTTGGGCGATCCGTTTATCGAGAGCAACTACGGTGTCCATTCAAGGCAGTTCGAGGGTCG\n") - f.write("GTGTTCTCGATTGGTTTGCTCGGTTGTGGGAGATTGAGA\n") - f.write("\n") - f.write(">gi|226792307|gb|GO545801.1|GO545801 Mdas9003I20_e214.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAN03474.1| syntaxin [Glycine max], mRNA sequence\n") - f.write("GGCGAGGATTTTTCTCATTGGCAAGCGGGACCCCACCCTAGCTGTGGCCTCCGGCATTTTCCAGATCGGC\n") - f.write("ACCGCCGTATCCACCTTCCAGAGGCTCGTCAACACCGTCGGCTCCCCCAAAGACACGCCGGATCTCCGCG\n") - f.write("AATAGCTGCACAAGACAAGACTACAGTATCGGGCAATTGGTAGAAGGATACTTCATAAAAACTGACTCTA\n") - f.write("GTCAGTGAAAGAGATCATCAGACCGAAGTTAATGCAAGCCAGAAGATTACAGATGCTAAACTTGCAAAAG\n") - f.write("ATTTTCAAGCGGTGCTTAGAGAATTTCAGAAAGCTCAACGACTTGCAGCTGAGAGGGAAACAACATATGC\n") - f.write("TCCTTTTGTTCCTCACGCAGTTCTTCCGACAAGTTACACCGCTAGCGAGATAGATGTAAACTCAGACAAA\n") - f.write("AGTCTGGAACAGCGTGCTCTCCTTGTGGAATCTAGAAGACAAGAGGTCTTGCTACTGGACAATAGATTGC\n") - f.write("TTTCAATGAGGCTATCATCGAGGAAAGAGAACAGGGAATACAAGAGATCCAGCAGCAAATTGGTGAAGTG\n") - f.write("AATGAGATTTTTAAAGATCTTGCTATACTGGTTCATGAACAACGAACAATGATTGATGACATTGGCTCCA\n") - f.write("ATATTGAGAGTGCTCATGCTGCTACTGGGCAGGCAAA\n") - f.write("\n") - f.write(">gi|226792306|gb|GO545800.1|GO545800 Mdas9004H09_e283.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P49313|ROC1_NICPL 30 kDa ribonucleoprotein, chloroplast precursor (CP-RBP30) pir|S26203 RNA-binding protein 30 - curled-leaved tobacco emb|CAA46234.1| RNA binding protein 30 [Nicotiana plumbaginifolia], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAATGATTTTGATGTACCAAATCTATAAACTGTCAAAACAAGTTGATC\n") - f.write("ACAATCAGTTCCTTAACTGGGCCAAGTCACTCGGAATATAAATCTTACAACTCTCAAAACAGTCTTCTCT\n") - f.write("GCTCTTGTCCATCTACAGGCAGATGTAAAAAAACCACCACTACCGCTCACAAAGCCAACCATGGCGCAAG\n") - f.write("GCAGCATGATCTTGTCACTAACCGCTCCTAAAAATCTGAAATGAGTATCAGCAGATATTATGATCCTAAA\n") - f.write("TGCAAACGGAAAGAAAAGAAACCCATCAAGTATTCTGTTGGCCAATGACTCTGCAAAGTTTACATTTAAA\n") - f.write("ACTGACGCCTCGGCCTAGGTTCTGCCGCAGACACTCGGATAGATCTTCCATTTAAGTCAACTCCATCCAA\n") - f.write("TGATTCAATGGCACTGTTCATTTCATCAGCAGTATCATAAGTTACAAAACCGAAACCCCTCGATCTGCCA\n") - f.write("CTGTCCCTGTCAAAAACTACCTTGGCTTCCAAAACCTTTCCTTGCTCACTAAACAAGTTCTCAAGAGCCA\n") - f.write("AATTGTCAACACCCCATGCAAGGTTACCCACGTAAAGGCGGTTGTTAGAGTCATAACCACCACCACCTCT\n") - f.write("GGGACCTCTGGCACCTCTGAAAGAGGAAT\n") - f.write("\n") - f.write(">gi|226792305|gb|GO545799.1|GO545799 Mdas9004D05_e269.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTACCCGCCGCTCGGTGGGAATTACGATTCAAGGCGGCCACCGCGGCTCGTCCGCCGCGAGGGCCAGACC\n") - f.write("ATCGACATGAGCCTTTGGGGGCCGGGGCCCCTACTGCAGGTCGGCAATCGGGCGGCGGGCGCAGGCGTCG\n") - f.write("CTTCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCACGGTAGCTTCGCGCCACTGGC\n") - f.write("TTTTCAACCAAGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGAATTACTATTG\n") - f.write("CGACGCTGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTATT\n") - f.write("GGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATC\n") - f.write("AAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACC\n") - f.write("TCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAA\n") - f.write("ATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTANG\n") - f.write("ACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACA\n") - f.write("\n") - f.write(">gi|226792304|gb|GO545798.1|GO545798 Mdas9004G02_e278.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTAGAAAACGATATAGACAATATAAAATTTCAAGATACACACGATGTGGAAGTACATATAGAAA\n") - f.write("CGATGAACTAGCGCATAATTTGTACTAGCTAGCTCGATCCCTCTTCCCTTAGCAAACAGCTTTATAAAGC\n") - f.write("TAGCAGTGGAAGAGCTAGCTAGATTAATACTATAACAACAAAAGGACAACTAGCTAGGGCATTTGTTTCC\n") - f.write("CATACATATATGTGTTCAAGCATGACATTTGACGGGCTAACCAGTCCCATAATAACGCTTATTATTGATC\n") - f.write("GGTTTACCGGTAGAAGTACGAGTACCATATACTTCTGTGATGGTTATCCCACCAAAGATTCTCGCTGCCT\n") - f.write("CATCAGAATTGATGAGCTTGTTATAATTATTAGGCCTCTGAAGGTTCTGTCGAGGTCCATGATTCTCCAT\n") - f.write("GTTGGCTGCAGTCGCCAGTCGTGGGTATCCTTGGTTATCATGATCACCGGTTGAAAGAGGTGTATTAGGA\n") - f.write("TGAAGAGAAGAGACTTGACTCGCCTGTCGTGGGTATCCTTGGTAATCATGATCACCGGTTGGAAAAGTTG\n") - f.write("TATCAGGATGAAGAGAAGAAATTTGACTCCCCATGTTAGCGAGAAATTCCAAATAATGAACTAGGACAAG\n") - f.write("TTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792303|gb|GO545797.1|GO545797 Mdas9004B01_e254.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD13683.1| major allergen Mal d 1 [Malus x domestica], mRNA sequence\n") - f.write("TTTTTTTTTTGCAAGTGAGACATTAACTGATTTCATTATATTTATAGATAATACACTTACAGTCTGCAAC\n") - f.write("TTTTTTTTCAAACAAATACATAAAGGGCAACCAGAAGATGATCACAACCATAAACTTATTTTTCAAAGCC\n") - f.write("AAAGTGCTCAAAACCATGGCTACTTTGGGCTGACTAGAAAAAGCATACAAAGAAAAGCCACACAACCTTC\n") - f.write("GACTGAAGGGTGACACCCAAAATACCATAGAAACATATTAATTTAGTTGTATGCGTCGGGGTGGCCCTTG\n") - f.write("AGGTAGCTCTCAATAAGCTTGAACAAACCATGAGCCTTCTCTTTGCCAGCCTTGACGTGCTCTTCCTTGA\n") - f.write("TCTCAACATCACCCTTGGTGTGGTAGTGGCTGATACTCTTGATGATGGAACCACTTCCAGATGCCACCAA\n") - f.write("CTTGGTCTCGTAAGAGACCTTCTCAATGGTGTCTGTCAAAGCATCTCCTTCAATCAAAGTGTAGGCGTAT\n") - f.write("GAGTAGTTTGCTTCGTCAACCGAGTCGATCTTGTGCTTCACGTAGCCGTATTGGCTGCCTTCACCAAAAG\n") - f.write("TGATCTTCTTGATGGTTCCAGGGCCACCGTCTCCTTCAAGGATCTCAGCATGCTTGATTGCCTGGGGTGC\n") - f.write("AATCTTGGGGATGAGGTTATCAG\n") - f.write("\n") - f.write(">gi|226792302|gb|GO545796.1|GO545796 Mdas9004D23_e271.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF73132.1|AF149017_1 homogentisate 1,2-dioxygenase [Lycopersicon esculentum], mRNA sequence\n") - f.write("TTTTTTTTGAAGGCCTATACCACTAGCACTGGTGTGGTGATTATTATTATTTTGCAAATTTAAGTATATA\n") - f.write("ATAGGCATCTGTTTACATGTAAAGAAACTTTGGGGGCCCATACGAATCCGGGGCACCTTTTGCACACCCT\n") - f.write("CAAGGCCGGCTCAGGTGCTTTAATACAGAAGTGGATACAAATAAGCATATTTGGTACACTTAACACTTTT\n") - f.write("TATAGTACTATGTACTCAGTAGGATTGTATTTGCTTAGTCTTTGTATGAACTATAGTTTCCATTCGTCTA\n") - f.write("AAGCAGCCACGGCAGTCTCCACTTTAATCCTCTTTCTTCCCATTCTGGACATCTCCGTCTTCAGCATTCA\n") - f.write("TCCTTCCACGCGTAAAATGTGATTTCAGTCCAGTCCAGCACTGGTAATAATCACGATCGATGACTGGAGA\n") - f.write("CTCGAGAGCCCATGTGCATACTCTGGGGATTAAACACGATTCAAACATAAAAGCCAAAGTATCGGTGATT\n") - f.write("CTGAATGGTCCTGCCTCATTTCCACGCGCAATGGTAGCCTCATATGTTTTGGTATCAGGACCATGGGGAG\n") - f.write("TCATGCAGCTATGAAGGCTTGCACCACCAG\n") - f.write("\n") - f.write(">gi|226792293|gb|GO546055.1|GO546055 Mdas9010K09_e770.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GGGGGCCTTCCCCGGGCAGCGAACGTTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAAT\n") - f.write("TAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGT\n") - f.write("CAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAA\n") - f.write("TGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCC\n") - f.write("AGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACT\n") - f.write("CTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGTATAAGTGGGAGCCTCGCGGCGAAATTGAAATAC\n") - f.write("CACTACTTTTAACGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCATCGCCCCTCTTTTTGGAACCA\n") - f.write("AGGCCCGCTCGCGGGCCGATCCGGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCT\n") - f.write("GTTAAAAGATAACGCAGGTGTCCTAAAATGAGCTCAACGAGAACAGAAATC\n") - f.write("\n") - f.write(">gi|226792292|gb|GO546054.1|GO546054 Mdas9010G23_e750.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB90634.1| protein phosphatase 2C (PP2C) [Fagus sylvatica], mRNA sequence\n") - f.write("TCACTTGTCACAAGAGCACAATGCCTGTATAGAATCTGTGAGACAGGAGCTGCAGTCTTTGCACCCTGAT\n") - f.write("GATCCACATATCGTTGTTTTGAAACATAATGTATGGCGTGTGAAAGGCCTAATACAGATATCTAGATCTA\n") - f.write("TTGGTGATGTGTATTTGAAAAAGGCTGAATTTAACAGGGAGCCTTTGTATTCCAAGTTTCCTCTTCCGGA\n") - f.write("CCCTATCCAAAGACCAATTTTGAACGCTGATCCAGCAATTTCAGTGATCCCATTGCAGCCACACCATCAA\n") - f.write("TTTATTATATTTGCATCTGATGGGCTATGGGAACACCTCACCAATCAGGAAGCAGTGGACATAGTTCAAA\n") - f.write("AACATCCACGAAGTGGAAGTGCAAAAAGGCTGGTGAAAACCGCCCTGCAAGAAGCAGCAAAAAAGAGAGA\n") - f.write("AATGAGGTATTCGGACTTGAAGAAGATTGACCGCGGGGTTCGCCGCCATTTCCATGATGACATAACCGTG\n") - f.write("ATTGTTGTGTTTATTGACTCAAACCTTGTGAGCAAGGCTAGTTCTGTCAAGGGCCCAAATCTATCGGTGA\n") - f.write("GAGGAGGTGGAATCAACCTGCCTCCTAACACTCTGGCTCCATACGCCTCGGCCACGGAAGCTGGCAATAC\n") - f.write("CTGATTAAACTGTATCTCTCATGTGTGTTCTGTTGCAC\n") - f.write("\n") - f.write(">gi|226792291|gb|GO546053.1|GO546053 Mdas9010J19_e765.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO63778.1| unknown [Populus tremuloides], mRNA sequence\n") - f.write("TTTTTTTTTATTAATGAAATTGCTAAGACAGCTGATTTTCATTCACTGATTATTCGAGTAAATACTATGT\n") - f.write("AAAAGAAATACAAAGTAATACATCAAAAATACCTCAAAGACTTCTGGATCATGGAAAATTCAAGACCAAC\n") - f.write("CACAATATTTTAACCAAAATTTTATCCCAATTTCAACCACTGTACATATGATTTCTCTCCTTGAAAAAAC\n") - f.write("ACCGTATCAACTGAATTTTGCCAACCATTTAGCAAATGACACAAGCATTGGGATCCTCTTCTGAACTTCT\n") - f.write("TACGTAATAATACGCAGGCATTGGAGGATAAAGTGCTGGGTAGGCCTTCATAAGCTCAAGCATTTCGTCC\n") - f.write("TTTGGATCTTTCTTCTTCGGCTCCTCCTTCTTCGGCTCCTCTTTCTTCTTCTCCTCCTTTGCCGGTCCGA\n") - f.write("CTGAGACTATCTCCGTCCGGCAAAGCTTCCTCAATCTTCCCACCAAATGCACGGGATCTATGTCCCCTGT\n") - f.write("GGCCGTCAACTTCTTGTCCTTCATATCCATAGAAATTGAATCAAGGCCTTCAAGCCCCGAGACGGCCCTC\n") - f.write("ATGACTTTCTTCTTACACTTCTCGACGTATAATTCCAATTTCAACACTACTTTCTTCATTTTTCTGTGCA\n") - f.write("GCTTG\n") - f.write("\n") - f.write(">gi|226792290|gb|GO546052.1|GO546052 Mdas9010M15_e783.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC55114.1| S-adenosylmethionine decarboxylase [Malus x domestica], mRNA sequence\n") - f.write("TGACGGCCATTTTGGCAAGCTTGGTTTGGCAAGCAAGGCATATGTTATGGGAAGCCCTGACAAAACTCAG\n") - f.write("AAATGGCATATTTACTCTGCATCGGCGGAGTTGGCAAGCTTATTTTGGGGTTCACGCCAATCAGGCCCTA\n") - f.write("CATACACTCTGGAGATGTGCATGACTGGTTTAGACAGGAAGAGGGCTTCTGTCTTTTACAAATCCGACGC\n") - f.write("AAGTTCAGCTGCTGGTATGACCGTAGAATCCGGCATCAGGAACATCCTCCCGCAGTCCGATATATGTGA\n") - f.write("\n") - f.write(">gi|226792289|gb|GO546051.1|GO546051 Mdas9011B22_e817.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("AAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAGCTTAAAGATCATCTAT\n") - f.write("TGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGGCCCAGGCATTGTTGGT\n") - f.write("AACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAAG\n") - f.write("AAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCCT\n") - f.write("CTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAAG\n") - f.write("GGGTCCTCCGGCGATGCGGTAACCCTCAACCGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAGA\n") - f.write("ATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCTC\n") - f.write("CGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGCC\n") - f.write("CAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTT\n") - f.write("\n") - f.write(">gi|226792288|gb|GO546050.1|GO546050 Mdas9010G22_e749.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTGTTTAATACACTGAGAAATATATTCTATGGCTTAAATTGTGCCACTTGTCAAAGGATTG\n") - f.write("GAATGTTAGTTACTCAAATTCGTTAGTGAGCTGGTATTATCTACAAATTAATACATACTAAAAAAAGGGG\n") - f.write("ATATCACAATCTTCAATTCTACGTTGACGTATTAACTTAAATGAGATTGAAACTTTACACTTCTTGGAGC\n") - f.write("ACTATTTTGATTCTCATCAAGGTTGATCACTCTAATGAAGGGCCTTCCTCCTTTGTGTGCATGCTCCATC\n") - f.write("TCTAAAGACCAAGAACACCCTTCATAGATTTTCGGTTGCACCTAGCCTTGTCAAGAGTAGGTTGCCTACT\n") - f.write("TACTTCATCTCCAACAAAGATCAAACCGTCGTATTTCAGCCTCAGAACTAACGTAAGGATGGAGGAGGAG\n") - f.write("CAAGAGTGTTAAACTAGGACACACTCAAAAGAGATGGATGGCTTTGGATGTGTTTAATAAGTGAT\n") - f.write("\n") - f.write(">gi|226792287|gb|GO546049.1|GO546049 Mdas9010N22_e795.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198367.2| adenylate kinase -related protein [Arabidopsis thaliana] gb|AAL49859.1| putative adenylate kinase [Arabidopsis thaliana] gb|AAM91697.1| putative adenylate kinase [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGAATGTGGAACGTTATTCAATTTAGTAGGAATTCCCCTCCAGTTATCCTCAACTGAAGACGGATTT\n") - f.write("GAGCTACTCCAACTTTTTCCTAATTTGATCTTCATTTCTTTATCTTTCTGCACTTGCGATAGTATAGAGT\n") - f.write("CTATTACTTCGAAAACAACATCCTTCGAATGGTTTCCATCGATCTTTTTCATGATATTCGAGTATGCGGC\n") - f.write("TGAGATTGAATCTGCATTTTTCTTGTATATTTCAAGACGCGACTTCACTTTTTCCTCGGTGTCATCAGGA\n") - f.write("CGAGTAATAAGTCTTGCTTTAATCTCCTGATTCTCCGGAGGGAAACTTTTTATATGGTAGATCTTCCCTG\n") - f.write("TAACTGGGTCTAGCCTTCTTCCAACACATCTGTCGATTAGAGTTTCATCAGGAACATCTAACACAATGTA\n") - f.write("CACATCTGGTATAATCTTCAATTTTTGCAGACTTTGCGCTTGGTTAAAACTCCGCGGATATCCATCAAGA\n") - f.write("AGCCACCCTTTTTCCTTCGCATCATCGCGTGATAACCGTGCTGTCACCATCGCTGTCACGACTTCATCGG\n") - f.write("GGACCAGACGACCGGCATTCATGAACTCTTTGGCCTTGTTTCCAATTTCCGTCCCGGAATGACACTTCAG\n") - f.write("CTCTGAGAAGGTCCCCCGTTGATATGT\n") - f.write("\n") - f.write(">gi|226792286|gb|GO545795.1|GO545795 Mdas9003L23_e224.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568299.1| 30S ribosomal protein S13, chloroplast precursor (CS13) [Arabidopsis thaliana] sp|P42732|RR13_ARATH 30S ribosomal protein S13, chloroplast precursor (CS13) pir|S59594 ribosomal protein S13 precursor, chloroplast - Arabidopsis thal, mRNA sequence\n") - f.write("TTTTTTTGTAAATAATTTCAGCAAGTTCATCACTTCTGATTAAATTTCATAGCATTCCAAGTAGTCAAGA\n") - f.write("ATCTACTGCAGTGTGACCAAGTGATTAGACAACATTTCCTTCTCAACATTTGACAATCCTATGAATAAAA\n") - f.write("CTGTGATCAAACAGGTACACCGACATTCACCTCTCCCAGACCCTGTGTAAAGCGGGAGCCTTGTGCACTG\n") - f.write("GGTACGACCTTATACATTGATGATCCCAACTACATTTCCAAAGGTGAGGGCACAGCTCAACGAAGCAAAA\n") - f.write("GCGATCAGAACAATTGTAGTTAATACTAAAACACAAAACCAGACAAAGGAATTCATTACCAATTACAAAA\n") - f.write("AGAGTCGAAAACCCATTCAATTACTTAACGGGCCTTTTTCTTTCCAGCAACAGTGACCCTCTTACCCTTC\n") - f.write("AGGGTCCTAGTGTTGTTCTTGGTGCGCTGTCCTCTGCAAGGCAATCCCTGGCTGTGGCGTATGCCTCTGT\n") - f.write("AGCACTGAATCTCCTTGAGTCTCCTTATATTCAAGGCATTGAACCTCCTCAAATCCCCTTCAATCATGTA\n") - f.write("CTTGGAGACTTCATCTCGGATAATGGTGAGCTCTTCTTCCGAAAAATCTTTGGTGATTTTGTTCT\n") - f.write("\n") - f.write(">gi|226792285|gb|GO545794.1|GO545794 Mdas9003H05_e208.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TACCATTCCATGATATTATTAGTTTTTTGGGAAATACATGCATGAGTTTTTACTATTTACTATTTACATG\n") - f.write("CACAACAAGATGAAGTAAATGCAGATAGGCTAGTCAACCCTGCATGAACTCCCATTAAATAGCTAATCAA\n") - f.write("AGGCCTTGAGACGTTAGATCGCCATCTGACGAGGATTCGGAGATGCTACACTTGATACTTTCCAGCAGTG\n") - f.write("GGCTGAGTAGATATGGTGGTGTATTCATCTGCCAAGTATTCTCGCTAGTACCAGTAGTGGTAGCAGTGCA\n") - f.write("CTCAAAGTCGATGCTGCTTGGTTGGTACCCGACATTGATAGATTTATGATGATGATCGGCTGCGCCTAGG\n") - f.write("TGTCCATTTTGTTGATCGAATGCTCTCACCGTTGCATGAGGATGATGGTTCGGATATTGCTCCACTACAT\n") - f.write("GATCCCCTTGTGTCAATAAAGCAGTCTCATTCAACATTGCATCGACCACTTCCAACGAATTCCAGTTTAC\n") - f.write("ATAGGCTTCCCTTGCTAAATTCTCAATGTAGGTCCTATTGATATTGCTGAGGTCTCGAATGGGGAAATTT\n") - f.write("TGGCCATTAACCACGGCCCTCAACACTTGACATATAGGATTTAGGAAAATCAAGAAATGAGAACCGCGAA\n") - f.write("ATATGAACATTTTGTTACCCATCACGCAGGTTTTGGCGTGCTTTACTGTCACTCCC\n") - f.write("\n") - f.write(">gi|226792284|gb|GO545793.1|GO545793 Mdas9004A01_e249.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27878.1|AF139466_1 chlorophyll a/b binding protein CP29 [Vigna radiata], mRNA sequence\n") - f.write("TTTTTTTATGATAAGCTCACATGCCATTGCATACACTAATCCTTTGATCCCATCACAATCTTTACAAGCT\n") - f.write("TAAGCAGTACATATCATGATTCAGATAATTAATCATGGTCTACTGATTAAAAAACCAAACATGATATGCA\n") - f.write("CATAAAGATACTTCTCTAAGAAGAGAAGGCGTCAATAATGGTGGTGTGGAGCGGGTCACTCAAATGGGTA\n") - f.write("GCCCAGTTGTTAAGTGGTCCCTTCCCGGTGACGGCGGCTTGCACGGCAAACCCCAGAAACGCAACCATGG\n") - f.write("CGAGGCGGGCGTGCTTGATTTCGGCCAGCTGAAGAGTGGCCTTCTTTTCCGGGTCAGCAGCAAGGCCCAA\n") - f.write("CGGGTCGAAGAACTTGCCACCCGGGTACAACCTCTTTTCCGGGTCGAGCTCGGCGTTCCTCTGGAACTCG\n") - f.write("ATGTAGCCAATCACTAGAACTTCGATCCAGATCAACGTGGTTAGTGAGAAAGGGAGTGGTTGACCCAAGT\n") - f.write("AGGACGACCCTTCGATGAGCTCCACCTTTCCGGCGTCTTGCCATGTGATCCCGGTGACGGACTCGACAGT\n") - f.write("GAGAGCACCGAGCGTGGCGAGCATGGCCCACCTTCCATGAATCAGCTCGCACTCCCTAAACCTCTGCAGC\n") - f.write("CCAAACACCTCCGAGTAAGGCT\n") - f.write("\n") - f.write(">gi|226792283|gb|GO545792.1|GO545792 Mdas9003M19_e231.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GCAAGATAAATCTCTTTACTTCTTAGATATCGAGGAAATTAGATTATGCAGATACATACATGATATATCT\n") - f.write("GAATCGGAAAATCTGTAAGGCTTTCAAATTAAAATTTACAGATGGGCATAAAATCTCTTTAGCTTAGTCA\n") - f.write("TACGTAATTGAATCATATGCTGTTTCCTGCCATATAGAGTTGTACACATGCTCCTCTTCTATGCCAACTC\n") - f.write("CATTATAATAAACATGAGAATAATCACGAACCCATTCACAATGATCTTTTGGACAATTATCCATCTGATC\n") - f.write("ATACTCACAAGAATCCGCATACCAATTCATGCCATTACTTGGTGAGCAAGCCACCTGATCCATTTCAAAC\n") - f.write("CATCCCAACGGATCGCAATCATCTGATGAAGGTGATCGTAAGCAATCCTGACCGTCCAAGCCTCCTACGA\n") - f.write("TGTTCCACAAGTTACTATCTTCCAAATCTTCGATGGTGATCCATTCAGTCTGTGTTACTCGAATCATTGC\n") - f.write("GGTCCATGGTTGTTTTGATTATTTCTGCCTCTAGAGATTGGATCACACTGTTTAATCTCTCCTCATCTCG\n") - f.write("ATCTTCCTCCTGCCATTCTTCTAGCAACGACATGAGAATGG\n") - f.write("\n") - f.write(">gi|226792282|gb|GO545791.1|GO545791 Mdas9003O20_e241.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTAGGGTTATGAATTGAAATCAAATCTTGTATTTGATCTCGTTTTT\n") - f.write("TTTTTTTATTATATTACATAAGCATTACATACATAAGAGGGGCAATACACGATCGCCTCCTTCGCTACAA\n") - f.write("GCATGCTACTACTAATAACCCAGTACGTACTATAATTAATTTAGCTTATACCCACATTCTAGGGCATAGT\n") - f.write("TGACAAGGTCTTTGATCTCCTCTTTAGAAATGGTCCCGTCACGGTTGGCATCTGCATGACCCAAAGCTCT\n") - f.write("CCTCGCCCTGAAACCACCCCAACGCGACCCGAGCTTTTTGAAGGCTGCCTTCACCTCCTCTTTGGACAGC\n") - f.write("ATGCCGTCGCCGTCCAAGTCAAAACTATTGAAGAGATTCACCACCTGCTCCCTAGTCCATGGAACACCGG\n") - f.write("TTGGCTCCTTATAAATGACATCCCTAACCATGATACTATATAGATATATATAGTGATCTTGAAATTTTCT\n") - f.write("TCTGTGTTTTGTTCTACACACTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792281|gb|GO545790.1|GO545790 Mdas9004E19_e273.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188937.1| expressed protein [Arabidopsis thaliana] dbj|BAB03045.1| gene_id:F5N5.17 pir|G71408 similar to unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TGTTATTAACACTTACCCTCCAAACTTTATATATTAAAAAAAAAAAATACACTTGTGAGGAGTGTAAATT\n") - f.write("GAAATTTTTTGAGTACCAATAATACTTCTCTAAAAAAAATGATTGTCAAAAATTAAATTAAAAAGTGGGG\n") - f.write("GCCCCACAACCTTCAAATCACCGAATCCACCTTCTTTTCTAACATCTCCCCAATCAGTCTGGAAATCTCA\n") - f.write("AATTCCGATCTGAAATCGAGGTCCAAACTGTTGTTGCAGTTTTCATTGAAGCAGTTGCAGCGGTTCTGGC\n") - f.write("TACACCTCGTCACAGCCAATGATTGCTTTTCGTTGCTTTCCTCGATGAAATTCTGAACCATCTTTGTCAA\n") - f.write("AAACATGGAGCTCGGCTCGAACTCGGCTGATCCTCCGCCGTCCCCGTCCCCGTCATCTTTGTTGAAATGC\n") - f.write("AGCTCTTTGATTCCAATTCCACCGTTGGGCTTCTCCGTGGCCACCGAGCTTTTCAATACATTCGTGAGCT\n") - f.write("TAATCGAATTTCCCTCATTTCCACAAAGTTAAAGCTTCCTCTTGAGCTTAATAAAAAAATCAAGCTTGAT\n") - f.write("TCTCTACCTATTATACAATCAATTTTCTCTCCCAATCAATT\n") - f.write("\n") - f.write(">gi|226792280|gb|GO545789.1|GO545789 Mdas9004J06_e292.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB40142.1| plasma membrane intrinsic protein 1-1 [Pyrus communis], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGGGGTGAAATAAAGGTTGGTGTTATTTCTGAATTGAAAAATA\n") - f.write("CACAAATTCACAGCCACAGGATACAAAGGAAATGAGCACTCACATCAGACGGACGGGATTGGTGGGGCCT\n") - f.write("CTCCCTAAAAAAGAAGGAACAGAGGGCCCCTTGATTCTTGAGACATATCCATCAACACACATGCCTTTTG\n") - f.write("CTTGCTCATATCACAATAAATTTAACAGCTTAATCCCTTAATTACGTACAAAATACGCTTAAAACAACAA\n") - f.write("GCATTACAGATGAAAAATAACACAAACTTGATCGAAGATTGGCTTGAAAGACGATCATAAAACCGATTTA\n") - f.write("AGACGTAATTAACAGTAATCACTTGGACTTGAAAGGGATGGCCCTGATCACAACCACGTGGTACAAAGCT\n") - f.write("GCAAGTGCTGCCCCAATGAACGGTCCAACCCAGAATATCCAGTGGTCATCCCAGGCATGCCGCTTGTTGT\n") - f.write("AGATGATGGCAGCGCCGAGACTCCTGGCTGGGTTGATGCCAGTTCCGGTGACGGGGATGGTGGCCAAGTG\n") - f.write("CACCAAGAACACGGCGAACCCAATTGGCAACGGAGCCAAAATCGGAACGTGGGAGTCTC\n") - f.write("\n") - f.write(">gi|226792272|gb|GO546048.1|GO546048 Mdas9010P15_e808.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192772.1| light-harvesting chlorophyll a/b binding protein [Arabidopsis thaliana] sp|Q9XF89|CB26_ARATH Chlorophyll A/B-binding protein CP26, chloroplast precursor (Light-harvesting complex II protein 5) (LHCB5) (LHCIIc) pir|T04049 chlorophy, mRNA sequence\n") - f.write("TTTTTTAAGGATCAAGGTTAAAAGCCTTTAAAAGGACTCAATTTGATATACAATGCTTTTAATTTTGATT\n") - f.write("GGAGGAGAATAAGGAGGAAACTTAAAATTACAGGGTTGGAGCTCTTTCGATAGATCCACCAATGACAGTA\n") - f.write("AGCAAGTTGTTGCCGAAGGGATCGCTCAGATGCTTTGATAGGTTTTCGACAGGACCTTCTCCGGTGACAT\n") - f.write("ACGCTTGGAGGAAGAAACCGAGCATGGAAAACATGGCAAGTCTTCCGTTCTTAATCTCCTTCACCTTTAG\n") - f.write("CAATGCAGCCTGGTCTGGATCCTTAGCCAGCCCCAGTGGGTCAAAAGGACCACCTGGGTGAAGCTTGTCC\n") - f.write("TCCAATTCCAGACCGTTAGTGATTCTGTA\n") - f.write("\n") - f.write(">gi|226792271|gb|GO546047.1|GO546047 Mdas9011C03_e820.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTGCAAACCAGTTTTGCTTATTTAGGCATCGGCTAACATCCAATAAAAGGTACAGACATTAA\n") - f.write("CCCAAATCGAATACTGCAATACTAAATTCACATTGTAAACACCCACCAATCTGCTCATTTACTGCAGAAC\n") - f.write("AATGCATTCTTGTGTCTCACCAACCATAGCAGCGCGGGAGCTTTTGTTAATGGTAGCGTCGACTTCTTCA\n") - f.write("TGAGAACGAGGCTTAACTTCTGGATCCTCCGGCAAATTTTCATTCCCATTTATTACCGGAAGCAATACGT\n") - f.write("TCGAAAATAAGAGCATTCACTTCTTGGAACCTCTCTTCAGAAAGGGAAACCTCTGCCAG\n") - f.write("\n") - f.write(">gi|226792270|gb|GO546046.1|GO546046 Mdas9010J15_e764.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197427.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("ACAAAATTGTGAAAATTTGATTACACGGCTGAAAGATCCAATATTATACTTAATAAACTTTTAATTATTA\n") - f.write("ATAATCCAACTTAAGTAGCCACCCAAAAGGGCTCCCAATACTTTAACAATCCTTTCTTCTCACACTCACC\n") - f.write("GCCACCTTCTTTGCACCTGCTTGGCCTTTCAAACTTTTCTATTCCATCTTTACCCCTAACATTCAAACTA\n") - f.write("TTCCCATCCACCTCCTCACCCTCTATCAAACACACATTTGAACTATTCCCTTCTTCTTCTTCTTCTTCTT\n") - f.write("CTTCCTCTTCCTCCTCCTTATCGCCTTCTAATTGTTCTACCAATTCTTCTTCTGTATTTTCTCCCACCAC\n") - f.write("TTCTTGATCTTGCTCTTCTGTTTCCTCCTCAATTATGTCATTTTCACACCCTTCATTGTATTCTTGAATG\n") - f.write("GCTGCTGCTTCTTCCTCTGAGTCAAAACTGGGAGTAAAGGTTTTTGAAAGGCACAATCGAAGGCGGCCAT\n") - f.write("TGCTTCTTTCAGCTTGGAAGCATGAATGACTTAAAGGGGCCTTGACAGCTTTGATGATCAGCCTCCCATC\n") - f.write("TTCCCTGTGAGGCCTAAAGGGTAGAGAATCCTCGCCGCTTA\n") - f.write("\n") - f.write(">gi|226792269|gb|GO546045.1|GO546045 Mdas9011B15_e816.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB91757.1| putative 60S ribosomal protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("CGACATCCAGTTTTAGGGTTTCCTTCTTCAGGAAGTTTTTTCGCAGCGAGGACAAAGATCTAACTAACCA\n") - f.write("TGAGTAAGCTTTCAAGTGATGGGCTGAGGGAGGCCATTTCTCAGATTAAGACAAATTCTGAGACAAAGAA\n") - f.write("GAGGAAGTTCACTGAGACGGTTGAGCTTCAGATTGGTCTGAAGAACTATGACCCACAAAAGGACAAGCGT\n") - f.write("TTCAGCGGTTCTGTCAGGCTTCCACATATCCCTCGCCCTAAGATGAGGGTTTGCATGCTTGGAGATGCTC\n") - f.write("AGCATGTTGAAGAGGCAGAGAAGATGGGTTTGGACTACATGGACGTTGAGAGCTTGAAAAAGCTTAACAA\n") - f.write("GAACAAGAAACTTGTTAAGAAGCTTGCCAAGAAATACCATGCATTTTTGGCTTCTGAAGCTGTCATTAAG\n") - f.write("CAGATTCCTCGTCTTCTTGGCCCTGGTCTTAACAAGGCAGGTAAGTTCCCAACCTTGGCGAGTCATCAGG\n") - f.write("AATCTCTGGAGGCAAAACTTAACGAGACCCAA\n") - f.write("\n") - f.write(">gi|226792268|gb|GO546044.1|GO546044 Mdas9010P11_e807.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_200125.1| cyclic nucleotide-regulated ion channel (CNGC1) [Arabidopsis thaliana] pir|T51354 cyclic nucleotide-regulated ion channel 1 [validated] - Arabidopsis thaliana emb|CAA76178.1| putative cyclic nucleotide-regulated ion channel [Arabi, mRNA sequence\n") - f.write("ATCGACTTCTTGCAAATAATCCACTGTGGAACAAAATATTTATAATTTCATGTGTGATTGCTGTGTCACT\n") - f.write("GGACCCTTTGTTCTTTTACATTCCAATCATCGATCAAGACAACAAGTGCCTTGGAATGGACAAAAAACTG\n") - f.write("AAGAATGTAACTCTTGTTTTGCGACTGCTCACAGATCT\n") - f.write("\n") - f.write(">gi|226792267|gb|GO546043.1|GO546043 Mdas9010L02_e776.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n") - f.write("TCGAGAAGCTTCAGATAGATTATCTGGATCTCTACCTGGTTCACTACCCAATGCCCACAAAGCACAATGC\n") - f.write("AATTGGTAAAACTGCCAGTCTTTTGGGCGAGGATAAGGTGTTGGACATCGATGTAACAATTTCCCTTCAA\n") - f.write("CAAACCTGGGAGGGCATGGAAAAGACCGTCTCTTTGGGCTTAGTTCGCAGCATTGGTCTCAGCAACTATG\n") - f.write("AGCTCTTTCTAACTAGAGATTGCTTGGCTTACTCCAAAATAAAGCCTGCTGTGAGCCAATTTGAAACCCA\n") - f.write("CCCCTATTTCCAGCGCGACTCTCTCGTCAAATTCTGTATGAAACACGGCGTTCTTCCCACAGCTCACACC\n") - f.write("CCTCTCGGAGGTGCTGCTGCCAACAAGGATATGTTTGGTTCTGTTTCACCTTTGGATGATCCAGTTCTCA\n") - f.write("ATGATGTGGCTAAGAAATACGGAAAGAGCGTGGCACAAATCTGTCTGAGGTGGGGAATTCAGAGGAAAAC\n") - f.write("AGCAGTGATTCCAAAATCATCGAAAATTCAGCGATTGAAAGAGAATTTGGAGGTTCTTGAATTCCAGCTG\n") - f.write("AGCGATGAAGACATGCAGCTCATCTACAGTATCGACAGGAAGTATCGTACCAGTCTACCTTCCAAGACTT\n") - f.write("GGGGCTTA\n") - f.write("\n") - f.write(">gi|226792266|gb|GO545788.1|GO545788 Mdas9003G21_e205.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGAAAAGTTGTGTAAATTGTCCCAATGGAAAGTGGACCAAAGGGTTCTTGGGGCATTAGAGGGCACA\n") - f.write("GGGTTAGATAATCTATATACTTTAGCAACTATTGTTGGTAGAAATGCCCATGACAATAGCATGATAGATG\n") - f.write("CTCTTGTTAGGCATTATGATGTTAGAGATAGGTGTTTTAAGATTAATAATCAAAATTTATTTTTCGGATT\n") - f.write("AGAAGATGTGCTTTTAATCACTGGGCTTCCAGTAGAAGGGACCCCGGTGATAAAGTCAACAACAAACATT\n") - f.write("CATGCCCTTGAAAACTTGTTAGGGGGAGTGCCTGAAAGTGAGTTGAAGGATAAATCAAATGCTGTGAACC\n") - f.write("TTAGTTGGTTACAAAAAGAGTTTGAGCATGTACCTGAAAATGTAGATGCCGATAGATTTTCCTGTCATGT\n") - f.write("TAGAGGATTTGTCCTCTACATATTAGGCACGGTAATGGTTCCCAGTTTAGACCATGTGCACGTGAATCTG\n") - f.write("GGCTACTTGGGCTGCATGTCCGAGATAGGTGAGATAAAGAAGTATGCATGGGGAGTTGCA\n") - f.write("\n") - f.write(">gi|226792265|gb|GO545787.1|GO545787 Mdas9003N07_e234.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196452.1| expressed protein [Arabidopsis thaliana] emb|CAC08335.1| putative protein [Arabidopsis thaliana] gb|AAM63112.1| unknown [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTCATGAAATTGACATGATTGATATTATAAACCCAGGCAAAAAAAGGGTAAAAC\n") - f.write("TAAAACCTTGAGGAAAATAAAAACACATGTAGAAGCTAATTACCGGAGATGAGCCAGCTCTCGTTAATTT\n") - f.write("GCTCATCCCCAAATTACAAAACACGTCTTGCTAATTGCTAATGTGCTGCCTGCATTTTCTAGTTGTGGGA\n") - f.write("CTGGTTGTGGTTGGCAATGGAAAGGGCCTTGTGAAGATTTCTGAAAGCTTTCTCGTAGCGCAAGAATCCC\n") - f.write("ATGAACCAGAAGTCGAAATCATCGTGGGTAACTATTTCAATGTACTTCTGTTGTGGTTTGTTGACATTCT\n") - f.write("CGCTTTGGTTCACTGTTTTGATCTTCCTTATTGGTATCCGAACTTTGTAATGCGTTCTGAGGAGTTGCAG\n") - f.write("TTGTCCAGCAGCAGCAGGACCAGAAGCAGGAGGAGAAGGGAGAGTGATGGGTCTTTCGCTGCAAAAAGCA\n") - f.write("AGCTTTTGGGTAGAAATGAAAAGGAGGCCAGGAATGGGACCGGCGGTGGTGGATAGGTAGCATTGGGAGG\n") - f.write("CCTTCAAGAGCTCTTCTCCTTGGCTGACACCGAATATCTGTTTAAAAATATTGGCCCTCCCACCCTCTTG\n") - f.write("AA\n") - f.write("\n") - f.write(">gi|226792264|gb|GO545786.1|GO545786 Mdas9003K17_e220.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172258.1| histone H2B, putative [Arabidopsis thaliana] pir|D86213 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF75074.1|AC007583_10 Strong similarity to histone H2B like protein from Arabidopsis thaliana gb|Y07745. ESTs gb|R8, mRNA sequence\n") - f.write("TTTTTTTTTTTGTTTTTTTTTTTTAGGTAAATCGTACTTTCATTTAGAATTTAAACCGCAATAGCACAAT\n") - f.write("ATCAGTACTTAATACTTACATAATCAAAAGCATTAAAACCCATAAACCCCTAACCCTAACCCTAATTCCT\n") - f.write("TCACAACCAATCTCAAACCCAAATCCACAGAATTAAACACATTAACCCTAACTCTTCAAGAGCTAGTAAA\n") - f.write("CTTAGTCACCGCCTTAGTCCCCTCAGACACCGCATGCTTAGCAAGCTCACCAGGCAGCACCAATCTCACA\n") - f.write("GCAGTCTGGATCTCCCGGGAAGTAATCGTCGGCTTCTTGTTGTACCTCGCGAGCCTGGATGACTCCTGGG\n") - f.write("CGAGCTTCTCGAAGATGTCGTTGATGAAGCTGTTCATGATTCCCATGGCCTTGCTGGAGATCCCGATGTC\n") - f.write("AGGGTGGACCTGCTTCAGCACCTTGAAGATGTAGATCTTGTAGGTCTCCACGCTCTTCTTCGATCTCTTC\n") - f.write("TTCTTCTTGTCTCCGGCGGCGGCTCCGGCCTCCTTCGGGAGCTTCTTCCCGGCCTTAGGCTTCTTCTCGG\n") - f.write("GCGGGGGCTTTCTCCGCCACGGCGGACTTCTTTTCCTCCGCGGGCTTCTTCTCGGCGGGGCTCTTCTCAG\n") - f.write("CT\n") - f.write("\n") - f.write(">gi|226792263|gb|GO545785.1|GO545785 Mdas9004B14_e259.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAP47161.1|AF514908_1 dehydration responsive element binding protein [Glycine max], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTGGCCATAAAATTCAAAGACTATAATTTCAAGAAAAGAAACATTACTGATTGCCCTT\n") - f.write("CAGTTGGTTTGTTGTTACAATTGAGAAACTATATCAAATTACCAATCGAAACGGAATTCTTGTGATTCCA\n") - f.write("TTTCCTGATCGGACCCAATAAACCCTTCTCTGTATTTTTACTTTATTGCACACCTAAATACCTACTCATA\n") - f.write("ACAATAAACAGCTGGTGATCGGTCGGCCTTCTCAATTAACTTTCATCGGAGTTTTCTGGGTCGGGGTACT\n") - f.write("CATTTAAGTCGGGCTTCAAAGAGCCACCCCGGCTCAACGTTGTTTTGGACTGCGACGTCGGCGATGAGCG\n") - f.write("GAGAGCGGTTTGAACAGCGTCGACCTTAGCCCCGACCTCCGTAGCTTTCTTCCGTATCGAAGCCGCCGAC\n") - f.write("ATGTCGTGGAGCTGCTGGCCGTCGTCTTGGAATACAAGTTCCGGGAAGTTGAGGCGGGCAGAAGGGCCTC\n") - f.write("GAAGATAGAAAACGGCGGTGTCGTAAGCTCGGGCGGCAGCCATGGGGGTCGTGTAGGAGCCGAGCCAAAT\n") - f.write("TCGAGAGCGCTTGTTGGGTTCTCGAATCTCCGCCACCCACTTCCCCCACTTCCTC\n") - f.write("\n") - f.write(">gi|226792262|gb|GO545784.1|GO545784 Mdas9004I10_e289.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188060.1| glycolate oxidase -related [Arabidopsis thaliana] ref|NP_850584.1| glycolate oxidase -related [Arabidopsis thaliana] sp|Q9LRR9|GOX2_ARATH Probable (S)-2-hydroxy-acid oxidase, peroxisomal 2 (Glycolate oxidase 2) (GOX 2) (Short chain, mRNA sequence\n") - f.write("TTTTTATCCATGGAAATATTATCTCACCATCCAGTAATCAGTATCATTACAGAAAACGCAGAAATAATAA\n") - f.write("GGAATCCAAGAACAAAGGTTTATCCACCGCTGTTCATTTGAATGTTTCTATAACCTTGGCTGATGGCGAG\n") - f.write("GGCGAGGAGCGTCCCAGTCAGTCACAATGTGATCGCGGGTGATCTCTTTGAGCGAACGGCATCCACTTAA\n") - f.write("TGTCATGGTTAGCTCAAACTCTTCGCGCAGCATTTGGAGTACCTTTCTAATGCCAGCCTCTCCTTCAGCC\n") - f.write("GCGAGAGAGAACACCACAGGGCGCCCAATAAATATGCCAGAGGCACCCAAAGCTAATGCTTTGAAGACAT\n") - f.write("CTGTTCCTCGACGAACACCACCATCCAAGAAAACAGGAATGCGTCCTTGTGCACCTTTAACAACCTCTTC\n") - f.write("GAGGGCCATGATAGTCGAAGGGACGTAATCAAGTTGGCGAGCTCCATGGTTGGACACAATAATCCCAGCT\n") - f.write("GCTCCAGCTTGTACTGCAATCCTTGCATCTTCGGCAGTGAGAACACCCTTAACTAGGATAGGCAGTGAAG\n") - f.write("TGATTGTCTGAAGCCACTGCACATCCTTCCAGCTAAGAGAACGATCGATTTGACCAGCAACGTATGAAGC\n") - f.write("AAGTCCAGAGTCAGCAGCTTTGTCATCTTTCCGAGG\n") - f.write("\n") - f.write(">gi|226792261|gb|GO545783.1|GO545783 Mdas9004E14_e272.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC24587.1| AP2 domain containing protein [Prunus armeniaca], mRNA sequence\n") - f.write("TTTTACACGAAACGAAAATGGCATGGCCTTTTGGTAATTCCGTCATCCTCAAAGGTCAGATTGTCATACA\n") - f.write("GATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTACAAACACCAAGTCAAAAGTACATAGAACTG\n") - f.write("AAAACCAAACAATGCAAAATCTGATGGCCTCTTGTAAAAAGGAAGACCGAAATAAATTTAAACAAGTACA\n") - f.write("GAATTATGAGGTTTCAGTATCATCATAACTCACACAATTTCATCGTTACAAACATGAAAGTTCAGAAACC\n") - f.write("ACAAGTTCTTTGGACGAGAAAGTGGACCCATTACCTATACGATCTCCATACGCCATTAGCTACGGCTTAA\n") - f.write("ATGCTCCCCCGTACAAGCCTTATCCATGTCAACAGCTTGCACAGATGTACTCCAACCCGAAACACATCAT\n") - f.write("GTAGCTTTATTTACATAAACTGGAAAGCTGGGGTAAGGTTCATCTCTCAGAAAGTTCCTCCAACAATTGC\n") - f.write("GGGCAGATCGTCAAAGGTCCATAGGTCCCCCGGATTACCACCATCCTGAGTTGCGTCTCCGTTAAGGAAG\n") - f.write("GCGTCCACTGAAGCATCCCAGCTCCCATCAAGATATGGGGTCTGAAAGTACTTCATCTCAAAAGCTGAGA\n") - f.write("GCTCATCAGAC\n") - f.write("\n") - f.write(">gi|226792254|gb|GO546042.1|GO546042 Mdas9011B07_e815.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S28827 chlorophyll a/b-binding protein type I - common tobacco emb|CAA45523.1| photosystem I light-harvesting chlorophyll a/b-binding protein [Nicotiana tabacum], mRNA sequence\n") - f.write("GCTGTGGCATCGCCACTACTGCCTTCCCTTCAGTCCTCTCATCCTCCAAGTCTAAATTTGCGACCAGCGC\n") - f.write("AGTCCAGCTCCCAAGTATTGGTGCCAATGCCTCCTCCAGGTTCTCCATGTCCGCCGAGTGGATGCCCGGC\n") - f.write("GAGCCCCGCCCTCCTTACCTCGACGGCTCTGCCCCCGGTGACTTTGGATTTGACCCACTTCGGCTAGGAG\n") - f.write("AAGTGCCAGAGAACTTAGAGAGGTTCAAGGAGTCCGAGCTCATTCACTGCAGATGGGCAATGCTTGCTGT\n") - f.write("TCCAGGGATTCTAGTACCAGAGGCTTTGGGATTGGGCAACTGGGTAAAAGCACAGGAGTGGGCTGCCGTT\n") - f.write("CCAGGAGGCCAAGCCACCTACTTAGGCAACCCAGTTCCATGGGGCACTTTGCCTACAATTTTGGTCATCG\n") - f.write("AATTCCTTTCCATTGCCTTTGTAGAACACCAACGCAGCATGGAGAAGGACCCTGAGAAGAAGAAGTACCC\n") - f.write("TGGTGGCGCTTTTGACCCCTTGGGCTACTCCAAGGACCCCAAGAAGTTCGAGGAATACAAAGTCAAAGAG\n") - f.write("GTCAAAAATGGCCGGCTTGCGTTGTTGGC\n") - f.write("\n") - f.write(">gi|226792253|gb|GO546041.1|GO546041 Mdas9010G14_e745.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTCTTTTTTTTTTGGTTGAGATTAGTGAAATTGCTTTCATACCGAATTTTATCAATAAGCTAG\n") - f.write("TAGATGCTACAAGTACCTATAACTTTCTATCATGTGCCTTAATTCTAAAAAAACCTTGACGCCAACCTTT\n") - f.write("GAGCACAGGGTGACTTCAATATTTTTCACCTTCAGCAGTTCCATTGTGTTTCGGTAACTGAGTACCATAT\n") - f.write("AGGCTACCATAGCCTGTGTCATGCTCGCCCTCTGTCTCTGTCTGTCTAGCATCAAGCGTATTTTTGGTTG\n") - f.write("TTTCCGCGCTTGGAAAAATCG\n") - f.write("\n") - f.write(">gi|226792252|gb|GO546040.1|GO546040 Mdas9010M10_e782.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ATTATTGTTGTCCAATACTTGGTACCAAATTTACCTCACCGACAACTATACAAACGAAAGTACAAGACAA\n") - f.write("CTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGAGGCGTATT\n") - f.write("\n") - f.write(">gi|226792251|gb|GO546039.1|GO546039 Mdas9010J03_e761.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO61490.1| arm repeat-containing protein [Nicotiana tabacum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGAAATATATAAATGTCTATACTACCAAGACAATGGGGGCATAACATC\n") - f.write("AACAATTCCAAATACAAATTTGTCATCATAATCATGCCTAGCCGGACTTACAGGTATGCTATTAACTTTT\n") - f.write("TCTTCCCACATTCACGTAGGTATTTTACAAATCAGACGTACAAATCTTCTATCCATCGTTTGTTATTCTG\n") - f.write("TCTTCTCTTGTCTATGGTTTCTGAAGTAGCTAAGGAGTGTCTGTGCCTTTTCTTTTGCCCTAGGGGTGCC\n") - f.write("GGATTGTGACAATACCACTAATGGTGGGACAGCTCCTTCTTGGAGGACCTGACTGCAATATCTATTACTG\n") - f.write("TTTGTGCAGAGCTGTAAAAGAGCAGCAGCAGCGTTCTCCTTCCCTCTTGGAGAACCCAACTCAACAACCT\n") - f.write("CGACAAGAACAGGGATCCCACCCTCCTGACCAATTGCTGTCCTTCCCTCGGGAATTGTCGAAAGATTAGC\n") - f.write("CAAAACAGCAACTGCCTTGTCAACCATTCCAGCTGCAGGGTCCATCAACTCCACTAGGTACTTTACAGCA\n") - f.write("CCAGCTTGAACAATTCGACCCTTGTTCTCATGAAAAATTGACAAATTAAACAAAGCTGTGGCTGCATCTT\n") - f.write("TCCTCCCTCTGGGACTCCCATTCCC\n") - f.write("\n") - f.write(">gi|226792250|gb|GO546038.1|GO546038 Mdas9011A18_e814.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191019.1| histone H2A.F/Z [Arabidopsis thaliana] pir|T47615 histone H2A.F/Z - Arabidopsis thaliana emb|CAA73155.1| histone H2A.F/Z [Arabidopsis thaliana] emb|CAB77576.1| histone H2A.F/Z [Arabidopsis thaliana] gb|AAM64788.1| histone H2A.F/, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAGCTTATAAAAGTCGAATCATATAAATAAAGACAGAGAATACCAG\n") - f.write("GTTAAACTATCCAACAAAACACATAAAGATGAACAAACATACAGATAATGGTTCAAAGGGACAAGCACTA\n") - f.write("GATTGCCCATATGTACTACTAAATCCAGCTAACCTAAACAGCTACTAAAACACGAGAAATAAACAGTCAT\n") - f.write("AATATTAAACAACACCATCAGTTAATACCCGTTTGACTCATCAGATCTGAATTACTCCTTGGAAGTCTTG\n") - f.write("TTGATGAGGGACTTGTGGATGTGGGGGATGACACCACCGCCAGCAATGGTTCCCTTGATCAGAGTGTCCA\n") - f.write("GCTCCTCATCTCCCCTGATGGCTAGTTGCAGATGCCTGGGTGTGATTCTCTTGACCTTGAGATCCTTGCT\n") - f.write("AGCATTCCCGGCCAACTCAAGAACCTCAGCAGTTAGGTACTCGAGGATTGAGGCCAAGTACACAGCAGCA\n") - f.write("GTGGCGCCAACACGGCCATGAGCAGCAATTCGCTGTTTCAGCTGCCTATGAATTCGACCCACCGGAAACT\n") - f.write("GGATACCAGCGCGAGATGAACGAGAAACAGGCCTCTTCTTGTCCTTCTCCTTTTCTTTGTCCTTGTTAGC\n") - f.write("CCGCTGTGGGTATTCGCTGCAATAAGCCCCTTCCCGCCTTTGCCCGCCA\n") - f.write("\n") - f.write(">gi|226792249|gb|GO546037.1|GO546037 Mdas9010F06_e738.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TCTCATCAACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGG\n") - f.write("GACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACC\n") - f.write("ACCGGGACCCTTGGCTAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACA\n") - f.write("ACTTAGACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGA\n") - f.write("TGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTC\n") - f.write("GGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGG\n") - f.write("TTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGT\n") - f.write("AGTCAACTTCCTTGGCCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAG\n") - f.write("TCCAAGTGGAGGCCACACCTGCATGCATTGCACTCTTCCTCCATTG\n") - f.write("\n") - f.write(">gi|226792248|gb|GO545782.1|GO545782 Mdas9004H05_e281.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q42434|BIP_SPIOL Luminal binding protein precursor (BiP) (78 kDa glucose-regulated protein homolog) (GRP 78) gb|AAA21808.1| ER-lumenal protein gb|AAA21806.1| ER-lumenal protein, mRNA sequence\n") - f.write("GAGTCCGATGAGAAGGAAAAGATTGAGACCGCGACAAAGGAAGCCCTCGAGTGGTTGGATGACAACCAGA\n") - f.write("CCGCCGAGAAGGAAGACTATGACGAGAAGCTCAAGGAGGTTGAAGCCGTGTGCAACCCCATAATCTCAGC\n") - f.write("CGTCTACCAGAGGTCAGGAGGTGCCCCGGGTGGTGCCAGAGCCTCGGAGGAGGACGATGAGTCACATGAC\n") - f.write("GAGCTTTAAAAGAGTAGTTTATTTCATTTTCATCGAACACGGTTGGAAGCAGTGAGGAGAGAGAGGGGTT\n") - f.write("ATAGGTTTAGGGGAAGAAGACTTTTACTGTAATTTTTCCGATGGGAATAGAAGAAGCTGAGGGAGACGAA\n") - f.write("TTTCGACTCTCTCGGCTTATCGGGTCTTTTTGTTAGAACGTGTAATTTCATTATTTTGATAAAAAAAACA\n") - f.write("CAGTTTCAA\n") - f.write("\n") - f.write(">gi|226792247|gb|GO545781.1|GO545781 Mdas9004I24_e290.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187919.1| chloroplast 30S ribosomal protein S10, putative [Arabidopsis thaliana] dbj|BAB01403.1| unnamed protein product [Arabidopsis thaliana] gb|AAK60293.1|AF385700_1 AT3g13120/MJG19_6 [Arabidopsis thaliana] gb|AAL16207.1|AF428438_1 AT3g1, mRNA sequence\n") - f.write("TTTTTAAAGTGAAATGAATCCTAGACATGGAGAATAATCGAAAAGATACACAATGCGGAACTAATATGCA\n") - f.write("ACAAGGATATCAAATAATGTCGAAAGAGGAACTCTTTATCTCTATTCTTCAACTGAGATCCAAGGGCAGA\n") - f.write("AATTGCTTACAATTGCTTACAAAATACACAAAAGAAATGAATTTCAGGAAAGGATCAAAATGCATTCGAT\n") - f.write("AAGCGTAATCCTGCAGTCATTCAGCCTCTACAAAATAAACGTGAACCTTTGTAATCTCTTTCCCATGTTC\n") - f.write("TTCAAAGAAAACACCTAAGCTGCTGCCCTGCTTCTTCACAGTTTGACCTCCACATCAACTCCAGCAGGAA\n") - f.write("GGTCAAGTTGCATTAAGGAATCTATTGTTTGTGCAGTTGGGTATAGAATATCAATGAGGCGTTGGTGGGT\n") - f.write("ACGAATCTCAAAATGGAACCTTGCATCCTTGTGGACATGGGGAGATTTGAGAACACAGTAGATTCGCTTT\n") - f.write("TTAGTTGGCAAGGGTACAGGACCCATTGTTTTCGCATTCGTGTTCCTAGCAGCATCCATTATCTGCTTGC\n") - f.write("AGGAATCTTCTATNCATGGCACAAAGTAAGACCTCAGTTTAATCCTGATTTTCTGCTTGAGTGAGGCCTT\n") - f.write("ATCTCCATCTTCACCAATACTGAGTGATGAAGTACTCGG\n") - f.write("\n") - f.write(">gi|226792246|gb|GO545780.1|GO545780 Mdas9003G22_e206.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S16294 chlorophyll a/b-binding protein type I precursor - tomato, mRNA sequence\n") - f.write("TTTTTTTTTTTTTGAAAAGATAGAGCAATTCCATTTAAGGATCAAGGTTAAAAGCCTTTAAAAGGACTCA\n") - f.write("ATTTGATATACAATGCTTTTAATTTTGATTGGAGGAGAATAAGGAGGAAACTTAAAATTACAGGGTTGGA\n") - f.write("GCTCTTTCGATAGATCCACCAATGACAGTAAGCAAGTTGTTGCCGAAGGGATCGCTCAGATGCTTTGATA\n") - f.write("GGTTTTCGACAGGACCTTCTCCGGTGACATACGCTTGGAGGAAGAAACCGAGCATGGAAAACATGGCAAG\n") - f.write("TCTTCCGTTCTTAATCTCCTTCACCTTTAGCAATGCAGCCTGGTCTGGATCCTTAGCCAGCCCCAGTGGG\n") - f.write("TCAAAAGGACCACCTGGGTGAAGCTTGTCCTCCAATTCCAAACCGTTAGTGATTCTGTAGTATTCAGCTC\n") - f.write("CACCAAGAAGAACAACCTCAGCAACAACAGCGAAGATAAGATTAATCGGTATGTTCTTCCCAAAGTAATT\n") - f.write("CAGTGTGTTCCCATCAAGGAGTAGAGCTCCTGTCTTGAACCAAACAGCCTCAGGGCCGCAGTTAGCTCCA\n") - f.write("AATTTGTTGAAGGCCTCTGGAATGATGAATCCGGCTGCACCAAGCATGGCCCACCGAGCGTGGATCAGCT\n") - f.write("CATATGCTTGGTATTTGCTGAAGTTTTCTGGCTTCTTGCCTAGGCCAAAAGGA\n") - f.write("\n") - f.write(">gi|226792245|gb|GO545779.1|GO545779 Mdas9004D14_e270.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198099.1| seryl-tRNA synthetase [Arabidopsis thaliana] sp|Q39230|SYS_ARATH Seryl-tRNA synthetase (Serine--tRNA ligase) (SerRS) pir|S71293 serine-tRNA ligase (EC 6.1.1.11) - Arabidopsis thaliana emb|CAA94388.1| seryl-tRNA Synthetase [Arabid, mRNA sequence\n") - f.write("TTTTTTAAATCAGCTCTGTTAAACATTACGTAATTAAGGTTTCTTGCGGCGCAAGCATACTCCTCATCAG\n") - f.write("ATATAACTGTGCATATCAGAAATCATAAGGCAAAATATGAATCTTGTAGGACAAACCAAAACAAAACAAG\n") - f.write("TTGATCTGAATATATTTAATTCATTACATCAAAGATGAAGACATGGAATTTGGGTTTCAGGGTTTCTCAA\n") - f.write("AACAATCATCAGAAGAGTTTACGCACGCCATGTATCATGAACTTCTCTTGTTAATCTATTCTTCATTAAA\n") - f.write("GACTGAAAAAATTACGAATTTTAGGCCTTCGATTTCTTCCCTTTGACTTCAGGGGCTGGTTTGGCCTTGA\n") - f.write("ATGGTAAGAACTCCTTTCCACCCATGAAGGGTTGAAGAACTTTCGGTACGTTTACACCCTCTTCAGTCTG\n") - f.write("GTAGTTCTCGAGAATGCAGCATACAGTTCTCTCACTCGCTGTAAGAGTCGAGTTCAATAAGTGAACATAT\n") - f.write("TGCTTTGTCTGCTCGTTGCTCTTTTTCTGCCCATATCGAATTTCTAACTTTCTTGACTGGTAGTCCGTAC\n") - f.write("AGTTTGAACAACACACCAGCTCTCTGTATGTCTGAGATGCAAGATACCATCCGTTCAGATCATACTTCTT\n") - f.write("TGCTGCGGCATCATTCAAAGCACCAGAGACGATGGACACAATATGATATGCGAGCCCTAACGCTTGATAA\n") - f.write("AAT\n") - f.write("\n") - f.write(">gi|226792244|gb|GO545778.1|GO545778 Mdas9003O19_e240.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192721.1| expressed protein [Arabidopsis thaliana] pir|T04031 hypothetical protein F17A8.180 - Arabidopsis thaliana emb|CAB39650.1| putative protein [Arabidopsis thaliana] emb|CAB78106.1| putative protein [Arabidopsis thaliana] gb|AAL6703, mRNA sequence\n") - f.write("CAGGGATAATATTTCAACATTAAAAGCAATGCCTAATAGAAACACAACGGTTTTTGGTAAAACAAAACGA\n") - f.write("AACAAAAAGCAATACAAAAAAGATGCTTACAGAAGATGGAGAAGACCAAGCTATTCTCAAACAAGACAGC\n") - f.write("AAAAGTAAATTAAATTGATTGCATTTACCGCTTCCATGTTGTGCCGTCTTCCCTTATGGAATTGCACCAG\n") - f.write("AGAGCAGCTTTGTATTGTCGTGGTTCTTCCAAAGACTTTTGACACCGTCCCATGGGAAATACTTGGATGA\n") - f.write("ACCAACTGAACGCTTTCAGTAGGTAGAGTCATGACCAGGACTATCTGCATGCATGTCCATCGAGGTATCA\n") - f.write("TTGGAACTTGGAGGATTAGCATCCCGGTTTGGGTGGAGAAAGCTAGGTTCATTGTTTCGGGCTCCATTTC\n") - f.write("CAGATGGCAGAACTGCTCCTGGATAATATCCATCTTGAGAAATGTGATAGTGCTGAAGACTCTGGCGAAC\n") - f.write("AGGGCTCGACAAAGCATTTGAGAAGACCGAATTCTTAGATTGATGATCGCACTGCTCAGAACGAATTCCC\n") - f.write("TGCCCAGTAAATTGTTGGGACAGATGAACCAGAAGT\n") - f.write("\n") - f.write(">gi|226792236|gb|GO546036.1|GO546036 Mdas9010N20_e793.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTCTTGGGGTCGCAGTCAGGGGAACAAGCAGTGGAGGTCGGATTCAAGTAACCAGTGGAATGGAGCACA\n") - f.write("CTATGGAGGACAGGGTTATGGCGGGTATGGACATGCTGTGCCACAGGGTGAGGACCTGAGCATGCACACC\n") - f.write("GCAGCTGCGGTTAACGGGGCTTCTTAACAGGGCTGTCGCAGTTGCCAACAGCGTGTAAACTGAACTTACA\n") - f.write("AAAGTGGCATTTTAGATATAGTTTATCAATGCCTTTAATTGAAGTAGGGTCGATTTAGCTAAATATGTAA\n") - f.write("TGTGAGGAATTTTTGATACCGGATTTAGCAGCCCTTGTGTGAGATGAATACTTGTGTCTATGCCTGGCAA\n") - f.write("TCTTGGAATCAACAGGAATTCTTTTGACCCGGAAAATACGTTTATACCGA\n") - f.write("\n") - f.write(">gi|226792235|gb|GO546035.1|GO546035 Mdas9010O21_e801.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172650.1| aminomethyltransferase-related precursor protein [Arabidopsis thaliana] ref|NP_849646.1| aminomethyltransferase-related precursor protein [Arabidopsis thaliana] sp|O65396|GCST_ARATH Aminomethyltransferase, mitochondrial precursor (, mRNA sequence\n") - f.write("AACCCAGCTTCCACCCCGAAACTGTCACTAGCACCCAGACCTGACAGCCTCACCTTCCCCTCGGATTTCT\n") - f.write("CACAGATTGCCTAGGCAAGATCCACTGCATTCTCATCAGGAACCGAGATTTCAAATCCACAAACAATGTA\n") - f.write("GCATACACGACATGAGTGATTAC\n") - f.write("\n") - f.write(">gi|226792234|gb|GO546034.1|GO546034 Mdas9011B24_e818.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P07030|PLAS_SILPR Plastocyanin, chloroplast precursor emb|CAA26709.1| precursor [Silene latifolia subsp. alba], mRNA sequence\n") - f.write("TTGCTAGAACACATTCAATCAACTACATACAATGGCCTTCGTCAACCCCGCCGCGGTCGCTATCCCATCA\n") - f.write("TTCACCGGACTTAAATCCGCCGGCGCAGCCAAGGTTAACGCTGCAGCTAAGGTCTCAGCCTCCCCAAGGC\n") - f.write("AGATGTGCATCGTCAAGTCATCCCTCAAGGATGTTGGTGTGGCCGTTGCCGCCACTGCCGCCAGTGCTAT\n") - f.write("CCTCGCCAGTAATGCCATGGCCATTGAGGTCTTGCTAGGCAGCGATGACGGTGGCTTAGCCTTTGTCCCC\n") - f.write("AACAGCTTCTCCATCGCCCCCGGTGAGAAGATTGTGTTCAAGAACAATGCTGGATTCCCACACAACGTTT\n") - f.write("TGTTTGACGAGGACGAGGTTCCCAGCGGTGTGGATGCTGGAAAAATCTCGATGAGCGAGGAGGACCTCCT\n") - f.write("GAATGCCCCCGGGGAAACCTACGCCATCACCTTGACCGAAAAAGGTTCATACTCTTTCTACTGCTCTCCT\n") - f.write("CACCAGGGAGCTGGCATGGTCGGCAAAGTTACCGTTAACTAATTCAGTTGTCTGATTAATAATAT\n") - f.write("\n") - f.write(">gi|226792233|gb|GO546033.1|GO546033 Mdas9010M04_e781.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF78526.1|AF195234_1 metallothionein-like protein [Pyrus pyrifolia], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTGATGAAAAATAAGATGGTAATTAACAGAGCCATAGCATGTATTCTAATATTTGC\n") - f.write("ATATAAATCAAAGGGCCATGAACATGGCCATTACATGACACAATCACAGAAACACAAACATATGAGTGAC\n") - f.write("ATGTTTTCACAGACGTACAACATGTCACTCGACAGACTCAAATACTATAAGCAAACAAGAGACAAAGCCA\n") - f.write("CAACGTTATTTTATCCCACAAACACTTTTCATTAATTAAGGGTCTATAATCCCTTAATTAATATGACACT\n") - f.write("TTTATTAATCACATCTTTAATTTGGTTATCTGGGCTTACTGACCACAGGTGCAGTTCACACATGGGCAGG\n") - f.write("TTGCGCCACACTTGCACTTTCCGTCGTTCTCGGCTGCAGGAGCGTCCACGACGACGGTGTCCATGGCGCG\n") - f.write("GTTCTCATTCTCCACGATCACCAAGT\n") - f.write("\n") - f.write(">gi|226792232|gb|GO546032.1|GO546032 Mdas9010J06_e762.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T12317 26S proteasome regulatory subunit S5A - common ice plant gb|AAC19402.1| 26S proteasome regulatory subunit S5A [Mesembryanthemum crystallinum], mRNA sequence\n") - f.write("TCGGGGAAGAGGATGATGGGAAGCCAGAGAAGCTGGAGGCCCTTCTGTCTGCAGTTAATAATAATGACAG\n") - f.write("CAGTCATATAGTACATGTCCCCCCCGGTCCAAATGCTCTCTCAGATGTTCTCATAAGTACACCTGTATTT\n") - f.write("ACTGGTGACGGAGAAGGAGGAAGTGGTTTTGCAGTGGCTGCCGCAGCAGCAACTGCTGCTGCTATTGGTG\n") - f.write("GCTCTGGGTATGACTT\n") - f.write("\n") - f.write(">gi|226792231|gb|GO546031.1|GO546031 Mdas9010K13_e771.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM63765.1| unknown [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTGGTTAGAATATGCTTATGCAAAGTTGCAAACAACATGAAGAATGTTCACATCCTTATGAACAATGCTG\n") - f.write("CGAGATATTTACGTATACAGATAGATGCTTCAAAAACCGGCCACGAGTTCTTATCTTAAACAACATTACT\n") - f.write("TTTCGGGTTGTTCTAGCTGCTGCCGATTATATCTTTGTATGTAGCTTTAATCTTCAGTGTCAAAGCCTCT\n") - f.write("CTGTCTGGTTTGTAAACAAGGTTCTTGTATGCAAACCACCCAGTGTAGCCAATTCCTACAAGCTCAAGAA\n") - f.write("CACCAGGAACTAAAGGAAGCCTATCAATTGCCGAAATCAGTCCAGTGGAGCCCCATAGTGCAGCAGCACC\n") - f.write("AGCTACTGCAAGTGAAGAAACTGCATATTTATCTTCCACTTTCTCCCAAGCTTCTTGAACGGTCTTCAC\n") - f.write("\n") - f.write(">gi|226792230|gb|GO546030.1|GO546030 Mdas9010P21_e809.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26889.1|AF317062_1 abscisic stress ripening-like protein [Prunus persica], mRNA sequence\n") - f.write("ACCGAGTAAACAGTATTATTATGAACAATAACAATGACATACATACATACATACATACATAGATGGCATG\n") - f.write("CTAAAAAAAAACCAAATAGCACCCATTAATTGAAAAGGACATTTAACCACTCAACTATTGTAGCGATATT\n") - f.write("GTTGAAATTAAGCATCACACTCTCACTGATCACACCACATGATAACTAGTAAAAACACAACATTGCATAT\n") - f.write("GTAGTCAAAAAATGATGTTCCACAATCCACATAAATCTAAAAGTGGTGGTGCTTCTTCTTTCCATAAGCC\n") - f.write("TCTTCCTCTTCTTCCTTTGTCTCTTTCTTCTCATGATGCTCATGGAAGGCAAATCCACCCGAACCAACTG\n") - f.write("CAGCTGCTGCAGCAATCTCCTCTTCTATCTTGTGCCTGTGGGCATGCTCTGGGTCTTTCTTTTCATTGTG\n") - f.write("CTTCTCATGCAAGGCAAAAGCGCCGGCAGCAGCTACACCGGCCTCGCCGAGGTGCTCGAGATGCTTGTGG\n") - f.write("TGCTTCTCCTCCT\n") - f.write("\n") - f.write(">gi|226792229|gb|GO545777.1|GO545777 Mdas9003K16_e219.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566036.1| protease inhibitor/seed storage/lipid transfer protein (LTP) family [Arabidopsis thaliana] pir|D84887 probable proline-rich protein [imported] - Arabidopsis thaliana gb|AAB82643.1| expressed protein [Arabidopsis thaliana] gb|AAL1, mRNA sequence\n") - f.write("CAGTGATATCCCCTTTTGTAGTAGTGTGAATAATCAATAATACAAAAACCATCAATGCTCAATGACTGAA\n") - f.write("AAGATAATAAGTTCACAATCCAAAGGGAAACACAAGAAACACAAGAAAATGTTCCTTGGAGGGAACACTT\n") - f.write("TACATATCAATTACACTTTGAAGGAAACATGCACAATGCATTAATGCAGCCAAAGATTAGTGCCCTTTGT\n") - f.write("ATTTTTATTCACACAAAGCTGTGTAAGGGCAGGTACTTACGTAGTATGCAGATGAGAAGATCATCGTGCA\n") - f.write("TGTCTCTAAGAGCATTGGAAGCCATTCGGGACAGACTTGCCACAGTAATTCAAAAGCAAGCTCAAGGAGA\n") - f.write("CTGGCACGTCAAGATTGATGCCCAAAACGTTGGCCTTAATTGCAGTGCAAAGGCACACAGCAGCTTCAAG\n") - f.write("ATCGGCAAGTCCACCAATGAGGCTACAGCATGGGGTCTTTGGTGGGGTCCCCACAACAATGGTCACCAAG\n") - f.write("TCATTTAACAAGTCGCCACATACCCCTAGCTTAAGGGTGTCCTTAGGGCAAGAAGCTTTAGCTGGAGGGT\n") - f.write("TTTGGGGGCTAGCGGGGGTTGCAGGAGGAGGACATTTAGGGGTTTTCGGGGGTGGTGGTGGTGGACATTT\n") - f.write("AGAAGCATGATGGTTTGCACTGACTGT\n") - f.write("\n") - f.write(">gi|226792228|gb|GO545776.1|GO545776 Mdas9004J18_e293.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTCCAGTCTCTCCGCGTCTTAAAAAACCCTAGATTCCCGAAAGAACACAGAGTTCGAAACCCTATCAACA\n") - f.write("ATGGCAGTCTCAAAGGCATCCTCCGTCATCGCTCTCATGGCGGTCCTCTTCGCCGTCCTCTCCGCCATCG\n") - f.write("GCGCGGCCCAGGAGTCTCCGGCTCCCAGCCCAACCTCCCCCGCCGCATCCATCTCCCCCTCGTTCGTCTC\n") - f.write("CGCCCTCTTCGCCGCCGTCACCGCTCTGGCCTTCGGATCTGCGCTCAGGGTTTGAGGTCGCGGTTGCTGC\n") - f.write("TTGTCTGGATGTGGCTGTGTAGAGCGGTTTGGGATTTTGTGATTCGTTTTGTTTGGTAGCGAGTGTCGTT\n") - f.write("TTAGTAGGTGGTGGTCATGGATCTATAGGGATTTCGTTTACATATGATGGATTTTATTATTATATTATTG\n") - f.write("CTACTGTGATGGATTTCTGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792227|gb|GO545775.1|GO545775 Mdas9004F13_e275.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ACGGATGGTACACCACGTGTTTTTATATAAGTGGTGGAAAATTGCATTTTTTAATACATATATCTCACCA\n") - f.write("TTTATATAACGACATGTAATATACCATGTATTCCGATCATATTGAAAAATCTCTAGTAGATGGGCTTTTC\n") - f.write("CCATCACATGACTCTAATCCACGTAACCACGGCCATCCATGTGGGTCCACCTCCCAAAAATCACATGGGC\n") - f.write("AGAAAAGAAAAAAGTTGAAAGGTCCACCATCCTAAATTGGGCCCATGTTATTGAATCACATGGCCCAACC\n") - f.write("AACAGCAACTCAGTTAGTTTGGAAATCTCAAAGAAACATTAAAAACCACTATTTTTTTACACTAAATCAT\n") - f.write("ATAGCACAGCATTGAAATCTCACCAAATTATAAAACGCAATTTTGCAATCTGTTGGAACATTCCAACTCC\n") - f.write("TACACTGGAACATTTCAACCCCAAGCGCTGCCGCACTCAAGATCGTCAAGTTCATAGACAAATCCTTCTA\n") - f.write("CAACCCACATGCCATCTATTACAAAGGTCCCAAGATAAAAGGGGTACATAGTACAAATTCTATGAACCAG\n") - f.write("AAGACCTGTTACTGTGCTTCACTGGATTCGCGCTTTGATGCTTCCTTGATTTCGTCCCCGGCATCATCCG\n") - f.write("TGATATC\n") - f.write("\n") - f.write(">gi|226792226|gb|GO545774.1|GO545774 Mdas9004C13_e265.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172536.1| expressed protein [Arabidopsis thaliana] gb|AAN41360.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTGAAAAATCAATCATAACGTTGTTATGTGCAAGTCTAAATGCCATAGCTGCTTCAGAAGAAC\n") - f.write("AATCATCTAGGGCAGCTAATTACAAATGGAAGCCTGAACCATCAAAATTTATCCTTTATCCAGGCCAAAA\n") - f.write("AAATCATTAATCTGTGGTGCCGCGGTGGCACCATGTAGCCTGGGATTTACAAACGCAGTTCTCATCCGCT\n") - f.write("TCCTCATCTCTCGTTCTGATAAGACTCCGGAAATGCTCTTGACAACAGCAAGTTCTTTATCCTAATAATT\n") - f.write("AGAGCGAAGACGCCGTAGCATGGGAGATGCATCAATCCAACCCCAAGATACCATAAGGGAGCATACGAGG\n") - f.write("ATGACAGGTCGAGAAATGGATCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226792225|gb|GO545773.1|GO545773 Mdas9003L22_e223.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P12372|PSAD_LYCES Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) pir|S00449 photosystem I chain II precursor - tomato gb|AAA34185.1| photosystem I subunit II protein precursor prf|160151, mRNA sequence\n") - f.write("CACAAACCAACCACAACTCTCTCTCTCTCTCTTTCCTCTCTCTAGTTCCTCATGGCCATGGCAACACAAG\n") - f.write("CCAGCCTCTTCACCCCAACTCCCTCAGCCCCAAAGACCACTGCTGACCGTACAACCACCCCATGGAAGCA\n") - f.write("ATCAGTCTCCTCCTCCTTCATGGCCCCCAAGCCACTCAAGCTCTCCACCGCAAGAACGATGAGGATCAAT\n") - f.write("GCCTCCGCTGAGGAAAAAACCGTGACCCCCACAAAGGAGGCCCCGGTAGGCTTCACCCCACCCGAGCTGG\n") - f.write("ACCCAACAACACCCTCACCGATCTTCGGTGGCAGCACTGGCGGGCTGTTGAGGAAAGCGCAGGAGGAAGA\n") - f.write("GTTTTACGTGATCACATGGGAGTCACCAAAGGAGCAGATATTTGAGATGCCGACTGGCGGAGCTGCCATC\n") - f.write("ATGAGGGAGGGTCCTAACTTGCTGAAACTGGCCAGGAAAGAGCAGTGCTTGGCTCTTGGAACTAGGCTTA\n") - f.write("GGTCCAAGTACAAGATTAAGTACCAGTTTTACAGGGTTTTCCCTAACGGGGAGGTCCAATACTTGCACCC\n") - f.write("CAAGGATGGTGTGTACCCTGAGAAGGTGAACCCTGGGCGCCAAGGGGTTGGCCAGAACT\n") - f.write("\n") - f.write(">gi|226792224|gb|GO545772.1|GO545772 Mdas9004G04_e279.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46280|EFT2_SOYBN ELONGATION FACTOR TU, CHLOROPLAST PRECURSOR (EF-TU) pir|S60659 translation elongation factor EF-Tu precursor, chloroplast - soybean emb|CAA61444.1| EF-Tu protein [Glycine max], mRNA sequence\n") - f.write("TTTTTTTTTGGGATGATGAAACCTACAAAATATATAACATTTCGTTGTGGAAATTGCTTGGAAATGTCAA\n") - f.write("AAGCTAGATAAAATTGAAGCTAAGAGAGTTCAAGTTTGACACCAAATTGCAAAAATAAGTTCAGACCACC\n") - f.write("ACATAATTTCTATTTTCTATCACTCGATAATGGATTGAATAACGCCAGCTCCAACAGTCTTCCCTCCTTC\n") - f.write("TCTGATAGCAAACCTCATCCCCTGCTCACACGCCACCGGAACAATCAGCTCGACAACAATCTTAACGCGA\n") - f.write("TCGCCAGGCATCACCATCTTCGACTCCTCATCCTTGTCGTTCATAATCGAAGTCACCTTCCCGGTGACAT\n") - f.write("CAGTGGTCCTCATGTAAAACTGAGGCCTGTAACCCGAAAAGAACGGCGAATGCCTCCCCCCCTCTTCCTT\n") - f.write("CTTCAGCACATACACAATGGCCTCGAATTTGGTATGCGGGGTAATAGTCCCGGGTTTGGCCAAAACCATC\n") - f.write("CCTCTCTGGATGTCAATCTTCTGAATACCCCTAAGCAACAACCCCACATTGTCACCAGCCATGGCATCAT\n") - f.write("CAAGAATTTTCTGAGACATTTCGACACCGGTGACAGTTGTGTTCCTGGTGTCCTTCAAGCCAACAATGTC\n") - f.write("GACGGTGTCTCCGACCT\n") - f.write("\n") - f.write(">gi|226791953|gb|GO546029.1|GO546029 Mdas9010L01_e775.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA04664.1| hypothetical protein [Citrus x paradisi], mRNA sequence\n") - f.write("GTCGATCTGAGTAGAGTTTGCAAGATGGAGAGCTTGAACAGCTTTTGGCAATTGGGTGATGAGCTCCGAG\n") - f.write("GGCAGTCAAAAGTCGCAGAAGATCACAAATGGTTAATGGCTGCTTCAAAATTGGCTGAGCAGACAAGGGT\n") - f.write("AAAGGGCGAGCGTATGAATAACCTTGATCTTTCAAAGGGCCCAGCTGAACAAAGGGCAAGGGATAAATTT\n") - f.write("GGGTTCCAGGAAGATAACAAATTTGAAGGCCAATACTTTAACATGCTGAGCTTGGATTCTAAAGTAAATG\n") - f.write("AAAATGTGAGCAAAAGTTCCTTCACGAATGGTATTTATAACATGAATGCAGTTTACCAGAAGAACAATGC\n") - f.write("AAGCATTGTGGGAAACATGACTGG\n") - f.write("\n") - f.write(">gi|226791952|gb|GO546028.1|GO546028 Mdas9011A09_e811.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_177142.1| expressed protein [Arabidopsis thaliana] ref|NP_849870.1| expressed protein [Arabidopsis thaliana] pir|F96720 unknown protein, 58197-59415 [imported] - Arabidopsis thaliana gb|AAG52556.1|AC010675_4 unknown protein; 58197-59415 [A, mRNA sequence\n") - f.write("GCAAATATTTTGATTAACTTGTAGACTATATTACAAAGTTGAAGCATCACCCTTCAGTTTCAAAAAGCCA\n") - f.write("AAACAAGCATAGAAAACTCACACTGAAAATTATATACGTGACGATACGTCCAATAATTCAACAATAAAAT\n") - f.write("TAACCACGCTGTTTTAGATCCTAAATCACACCCAAATTCGAGTCTAGCGTAACCGCGCTAACAAACCATC\n") - f.write("GGAAGCTTAAAGATGCCGAGCCTCCCACTACTTACCATGTAACGGCATTACACCCGACTTCCTTGAAGGA\n") - f.write("GGCCGTCTCTTATCTGTGAAGAGATATCTTTCACAGCACCGGGTCCGTGCGGGATGAAAACCGAGTTGGA\n") - f.write("CTTTGAGGACGCACCGACGTCCTTCAATGTGTCGAAGTACTGGGTCACCATAA\n") - f.write("\n") - f.write(">gi|226791951|gb|GO546027.1|GO546027 Mdas9010I01_e756.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564093.1| expressed protein [Arabidopsis thaliana] gb|AAK59521.1| unknown protein [Arabidopsis thaliana] gb|AAL15188.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTGCAGAGACCAACAAGTGCCATTACATTGCTAGTAAGTTTTACCTATGCTCTATACATACA\n") - f.write("TATAATTATTTACTATATTCACAAGCTTTTTACATCATATATTCATATATATATATATATAAGAAAAGCG\n") - f.write("GAGATGCGCGGCGGATTGCGGGTGTAGCCGATGAGCTGATCAAACTTCCAAGAATGCTGTTTATGTACAG\n") - f.write("TTTTAAATCCCTACGGGCGATCCGTTCATGCCAAGTTCTTTCTAACACGAAGTTGGAAGAACTTGGCCCT\n") - f.write("CCATTGAGCAGCATCTCTATAGCGTTCCTCCACTGCCGCAATAAGCATGGTGCGCACAAGAATAAACTCC\n") - f.write("TTCCTTTCAACACATGGTTGACCATTTGGCCGATCCAGTTGAGTAAATAATAATCCATCTGAAGGGCCTT\n") - f.write("GAGTGGAAAACTTTCCAGATTCGATAACTTTCATTCCATCACTGTATGCCAGGTACTTGTTGACCTGTAT\n") - f.write("GGGAACCTTGCACCGTACAGCAATGTTGATGGCGTCTGAAGGTCGAAGGTCGAAGCTGACACACTCTGTC\n") - f.write("TCACTACCTGCCTTTCTGAGGTATAGCTGAGCAAAATACGCCTCAT\n") - f.write("\n") - f.write(">gi|226791950|gb|GO546026.1|GO546026 Mdas9011A16_e813.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTGACATAAACCTTATTCTTCATAAAGCAAAAATAACAAAATACAAGAAA\n") - f.write("AGAGGGAGGGATATACACCTTACCCCTCTTGAACAAGAAAATACAAGAAAAAGAGAAGGGGAGACATAGA\n") - f.write("CTTTACCCCTATTAAAAAATAAAATACAATAAAAAGAGAGGGGCGAACATAGGACCAAACCCCTCTAAAA\n") - f.write("TAAAACTTAAAAGGTAAGAACCTGCAAGACAAGATATGGTTCGATCGGTTTAATGCGCACCCCTATTTTT\n") - f.write("TTTTTCCATGCCCCGGAAAAGGTACGGTCTTATAGTGCACCGGTTCCTCTTCCTTTGCCACAACATGCAG\n") - f.write("ATGCGACCTACTGATGATCTTTTCTGCTACATTGTGCTTTGGTTTTTCAGAAACATTGGCAAAGACTAAT\n") - f.write("TTGGATGAGAACAATAGCAATAGGATGATGGAAATCATGTAAACAAAGTTGGCCTTGTGAACCATATTGT\n") - f.write("ATGATCAGCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791949|gb|GO546025.1|GO546025 Mdas9010N10_e788.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P54260|GCST_SOLTU Aminomethyltransferase, mitochondrial precursor (Glycine cleavage system T protein) (GCVT) pir|S59948 aminomethyltransferase (EC 2.1.2.10) precursor - potato emb|CAA81081.1| T-protein [Solanum tuberosum], mRNA sequence\n") - f.write("AAGCCGCCCTCTGCCCTTCTTCTCTTCCCTATGGCCCATGTGAGTCCGTCCTCCACAGGTGTTGTGAGTT\n") - f.write("GCTCCATGTCATTGACGTATAAGCACAACCCAGCTTCCAGTCGGAGACTGTTACGAACACCCAGACCTGG\n") - f.write("CAGCCTCACCTTCCCCTCGGATTTCTCACAGATTGCCTTGGCAAGATCCACTGC\n") - f.write("\n") - f.write(">gi|226791948|gb|GO546024.1|GO546024 Mdas9010P08_e806.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_114288.1| cytochrome b6/f complex subunit IV [Triticum aestivum] sp|P12119|PETD_WHEAT Cytochrome B6-F complex subunit 4 (17 kDa polypeptide) dbj|BAB47064.1| sytochrome b/f complex subunit 4 [Triticum aestivum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTCTAAAGTTTTGTCTAAACAGATAAAAATTCGTTTTGAATCTTGAATC\n") - f.write("TTTAGCACAATCCATATATTCCGAATAGGTCCAAAATTAAATTGAATAGATGTATCTAGGGAAAATTCAC\n") - f.write("TTTGAAGCGACTATTCCCTAGATACACACGTCATAATATACTTTTTTTTATTTCACAGTTGAATCGATTT\n") - f.write("AAAAAAGACCTAAAGTTAAGGACTTATCAATAGGTAGTGTTGCTCCAATACCCAACCAAAGGGCTACTAC\n") - f.write("AGTACCAATCAAAAAGACGGTTGTCGCTACGGGACGACGAAATGGATTTTGGAATTTATTAACATTCTCC\n") - f.write("AAAAAAGGTACTGTTAATAATCCCGCAGGTACTGAAACCATTAAAAGAACGCCCAATAACTTATTTGGCA\n") - f.write("CTGTACGAAGTATTTGAAATACGGGAAAGAAATACCATTCAGGCAATATTTCCAAAGGAGTTGCAAATGG\n") - f.write("ATCCGCGGGTTCACCAATCATTGATGGTTCTAGAACCGCTAAGCCTACGTTACATGCAATAGTACCTAAA\n") - f.write("ATTACTACTGGAAAAATATATAAAAGATCGTTTGGCCATGCGGGCTCTCCGTAATAATTATGACCCATCC\n") - f.write("CTTTAGCCAATTTAGCTCTTAACACAGGATCGTTCAAGTCAGGTTTTTTTGTTACTCCCATAATCCAT\n") - f.write("\n") - f.write(">gi|226791921|gb|GO546023.1|GO546023 Mdas9007M09_e535.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCCAGTTTTTTTTTTTTTTTTTTTTTGGATATCAAGGAGAATTAAATTTATTCAATTTCCATACAAAGAA\n") - f.write("AATGAATTAATGCAGGAACAACATTTGTGCACATTGAGAATGAAATTAACTAATTAACTTACTATCCCCT\n") - f.write("ACTGCAAATTTCACAACTATGCTCAAAACAGATTTTGTAACCAATATCCCAAAAAAGGGGCAAAAGGAAA\n") - f.write("GAAAAAAAAACTTTTGTATGGTATACTGCAGCGTTATCTGTGTAACCGAACTCAACCTAGCTACCTCCTT\n") - f.write("GTACACTTGGAAAACCCAAACCAACAGTAGCCTTCGAACTCCTGTTAAATCTCAGATTTATCAGCGGAGT\n") - f.write("AAACCAAATGCAAAATCCGCTCTTAACCGACAAAGCCTCGACAAACTGAGTTAAATAAAAAAAAAATACG\n") - f.write("ATGATCTGAACAAAGATCGCACCCAGACCGCACCAAAAATTGGTCGGAAAGCCGATGACAATTGGGGAGA\n") - f.write("AACGATTTACAGAGATGCAAAACTTGTCTCAAAACAGAGAACCCAAACAAACTCCCCAGAAAAAAATAAC\n") - f.write("ACGACGATCTTGGCGATGAATATTTTGCAAGACGAAAAACACAGGATTTCAAACGAGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791920|gb|GO546022.1|GO546022 Mdas9007I12_e518.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGGACGTAAATTCTAAATTGCATTACAAAAGGCGCTACTTTTTACACT\n") - f.write("TCTACAGCGGTTAGCAGCTTTAATTACCCTCCAAAAACTCCAACTCATGAAAAACCCAACGCCTAAAAAT\n") - f.write("TGGCCAAAATCTTTGATTAGAGAAACCTTTTCCTTCCTCTTTTGCTATTTAACTCTTTACTACTTCTCCA\n") - f.write("TTCACTTGGCTCTTGTGGACGAGAAATTTTCATTGTGCCGGAAACATAACCCGATATACCAAATGTCATA\n") - f.write("ATACAATTGATTGAAAGCTTAAAAAAAAATCCCAACCAATGGTATTACAACACTTGGTGTACCAAATCGT\n") - f.write("GTTCCCGACCGACTGAAAAACCTCCCGTTGTTGAAGGGGGTTTTTTTCTCTTTCTTTTTTTTCACCCCTC\n") - f.write("CTTACTTTTTACCTTTTTTTTCTTTGTTACTTCATTTCTCTCCCAATTTGAAGAGGGAAAATTACAAGTG\n") - f.write("AAACAAAAAATAACCGACTCAAAGTTACCGACTAGAAAGTAGTTAAGTGAGCAGGGGAAAGAGTGTGTCA\n") - f.write("CACCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791919|gb|GO546021.1|GO546021 Mdas9008A08_e556.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P58419|NU4C_OENHO NAD(P)H-quinone oxidoreductase chain 4, chloroplast (NAD(P)H dehydrogenase, chain 4) (NADH-plastoquinone oxidoreductase chain 4), mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTATAATCATTCCAATAGCCATTACAAAAGTAAAATATTTGTCACTA\n") - f.write("TAAGATATTTTTTACTAGCATGTATTCCAAAAATAAAACACTAACAATTCATCAACAAAACAGCTCATGC\n") - f.write("CCGGTGATGCAAGAGAAGGCATTGGCATAATAGTTATCAAACGGGTCCTAAAGATTTCAGACGCTTTTTT\n") - f.write("GTTTGATGGAACACGAAATTATACCAACTATTCCACATATCACTTGTCAAACTACACTAAACTGGCTTGT\n") - f.write("CACAGTGTGTATGCGGTAATGCTGCAAACCGCGACATAACTCGGGAACTGAAACCACTTCCCTATATACA\n") - f.write("GCAAATGCTAGTTCACAGTAACTGTAATCTAGCTCGTGTATCCACTCGTGAAAAATAATAGGAAATGTCT\n") - f.write("ATGTAGTTCCATGAACCAGCATAACTTAATGAAATGAAACTCACTGGCTATCAGGCTTGCCCGAGCATTT\n") - f.write("CTTGCTCCAAACAACCGAACCTGCTTTTCGCTCCCCTCGCTTTCTCTTGTTTCTATGAAAACTTACATCT\n") - f.write("GAAGCCAAGCATGACTCTAGAGTCGATTGCTCCTGAGGAAGAGCAGCTT\n") - f.write("\n") - f.write(">gi|226791918|gb|GO546020.1|GO546020 Mdas9007K24_e528.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564931.1| expressed protein [Arabidopsis thaliana] pir|A96709 unknown protein, 35272-36292 [imported] - Arabidopsis thaliana gb|AAG52398.1|AC011915_12 unknown protein; 35272-36292 [Arabidopsis thaliana] gb|AAM65154.1| unknown [Arabidopsis, mRNA sequence\n") - f.write("TCCAGCTTTTTTTTTTTTTTTTTTTTTGACTAAAACACAAATGCTTTATTTACACACTAAACGACTGTTT\n") - f.write("AAATCGACTCAACAGCGGCTTCAATTTATACAGATTCGCTTCGCAAGCCGCTCTATGAAACTCCGAAACA\n") - f.write("CCTAAATGGAAACACAACGAAAATTTTCCCACAGTACTCTTTTTACTTTTTACAATACAAGAGGGTCGTA\n") - f.write("AACACTCCTAGACACGATCGATGAACCCGTTTATTATTTGGTTAACATCTCATTTACTTACACGACACTG\n") - f.write("ACATTTCATTTACACAAATCCCTCGTACATATATACACAAGGTAGAAGGATCGTCGTAGTCTTCTCGTGC\n") - f.write("TGAAAATTTCAAAATTTCCTCACAGTGCTATCAAAGTAATGTGGTTGGCTATATCAAACTTTAAGCTCAG\n") - f.write("TCTGTTCCTATGTACCTTCATCGATTGAATTGGGATCTCATGCCAGGGTAGGGATACTGCAATTACGTCG\n") - f.write("ATCCCTGTCCAGGCAATCAAACCCCTCGATCCTCACTGCTGGTTTGCTCCCGAAACTGGCCCGAGCATAG\n") - f.write("CCTCCTTTCCTAGCAGATGATGAAGGAGACGATGAAAGGCCCATTGCGGGAGCGGTTGGCGACAGTGGTG\n") - f.write("ACAATGG\n") - f.write("\n") - f.write(">gi|226791917|gb|GO546019.1|GO546019 Mdas9008A19_e559.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAAACCATGTACTTCAAACCGAATTTAAAGTTATTGAAAAGGAACA\n") - f.write("CTACCAATCTAACTGATTGGATATAAATTGACCGTGTTTACAGTTGAAACGTTGCAAAAAGGATGATAAG\n") - f.write("TTTTACTTCCAAGACAACTACTCTTTTTTTGATAAACATGCTCCCTA\n") - f.write("\n") - f.write(">gi|226791916|gb|GO546018.1|GO546018 Mdas9007E02_e499.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P29790|ATPG_TOBAC ATP synthase gamma chain, chloroplast precursor pir|PWNTG H+-transporting two-sector ATPase (EC 3.6.3.14) gamma chain precursor, chloroplast - common tobacco emb|CAA45152.1| ATP synthase (gamma subunit) [Nicotiana tabacum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCCTTAATTACATGATTAGCAGTATTATTAACTATGATGGAAAAA\n") - f.write("AATGACATACAATATATATATATGTGGAATGCTCTCTTTTGTTCTCATTTGTGCACACAAAGTTTATTGG\n") - f.write("CAGCTGAAAATTACAATGGAAGTGTTAAGTCTGCAAATTTAAAACAATTGGCACAACTCAAAGTGGAGGA\n") - f.write("AAAAACAAGTACCATGTTGTTCTTTGAATCGTCTAAACTAAAGCGTTGGCACCCGAAACAATCTCCAAAA\n") - f.write("TCTCTCCGGTGATTTTTGCCTGGCGCTGCCGATTGTAGGTCTGCGACAAGGTTTTCTTCAGCTCCACAGC\n") - f.write("GTTATCGGTTGCATTGCTCATAGCGGTCATCCTAGCAGCGAGCTCACTGGCTAGAGACTCCTGCAATGCC\n") - f.write("CTCAAAATCTGACTGTTGAGGTACAAGGGCAGCAAAGCGTCGAGAATCTGAACCGGATCCTGCTCAAACT\n") - f.write("GCAAAACCGGTGTGAAATCCACGGTCTGCGTCTTGATGACATCTCTCTCCACTGTCAATTTCCCTTCCTT\n") - f.write("TGTTGTCAGCCTGAAGAACTCATCATCCACGGCGTCCACACAAACGCCATTGATGTCGCAAATCTCTCCT\n") - f.write("TTTGGCGAGAGTGGAAGCAGGGTGTGA\n") - f.write("\n") - f.write(">gi|226791894|gb|GO546017.1|GO546017 Mdas9007P13_e550.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB62573.1| P0454H12.5 [Oryza sativa (japonica cultivar-group)] dbj|BAB64826.1| B1148D12.11 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTCTGCAAGTAAAGGGCTTAGATATTGACTCGAACTCTTCACGAAAA\n") - f.write("ATGGCGACGTATATGAGTTTTCGAGTTTAATCTCCAGTAGTAACAAAAAATATGACATAAAAGTTTATGA\n") - f.write("GAACCAAAAATTTATGTACCAACAAGTTATCCACATCTAGTGATTGTTCCATTCGCCTTTCACATTCAAT\n") - f.write("CAAGAAACAAGGGAAGAAGACGTACAAGTAATGTGCATTTGGGTAGGTCGAATTCCCGACTTGCAAGATA\n") - f.write("GAAGGATCAATCACTGTGTTTGGCCTTTGAAACAGTTTTGATCAAACCTTTGGTAATCTTCCAAAACCAA\n") - f.write("ATGAGATTCATCATAGACAACATTGGAGGCACCAGGAGCAAGCTGTAAAATCCTAAAGGGAAGATTGTCT\n") - f.write("TGACTTGATCGAAATGGATAAACATGTGGACGAAAAAGTAAATGAACAAAAGAATCCTTGCAACCAGCCG\n") - f.write("CCCGAGGAACAATGCTACGCCATTGAAGATGTACAGGTTAGAGTTCTTCTTACCAGCAACATCCAAATAC\n") - f.write("CATCTCATGTTTACGAGAGGAGTCGTGCTCT\n") - f.write("\n") - f.write(">gi|226791893|gb|GO546016.1|GO546016 Mdas9007K23_e527.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB03143.1| ankyrin-like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TACCCTCTGATGGAGTTTATACATATTACCTTCTGATGGGATTTATACAGATATCTCCGAAAGATAATAA\n") - f.write("AAATAAATTACATCATTCGGGTGGGGTGTTTATTCTTTGCTTTTGCAGTGTTTTTCTGCTGCCCTCTTCC\n") - f.write("TGTATCTTCACCTGGTAGACAGAAGGAATCATAATGATATGAAAATCTTTGATTTTCTTCTTTTCTCTTT\n") - f.write("TCCTTTTCCTTTTCACTTTTGCTTTGCACCTCTGTCTTTGCTTTTCTCCAGACATCATTGTTTTTCTCTT\n") - f.write("TGTCTTTGTCTCGGCATGGGTCAGGCAAATTATTGAAACAAATGGGAAATTATAATCTTTCCCTTGAAGC\n") - f.write("TCCGTGTTGTTATGCCGCCCCGTCACCTGCTTCATGTACTTCTTCTTCTTCGCCTGGTCAATCCGTTTTC\n") - f.write("CTGAGTTAGAAAACACTAAAGTCGGCGAGTTGGAAGTCAGAGACGACTGGCGAGTTGGAAGTCAGAGACG\n") - f.write("ACGTGGAAGTCAGAGACGACGAATTGGAAAGCACCAAAGCCGACGCTGACGCAATGGAAGATGGAGACGG\n") - f.write("CGATGACGATGGCTCGGCCAGAGGGTTTTGGCTCGGCTGTGCAGATGAAAGATGGTAGTGCAGAGCCCGT\n") - f.write("TTGTGATGGCTGGTAATGCAAAGCACATTCCTC\n") - f.write("\n") - f.write(">gi|226791892|gb|GO546015.1|GO546015 Mdas9007L11_e530.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92380.1| P0512C01.35 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGGTGAAACTGAACTGTATTGGGAATATACTTCTACAATCTAAACACC\n") - f.write("TTCTGTAATTTATTGGGGAAGCAAATCAAATACAACGAAGGGGAAGAAAAAATGCACAACAGGGAACTTT\n") - f.write("GCTAGTGGCAGTTTCATCTCTCACACCAACAAGGTCCGACCTCGGCCATTCTGACCAGTTATCGACTTGA\n") - f.write("AAGTGGCTTACAAAAGCTCCAAAACAAGGGCAGATGCACCTCCTCCACCGTTGCAAATACCAGCAGCACC\n") - f.write("GTATTTCCCGTTCTTCTGCTTCAGTACCCCTAAAAGGGTGACCAAGATACGAGCTCCACTGCAACCAAGA\n") - f.write("GGATGTCCCCCTCGTGCCGAATTCGGCACGAGGGTCATCCCTCTCCCAAACCCTAAAGCGCTACCTCAAG\n") - f.write("AAACCGTGGGAGATAACCGGTCCGTGCGCGGATCCGGAGTACAAATTGGCCGTACCCGGCGCGCTCGAGT\n") - f.write("ACCGGCTCGAGTGCCCTGCCACCACCAAGGTCCAGGCGTGCGTGCCCACCTCCAACCCGGAAACCGTTTA\n") - f.write("CGATATCAAGTATTTCGCCCGCGACCAGCGGCGCAAC\n") - f.write("\n") - f.write(">gi|226791891|gb|GO546014.1|GO546014 Mdas9008E07_e580.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191320.1| adenylosuccinate synthetase [Arabidopsis thaliana] sp|Q96529|PURA_ARATH Adenylosuccinate synthetase, chloroplast precursor (IMP--aspartate ligase) (AdSS) (AMPSase) pir|T06759 adenylosuccinate synthase (EC 6.3.4.4) - Arabidopsis th, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAATGGAGACAAAAGTGAATGCGATTGATTTTCTCACACATAAATTG\n") - f.write("TCATATTAATGTGAGATGAGCCTAGGCATCTGTTACCTGCTATCAAATAATAGTATAGCCCATAACTAAT\n") - f.write("ACATGAAAACTACGATAACGACCGACCCCGAGTACTCTGACCTCAATTCATTCCAACAAATTCATACCCT\n") - f.write("AGTAATCCATGCATTACAACAAGCAATCCTAAACACAACATAGATTTCTTGTGGCCGCCTCGGGTGGAAA\n") - f.write("ATGTGTTGAATCAAACTGTGTCTTGAAAATTACTTCTAATCCGAAAAATCAACTCAAGTATCAAGGGAAA\n") - f.write("ATCGAGATTACTATTTGTAAATCAGTGCATCGCGTCCAGGCCCTACACCAATGTAATGGACGGGTACACC\n") - f.write("AAGAAGTTCTTCTATCGTTTCCACATATTGACGTGCGGCCTGCGGAAGGTCGGAGTAATTTCTGACAGAA\n") - f.write("GAAATATCCGATTCCCATCCGGGCAATTCTTCATAGTCGACCTCTAATTGCTCAAGATCACGAAGGTCTG\n") - f.write("AAGGGAACGATTTAATCGGTGTACCATCCTTCTGTTTATAGGCAACACCCAACTGAATTTTGGGAAGATC\n") - f.write("AGACAAAACATCAAGTTTGGTGAGATTGAGAGAAGAAAATCCATTGATCTGACAGCAA\n") - f.write("\n") - f.write(">gi|226791890|gb|GO546013.1|GO546013 Mdas9008A06_e555.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_173710.1| expressed protein [Arabidopsis thaliana] pir|G86363 F19G10.8 protein - Arabidopsis thaliana gb|AAB72164.1| unknown protein [Arabidopsis thaliana] gb|AAL49950.1| At1g22970/F19G10_8 [Arabidopsis thaliana] gb|AAM70551.1| At1g22970/, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTACCGGAAAAACATAGCTTTATTGATTGATATTTCAGAAACA\n") - f.write("AAACAAAGAGGTCTTTATATAGAGAAAGACCAAAGCAAACCCTAGACTAAAACCCTAAACCAAATCCTAA\n") - f.write("ACAAACTCAAATACTTAATGGGCAAGTAACTAATCCTTGGCCCGCAAGATAACAACCTAAATTCCAAACT\n") - f.write("AAATTCCAACAATATGGACACAAGAAGCCAGCATAGGCCCTGCACCGACTGTACTCCCATGTGATAGCAG\n") - f.write("AAGAAAACCTTGCAGGGTATTGAAGTAGGAAACCATGTTTTCTTCAAGTGCTCTAACTTGCGGTGTTTCT\n") - f.write("CCTCCGGTCCAAAGCATTCCAAAAATGGTGGCTTGTTTGGAGACTTGATCGCCCATCTTTGTGACCTCCA\n") - f.write("CCCAGCTCACCTTCTCAAGTTTTGAAGGTGCAGTTTGATCCAACACCTGGAAGGTCTCGTGGACGGTGTT\n") - f.write("GAGGTGGTGATTGAGAGTTCGAGTCAGTTGGTCACTCTCGGCTCGGCCCATCGCTCGGCGTTTGACGGAA\n") - f.write("GGAATTGCAGCTGCAGCAGTGGCGTTTGACGAGGGACTCGGCCCACTGTCCATCACTCGGATTTTTTTTT\n") - f.write("ACTATTTTTCCACGACTGGCAATGAAGTGAGAGATGGCC\n") - f.write("\n") - f.write(">gi|226791860|gb|GO546012.1|GO546012 Mdas9007F15_e504.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAAACTTCGTAACTCATTCTATTTGTGCATATTTCTTGCAAAGCTAT\n") - f.write("GAACAACAGCAGAGATTTCGTGTATGCACCAAG\n") - f.write("\n") - f.write(">gi|226791859|gb|GO546011.1|GO546011 Mdas9007L14_e531.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_187796.1| amino acid transporter family [Arabidopsis thaliana] gb|AAF23206.1|AC016795_19 putative amino acid transporter protein [Arabidopsis thaliana] gb|AAP37661.1| At3g11900 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGATTTCTGCATCATTGGGCTGAAGAATATTATACACTGGTGGTAC\n") - f.write("ATCGAATATTGGAATCCAGATACAGATTAAAGTTCTTCTGCTTCCCCATTGTACAGTTTGTATTCATGTA\n") - f.write("TCTCTTACTTGTAAAGTACTAATTACGACAAGCGATTCAAACGCCAACTACGGCATTGTAAGCGCCGTAT\n") - f.write("GCGGCAAAAAGCATTCCGCAAAATAATATGCAACAATCCAAGGTTCTTTGCCACAATTTTAGGGAAGAAC\n") - f.write("CCAACAATGCTAAGTGAAATGAAGCAGGTAGAACAAATGAGATCAGTGCACATACAGTACTTCCCACGAG\n") - f.write("CGACGCAAATACTGCAAACCCTGGAACGCACGAGGCCAAGACGGCCAGTATGATCACCACTATTGCTCGA\n") - f.write("CTCACGTACACTGCAAACCTTCCTAGAGGCGGCATCGTTGAATAATCGTCATTGTCATCATGAGCTTTCT\n") - f.write("GAAACCATTTGCCTTTTACCAACTTCCCTTCTATGATCTCGTTTATCGGGTGTAGCATGATATGGGAGGG\n") - f.write("TAAATATTAGCCCCAAGCACAAACCAATCTGAACCACCATGGCAGACCAA\n") - f.write("\n") - f.write(">gi|226791858|gb|GO546010.1|GO546010 Mdas9007E17_e501.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191612.1| GATA zinc finger protein [Arabidopsis thaliana] pir|T47864 GATA transcription factor 4 - Arabidopsis thaliana emb|CAA74002.1| homologous to GATA-binding transcription factors [Arabidopsis thaliana] emb|CAB81839.1| GATA transcript, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAATTAATACATTTTCTTTTAATTAATTAAATATCCAAAATAGTAATG\n") - f.write("GAAATTAATTTCAACTTTTTTCTTTGCCTCAAAAACAAAAAATTCCCATTGTTTATGGTCAAATTTCCAC\n") - f.write("ACGGCCCATCAACTGAGAGACCGCCACGTGTTCCACACGTCAGCAAACTCGAAACTCGTCGCGGTGAAGA\n") - f.write("TAGAATTGCTGCTGATGCGGACGGTGTTGCTGTGGTTGCTCTTGCGGTGCCTGCTGCTGAGAAGCCTCCT\n") - f.write("TCTGGCGACGGAGCTCCAGAACCTTCCGGTGCGAGTTCGAGTGCTGAGTCAGCACGAAGGTCGGACTCGC\n") - f.write("CGCCGGCCGGTACTCGGGCACGAGCCGACCCGACTTGTACCGGACCCCGCACGCGTTGCAGAGAGTCTTG\n") - f.write("GGGCCCATCGGTCCTGCCCGCCACTGCGGCGTCTTCTCCGAGGCGCAGTGCGTGCACCTGAGCGGTGAAG\n") - f.write("GGGACGCTTCCGACGGCTCTCTCTTAGGCCTGTTGGGCCTC\n") - f.write("\n") - f.write(">gi|226791857|gb|GO546009.1|GO546009 Mdas9008C11_e569.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAATTTCTTACAAAAAAGTTGGCATCAAATAATCCATGTCCCACCCACATTTGGGTGATTTTAAAAAACT\n") - f.write("TATTTTAATTATCTTTTTACAAAAGATAAGCTTAATAACCAATACACAGCAATACATGGTTCTGTTCATT\n") - f.write("GAGTTCCCCATTTGCCTGCTACTTAAAATACGTTTGAAGATCCAACCCCAAGACCAAAAATACCAAACGA\n") - f.write("AATCGGAAAAAAAGCAAATTACCTGTCAACAACTACCGGTAAGCATATAGCAGTAGGTACCCCATGGCTT\n") - f.write("CAATTGTTCAACATTCCTCCACCCCCCCATCGTTTTGTTCCATCATTGTCCCCCTAATTTTTCAACAGAA\n") - f.write("AACTAATGCAGGAACCCCGCTGTATTCGGCTACATCAAATCTACATCGGCAGCACAATGTAAATAACAGG\n") - f.write("GGAGGGAGAAGGCCAACAAATTTCTGAAGAAATGAATTCCTCTCAATTTACAGGCCT\n") - f.write("\n") - f.write(">gi|226791856|gb|GO546008.1|GO546008 Mdas9007G24_e510.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568305.1| mannosyltransferase, putative [Arabidopsis thaliana] gb|AAK91470.1| AT5g14850/T9L3_150 [Arabidopsis thaliana] gb|AAM52236.1| AT5g14850/T9L3_150 [Arabidopsis thaliana], mRNA sequence\n") - f.write("ACATTTTCAAACCACATCACTAAAGGGGTCAAAACTGATATCATGTTTAACCATGACAGCCTATCCATGC\n") - f.write("TCACAGGCTGTATCCAGTTGAAAAATCAAGTTTAACACAACATAAATAGACACACAAAAACGCAGGAAAA\n") - f.write("ACAACAAAAACAAAGCATTTAATAAAATCCGGGGTTAATGAATGGAAAAAAATTTGTTACATACTAATTG\n") - f.write("GCGGTCTGAAATTGGAATCTGCTGAAGCGGGCATGTCTCCAATAAACCCCCATGCTCTGGCCATTCACTC\n") - f.write("CATTCATCAAGACATAAAGTCAATAAATTCTTCCAGCCCATCATACTGGAATGGTTCTAGTTGCACATAC\n") - f.write("AATAATCAGTCGCCTGTCAAACCGTACACAACAACTGACGCTTGCAAATCACGGTCCACTTTGAAGTGCG\n") - f.write("CATGGAAAAACCTTTTTATCTTTTTGAAAGAATGTGAAATCAAAAAAGCCCTCAACTGTTTTTCTTCCGA\n") - f.write("ATCAAATACTACAATGTGACTAGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791855|gb|GO546007.1|GO546007 Mdas9008D01_e573.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191593.1| palmitoyl protein thioesterase precursor, putative [Arabidopsis thaliana] ref|NP_850728.1| palmitoyl protein thioesterase precursor, putative [Arabidopsis thaliana] pir|T49229 palmitoyl-protein thioesterase-like protein F27H5.130, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGAAGTAATGGTCCGAAAGGTGGAAGATATAAAAGTACAATAAAGTTG\n") - f.write("GGAGTCATGTACATACTCTACAACGTAGAGTCTCCGTAAAATTACTTAACAAAGTACAACATCAATGATT\n") - f.write("ACGAAACAATATGGCAGCCGGCAGCCGGCAGCCGGCAGCCGGCAATCGTAAAAGGAATTGTCACTCACTC\n") - f.write("TCCCTTCTCCAATGGTGCAAAAAATAAACAGACATAACAAGTCCCGTTCGACTATAGTGCATAGAGTAGT\n") - f.write("AAGAATATACGTAGTAGCGATCATTTCAGAGCGTTCTTGTGTATATTTCGTGTTACCTTTAAACCCCGAA\n") - f.write("ACTCACATTACACGACCCTCAGCACCACCTTCTGATGCTCACCGAGTCCAACAAGATCCAAGTAGTTGTT\n") - f.write("CCAGATTAACGAAAGTGTCGTTGGAAATGAAGGCTCTGCTATCTTGTGCTGCGTTGAGTCTTCGTCTTCC\n") - f.write("AAGTATGGCACAATGTACGTTTTCATGTCGCTTCGAGAGATCTGCAGATGGCCCCCCGACACATTTATGA\n") - f.write("ACTTAACTTTTCCAGCTTCGTCCAAGGTTTTCAAACCAATCCAGTCTTCAGTGTACAACATGGTCTCTTG\n") - f.write("CGCAGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791828|gb|GO546006.1|GO546006 Mdas9008C21_e572.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92996.1| chalcone synthase [Malus x domestica], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTCATAATTATCATCTATTTGTACTATCTCTTTAATAAAAATAGGATCC\n") - f.write("GCCAATATATAGGGATTCCATCTCTATTAATAAAACGATACAAATAAATGATGAAAATAGCATTTTTGCA\n") - f.write("GCAAATATTACTCCAAAGTTTCCCCAAGTCAAAGTAAAAAATCCAAAAACCCAAAGAAATAACCACAAGA\n") - f.write("TATACCGGTGGAAAATTTAATACAAATACCACGCAGATATTATAAATAGTTATTGAAACTTCACCTTCAA\n") - f.write("CCCGTTAAACCCACGCTGTGAAGCACGACGGTCTCCACCGTGAGGCCGGGCCCAAATCCGAAAAGCACAC\n") - f.write("CCCACTCCTTTCCCTCCCCGGTCGTTTTGAGTCCTTTCTCGGAGGACTTCCTCCTGACCTCGTCCGAAAT\n") - f.write("AAAAAGCACACAAGCACTCGACATGTTACCGTAATCCGACAACACTTGCCTTGTTGCTTCTAGTTTCTCC\n") - f.write("GGCTTCAATGCCAACTTGGCCTCTACTTGGT\n") - f.write("\n") - f.write(">gi|226791827|gb|GO546005.1|GO546005 Mdas9007H11_e512.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_850250.1| expressed protein [Arabidopsis thaliana] gb|AAL67023.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTCCATTTCTTTTATTGGAGCTACATATGAAGATTATGAATGATACACCTGAAAAAGATTTCTTTAAT\n") - f.write("ACACAACACTATTTCTCCCAGTCTTAATATGGATGCAGTCCTCTTCGTTTCTATTCATGTAGGTAAGTTA\n") - f.write("GGAACTAATTCGTTTGTCAAATACTTTCCCATGCTACTCGTCTTTGTATTTCCTTTGACAGATACATGTA\n") - f.write("CACGTATCGCTCGGTTTCTCTTACGGTGGTGGGTGATCGTCCTCACGGGTTTGAGGAGGGATAGGTCTCC\n") - f.write("AACCTGGTTTCTCATCCCAGTACATGTCATAGTATATGTGACCAGGAGTGTGTTCGGCCACACAACACCA\n") - f.write("TATACCAACATACCGCTTCGCACGATTCCTGAATTTCTCTTCCCTTGCCTTGTCGGTGAAACCTGGGAAT\n") - f.write("GCATCTTGCATAGAAGAAAACTGAATTACTTTTACATCCTTGAACGAGGAGAATACTGTCTTGAACGTTT\n") - f.write("CTTCGTTGCTTCTCTTTGGAAATCTGAGTGCTCCTGAAGGGGTGGTAGTATTTGAAGCAATGCAGTCTCG\n") - f.write("CGTTCCTTGTTGACAAAGCTGGACATCAAGCCATGATTCTTTCACCTGTTTTGGCATCAATGGATTGTCA\n") - f.write("AAGAATGAGTATTCTCTAATACCGATTGGGGGCCCAAATAT\n") - f.write("\n") - f.write(">gi|226791826|gb|GO546004.1|GO546004 Mdas9008B14_e564.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTGCAGACAAAATATATAAAATATATGTATAGGTATAAAACAG\n") - f.write("AAATAGTAAACCCAGCATCCTACCAATTTATTTACATAAAAGGTTCAAACCATAATCATTGTCAATCGCC\n") - f.write("GTCACAAACAGTTTGCAGCAAACTCCACATTAGCCAACCGTTAAACGAGGAGAAAGATTGATTCCTTACC\n") - f.write("ACGCATCTTTATCAAAAGTTGCATTTATAGAATGACACACTTGGTTTCACCTCTTTTACGAAGCTCCTCC\n") - f.write("TCTGCTTTCATTAAATGTTCTCGAAGCTTTCGAATTTCATCATCAGACTTCAGCTGAGCCTGTTGAGCAT\n") - f.write("TCTCTTCTGCTCTCAGACGTGCAGCTTGTTCATCTGCCAACTGTTGCTCAAGCCTCATAGTGGTCTCTCT\n") - f.write("TAACTTTGACTCGACCATCTCAGTAATCCGCTTAAGCTGCTCGTCATGTGCACGCTGCATCTGATCCTTC\n") - f.write("AATTCAGATATTTCTCGTTTGGAATACCCCTTCAAGGAGTTGACCTCTTCTTGTTGATCACGAAGTTTAA\n") - f.write("TGGCCCCTTTCTTCACTTCAGCAAATATCTCATCTGTGTACGGTCGCCCACCATTTTGTGATATG\n") - f.write("\n") - f.write(">gi|226791825|gb|GO546003.1|GO546003 Mdas9007P19_e553.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196647.1| CBS domain containing protein [Arabidopsis thaliana] sp|Q9LEV3|UMP3_ARATH Protein At5g10860, mitochondrial precursor pir|T50795 hypothetical protein T30N20_130 - Arabidopsis thaliana emb|CAB96841.1| putative protein [Arabidopsis, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGTGAAAAAGAAATAAAAATTAGTACCATACTTACACGAATATGTGA\n") - f.write("ACGTGTGAACGTGCGTGATACAAAACGCACTACCATCTACCAGAGAGAGAGAGGATTTAAGCAAAAACAG\n") - f.write("AACGTACACTGCTTATTGTTAGGTACTTGACAGTCCCAAAGGTTTGTAATTAGACAGTGATTGGAAGTAC\n") - f.write("AGAACCAAACAACAACAACAACCGGAGATGCACAAACGAACACACAATACATACAAGCACTCGGGCTTAT\n") - f.write("TTCTGTTTGTCATTCCGGCGTGTCAACTAAAACAGCGTCTCACGTCTTCGTCATCATCATTATCTAGTAA\n") - f.write("CCACCTTGAATAAAAGCATTCAAGCGGTCTAGCTCCTCCCGGTGCTCGCTCACCACAGCACGAACCACGT\n") - f.write("CACCGATGGACACCATTCCAATCATTCCCCCGTTGTCTATTACTGGAATGTGCCTGATTCGGTTATCCGT\n") - f.write("CATAAGTTGCATTGCCCGCAAAACTTTGGTGTCAGGGGTGACAGTGATAAGCTTGTTCTCCTCAGTCATG\n") - f.write("ATATCCCCAACCTTTGTTGACTTGGATGATCTTCCCTGAACTATGATCTTCCTGAGATAATCTCTCTCTG\n") - f.write("TTATGATTCCTGCAAGAGACTTTTGCACTCCGGGTTTCACAACAACTAAAGCTCCAACATTGTGCTGGG\n") - f.write("\n") - f.write(">gi|226791824|gb|GO546002.1|GO546002 Mdas9007H05_e511.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568870.1| SKP1 interacting partner 1 (SKIP1) [Arabidopsis thaliana] dbj|BAB08860.1| contains similarity to N7-like protein gene_id:MTI20.16 [Arabidopsis thaliana] gb|AAG21976.1| SKP1 interacting partner 1 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTACAAAGAGAAAAGCATTAATACATGGTTTATACATGAACTCCATACA\n") - f.write("ATTTGACTTATTGGCGTTACCGAACAAGGTTTTCGATAAGTAGAAGTGAAAGAGATACAGAACCTTTTGT\n") - f.write("AAAGAGCTCCACACACCAGCATATACAATATGCTTTTCCCACAATTGATCAGAGCAACACAACACGGTCA\n") - f.write("TACATGTCTTATGTCCGAGCTTAACAGACTAGATTCTGAAAACATCTGTCTGGAATCGCTCGTCATACAA\n") - f.write("CCTCCAATGGCCATACCTCTCCGAATGGAAGACTGACCGTGGAATGTAGAAGTTTGGCTTTTTAATCTCC\n") - f.write("TTCAAATTCTTCAGATTGCATGTTGTGTTCTCAATATCCCGGCTAGTCAAGTTCACACACCCAAATAAAT\n") - f.write("CCAAGTACTCGAGATTTGGACATCCTACAGGTATCAAAGTAAACCCTTTAGCCGATACCTTTGAGAACCG\n") - f.write("AAGTTCAAGGTGCTCCAAATTTGGCATAGATTTGCCAATTGCAGCAGCTTCTGAATTTCCATCCTGAGGG\n") - f.write("CAAGTTTTTAAGTACTCATCTGGAACAACTCCAGTGTATTCGGATGGATCTAACCAGTTCAGCATATTCC\n") - f.write("GCTTTCAGATTTTCAGATTT\n") - f.write("\n") - f.write(">gi|226791823|gb|GO546001.1|GO546001 Mdas9007N23_e544.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ATCGCTCCAATAAAAACCACATTACATTTTGCAACTAAATACAGATGCAGTTACTCAAGCTACATCCAAT\n") - f.write("TACATCATGGATACAAATTAAAGTTCGACATTTATTAAATTAAGCTATCTATTTAGCTGCTCCTTCAATT\n") - f.write("AATTATCACAAAAAAAAAAAAAAACTTTTGGGTACCCAAATCAACAAAATGGGTCGGACCCACGACAATC\n") - f.write("AAGAAATTGCAGGAGGAACCCATTACACAAATTGCATTCAAAATACCAAAAATTGAGGGAAAAAAACATC\n") - f.write("AACGAAATTGAGAGGAGGGATCGGAGGATCAACCTGCATTCGAATCAATGCCGGTGTCTAGAGAGAGAAA\n") - f.write("AAATCGGATGCAATCTTGAAAATGAGGAAGCAAAGGAACGCGAAAAAGATCGAGAGGAAGAGGTAATCCA\n") - f.write("CGAAGACGAAGAACTCGGTGGAGCCGTGGCTCCTCTTCTTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791795|gb|GO546000.1|GO546000 Mdas9008B02_e561.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB89355.1| ubiquitin-conjugating enzyme OsUBC5b [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGACTTCCACCCGAATATCAATAGCAATGGAAGCATTTGTCTTGACATCCTAAAAGAGCAATGGAGCCC\n") - f.write("AGCACTTACTATCTCTAAGGTATTGCTCTCAATCTGCTCATTGCTGACTGACCCAAATCCTGATGACCCT\n") - f.write("CTCGTGCCGGAGATCGCCCATATGTACAAAACTGATCGAGCCAAGTACGAATCCACTGCACGTATCTGGA\n") - f.write("CTCACAAATATGCAATGGGTTGAAGAAGTCTTTTCCGCCAAATGTAGAGTTTGTATTTGGGGGGAGGGGG\n") - f.write("ACAGGTTCGGGGCTTTTCAATTGAGGAAGAACAGTTTCCTTAATTATATCAAAAAAAGAAGGGTATGAAT\n") - f.write("GGGATGTAATTCTGGCTTTACCAGAACTTTAATTTCTTGTTTGATGTTGTTCCTTCCAGATTTCTAGACA\n") - f.write("GAAACTTAAGTGTTCAAGTTTTAATTCCATCGACTGAGGAATCGGTGTTGATTTTTCATCTGCCATTTCT\n") - f.write("TGTTGTGTCTTGAAAGATTGAGAAATGTATAAATCCAATGAACTGCTATGTTTGCTATTTACTCTTCCAA\n") - f.write("TAAATTGTTCTTGCAAAAAAACAAA\n") - f.write("\n") - f.write(">gi|226791794|gb|GO545999.1|GO545999 Mdas9007N14_e542.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAACAATTACAAATTTCAAATTTCAATTTTTAATTTAAAAAATATAG\n") - f.write("TAACTTACATTATTACATTAATGTCAGGGACCTCAATCAAAAACTAAAAACTAACAAGGTTTCAATCAAA\n") - f.write("GAATATTGATAGTTAGGGACCGCATCCAAAGTGTCCCTTTTAAATAACATCATTTAATCAAATACAAGAG\n") - f.write("AGGGTATGAATCTGTTCCACTTATTTTAGCCGATCCAATCAAATATAATCTGT\n") - f.write("\n") - f.write(">gi|226791793|gb|GO545998.1|GO545998 Mdas9007M06_e534.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTAACTACATGAAGAAACAATTATGTTACAAAACCCTTACATAATTA\n") - f.write("TGCAGCAGTCTCGCAATCATATAACTCTCTCCCCCTTTCAATTACAAAGAATTAATACATCAACAGGTAC\n") - f.write("CTAACCTATATACTTAAATATTTAGCTCACAGAACACACTTGTATGAAACTTGACTTTGTGGTAAATTAG\n") - f.write("GAAGGAAATTTGAAAAGAGATATCGAGAACGAAAGGGCCCCATTTTCTCCCAAGTTCCACATTCCTCTCC\n") - f.write("CCATTTCTGCTCAGTTTCCCCCTCCCCTTCCTAGTGCAGGCACTCCTCCTCATCATGTCTGGCTCCGCCA\n") - f.write("CTCCAAACCGATGACTTCGGAATGTTAGAGCTTAGTTAGGTAATTAACTAAGTAGCATCAGAGGATGAGA\n") - f.write("GAAGGGGTTCATGTTCCCTTCCTTCTTCCAACTGTTCGCCATCTGAAATCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791792|gb|GO545997.1|GO545997 Mdas9007G21_e509.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196186.1| signal recognition particle receptor beta subunit-related protein [Arabidopsis thaliana] dbj|BAB09661.1| signal recognition particle receptor beta subunit-like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("GCATCCCAAATGCAATGAGCCATAATCACTTGGAACATCTTTTAACTTACAAGAAATTACCACAAATTCA\n") - f.write("TGAAATGGGATCAAATATCCTACGACTTTACGTTATCTCTGATAAATTGCTCCACCTGGGAAATTTCACC\n") - f.write("ACCAAGGCCAGAAGCTTCTCCAACTGTAACTTTGTTTTGACACTGCAAAAATGCAAATCGTTCTCCAGGT\n") - f.write("GCTCCGAGTGTAAACTCATTTGTAATATCAGCTGTTGATACTGCACTTCTTGATGCTCGTAATTTGTCAA\n") - f.write("TTTCCTTCTCCAATTGTTTTCGAATAAATTCCTTGCTATGTGCAGTCACTTTGTCTGTCTTATTGCAGAA\n") - f.write("AATAAGAACTGGAATTTTCTTCCTCACCACACTCGCCTTGGTCAAAATATCATACAGGTACTCTGAAGCA\n") - f.write("GCACGGCAATTTGGTAAGAATTCCACAGCATCAACCACAAACACTATACCAGCAGCTTGAGGGAGGAAAT\n") - f.write("CATCTAGTTTGGCTCTAAGGCGAGAATGCCCGGGAACATCAATAACATGAATAGGATTTAGCTTTCCATT\n") - f.write("CTTTGATTTTTCAGAATGAAGCACAAAAGTTCCCTCATTTGGTTCCATAGATGTGACAG\n") - f.write("\n") - f.write(">gi|226791791|gb|GO545996.1|GO545996 Mdas9007E08_e500.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566716.1| protein kinase, putative [Arabidopsis thaliana] dbj|BAB01250.1| kinase-like protein [Arabidopsis thaliana] gb|AAK59509.1| unknown protein [Arabidopsis thaliana] gb|AAL34187.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TGGAAAAGCTTGATTTCCCTACTAATTTACAATAAGAATGAAGAAGGAACCCCAAACAACAATATGGCTT\n") - f.write("TTCAAAAACGCTGTTTGTGCATTATTCAAAAATGAAAAGTGATTATTCAAAGACTGACTGCTGCCTGCAG\n") - f.write("TCTAGCGCTGAACTGGTAAACTGGTTTTAATATGCAATGCACAGTCTGTAAAGCTATATTACACCAAACA\n") - f.write("AAGAAGGTTATGGACCGCGAGGTGTGCCGAAACAAAAACAGCCGGTTGACTGGTCTTCAGGTATCATGCC\n") - f.write("CCCTCCCTTGCTCGTATCTATTGCGTACAACAGTTTCACAACCTCTTCCATTTCAGGGCGTTTATCCGGG\n") - f.write("CTTGCATCCCAGCATTTTCGCATGACGCTAGCCAATGTGCTCGGACAACATCTTGGGATTTCTGGTCGTA\n") - f.write("AATTCTGTCGCACTACTGCAGATGAAACATCAGCAAAACTTAAATTAAGATAAGGCATGTCGCAACAATA\n") - f.write("GATTTCCCATAAGCAAATACCAAAACTATAGACA\n") - f.write("\n") - f.write(">gi|226791790|gb|GO545995.1|GO545995 Mdas9007K19_e526.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|H71447 trehalose-6-phosphate synthase homolog DL4920W - Arabidopsis thaliana emb|CAB10557.1| trehalose-6-phosphate synthase like protein [Arabidopsis thaliana] emb|CAB78780.1| trehalose-6-phosphate synthase like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGAAGGCCAACATTAAGATACGAGAAAATTTTACAATTTCGCT\n") - f.write("ACTCACACACTAGTCACTGCATAATAACAGAACGGGGTTTCAATGAATAATCTATTTACTTTTCTAAAGT\n") - f.write("AAGTACTCGCTGAAAAAGTTGCCCTGCAGCGCTTTTGGCCGACTGCTCCGAAGCATTGGCCAGCCCCTGT\n") - f.write("AACATTCTCAAAATCTCAGTTGTGTCTTCCAGGTAGTACTTGGCCTTGCTGGGCTTCTGACCGACGGTGC\n") - f.write("AAGCAAACACTTCAGCCACCGGAGAGAGAGAGTCCCTTGAACTCATTATCGCCTCAAACATGTCTTCGTC\n") - f.write("GGACCTGTCATCCCCAATACACAGAACAAAATCTGGAAGCATTGCTTTCTGTTTCATTGCTACGAGGAGA\n") - f.write("CGTTCTGCTACAAGGCCTTTGTTGACACCCTGAGGTTTAACTTCTACAATGTGCTGACCACTCTTGACAG\n") - f.write("ACACTGGCTCATTGGCAAGAACACTTTCCAGGTGATCTAGAAGCTCCTTAGCCTGACAAAAGCCAAAATC\n") - f.write("TGGATCTGCGTATTGATAATTCCAAACAAGAGCACTTTCTTTG\n") - f.write("\n") - f.write(">gi|226791762|gb|GO545994.1|GO545994 Mdas9007K12_e524.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CAGGAGGTACTCTCTTGGCTTTCTTAATTCAAAAGTAATAAAGTAGTCAAAAAAGTAGTCAATAAAGTCC\n") - f.write("TCAATAAAGGTTCCCAAGTACTACAGTAAATGCCACTAAACAAAGTAAAATCCCTAAAAAACATGATTTC\n") - f.write("CCTGCCATCCAATCCAACCGCGGGTTGTAAATTTTCCATCCCCCCCCCCTGCTCTGGATTTCCTCTTCTG\n") - f.write("CCCTCTTGGTACCAGGCCTTCGCTTCATGTTCTCTTTCCCTTGAGGGTCTTAAAACTCTTTAAAAAAAAA\n") - f.write("CTGAAAACCCCCTTCAGGGGAGCTTTCCTTCCTTCTTTAAAGTTCCAAAGTTCAAAAAAAACATCCCCCC\n") - f.write("CCCTTGGATTGGAATCATTAAGTTCTTTC\n") - f.write("\n") - f.write(">gi|226791761|gb|GO545993.1|GO545993 Mdas9007C18_e496.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567082.2| serine/threonine protein kinase, putative [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTTGCAAACAACATTCAGTGAAAAATATATCCACCTCACAATC\n") - f.write("CAACCCCCAAGTCAATTCATGGCGAAAAAATTAGACATACAGCACTCAGCAATGACATGAAACTGGCCAA\n") - f.write("ACCAATCCTACACATCCAATCTCATATATGAAATGTAAAAAAATGAAACTATATATAATGTTTACGATGA\n") - f.write("AATCAGCGGGAGGCAGTTGAAAGCAGAGTGTTTCAAGGACGCAGAAATTCCAGCACAAGGAAAGACTGAG\n") - f.write("GCCCTTGCCTTCAAGACTCCGGAGCTGCTGCTGGTGGCTTCAGAAGCGGTTGAAGAGCCTTCACAACAAT\n") - f.write("GCTCATATTTGGCCGGAATTCAGATTCATATTGCACACACAGTGCTGCAACGGCTGCCAGCTTCGCGACC\n") - f.write("CCCTTAGCAGGATAATCCTTTAGCTTTGGATCAACACATTGTTTAACTTTGTCTTCGCTCAATCTTGGAG\n") - f.write("TAGCCCAAGTAACAAGACTCTGCTGTCCACGAGGCATTGTATGATCAACAGGTTTCCTCCCGGTCAGAAG\n") - f.write("TTCTAGTAGAACCACTCCAAAGCTGTACACATCACTCTTCTGTGTCAATTGGCCTGTCATTGCATACTCT\n") - f.write("GGGGCATGATAACCAAATGTTCCCAAAAATCGAGTAGAATGAAGACGAGCAGCCATATCAGGAGCCTGA\n") - f.write("\n") - f.write(">gi|226791760|gb|GO545992.1|GO545992 Mdas9007L07_e529.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTGGACAACTCAATTTATTTAGACCGGGTCATAATGTTACACACT\n") - f.write("GAAATTCACTCGAGCATCTCGCGCACATTAGATGCTCGACAATAACATGAATTGAAAGACGTTAACACAA\n") - f.write("CAGAGTTCATAATTACAGCTCAAGAACAATATATTGTATCCCGGATTGGGGTTCGATAAACCCACTCATT\n") - f.write("TCTTCCCGCTTTTCTTGAGCCCAGAACCTCCGAAGGACCCTTTCTGTTGTGCCTTGGCTCTAAGCTCCTT\n") - f.write("CAGTGCCTTTTCCTCCTCTTTCTTCTTCTGAAGGTTGGCCAAATCGGACTCGTCGTACTCCTTCTTGTCG\n") - f.write("GCCTTGGGTGCCTTCAAGGGCT\n") - f.write("\n") - f.write(">gi|226791759|gb|GO545991.1|GO545991 Mdas9007H16_e514.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568754.1| expressed protein [Arabidopsis thaliana] ref|NP_851167.1| expressed protein [Arabidopsis thaliana] gb|AAK92812.1| unknown protein [Arabidopsis thaliana] gb|AAM14150.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("GGGAGTCGCTACGTTTGGAGCTCCAAGGAGTCCGAATATTCCTCCGCTGATCATCTCGTTGTCATGGTCC\n") - f.write("ATGGAATCATGGGAACTGCCGCGGATTGGAAGTTTGGGGCGGAGCAATTTGTTAAAACACTTCCAGACAA\n") - f.write("AGTTATTGTTCATTGTAGTGAACGGAATGGCTCTAGGCTGACTCTAGATGGTGTGGATGTAATGGGGGAG\n") - f.write("CGATTGGCAGAGGAGGTTATCGAACTGACTCGAAAAAAACCTAATCTACGAAAGATCTCATTTATTGGAC\n") - f.write("ATTCTGTTGGAGGATTAGTGGCAAGATATGCAATTGGGAGGCTATATAGACCCGGTCCCCCTAAAAGTGA\n") - f.write("CAATACGGAACCTAAAAGTGAGAATACGGAACATTCATCTCCTGATGGATGTGAAGAGGATGCAAGGAGT\n") - f.write("ACATTAGCTGGCTTGGAGCCTTTGAACTTTATTACTGTTGCCACGCCTCATCTTGGATCAAGGGGTAACA\n") - f.write("AGCAGGTGCCATTTCTCTTTGGTGTACCTGCCTTTGAAAGACTTGCTAGTGCGGTTATTCATTTGATATT\n") - f.write("TAGGAGAACAGGTCGGCATCTTTTTCTTAATGATGACGATGATGGGAAGCCCTCACTG\n") - f.write("\n") - f.write(">gi|226791758|gb|GO545990.1|GO545990 Mdas9008A20_e560.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB89355.1| ubiquitin-conjugating enzyme OsUBC5b [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("ACGTCTTCCACCCGAATATCAATAGCAATGGAAGCATTTGTCTTGACATCCTAAAAGAGCAATGGAGCCC\n") - f.write("AGCACTTACTATCTCTAAGGTATTGCTCTCAATCTGCTCATTGCTGACTGACCCAAATCCTGATGACCCT\n") - f.write("CTCGTGCCGGAGATCGCCCATATGTACAAAACTGATCGAGCCAAGTACGAATCCACTGCACGTATCTGGA\n") - f.write("CTCAGAAATATGCAATGGGTTGAAGAAGTCTTTTCAGCCAAATGTAGAGTTTGTATTTGGGGGGAGGGGG\n") - f.write("ACAGGTTCGGGGCTTTTCAATTGAGGAAGAACAGTTTCCTTAATTATATCAAAAAAAGAAGGGTATGAAT\n") - f.write("GGGATGTAATTCTGGCTTTACCAGAACTTTAATTTCTTGTTTGATGTTGTTCCTTCCAGATTTCTAGACA\n") - f.write("GAAACTTAAGTGTTCAAGTTTTAATTCCATCGACTGAGGAATCGGTGTTGATTTTTCATCTGCCATTTCT\n") - f.write("TGTTGTGTCTTGAAAGATTGAGAAATGTATAAATCCAATGAACTGCTATGTTTGCTATTTACTCTTCCAA\n") - f.write("TAAATTGTTCTTGTAAAAAA\n") - f.write("\n") - f.write(">gi|226791757|gb|GO545989.1|GO545989 Mdas9007D02_e497.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567082.2| serine/threonine protein kinase, putative [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTTGCAAACAACATTCAGTGAAAAATATATCCACCTCACAATC\n") - f.write("CAACCCCCAAGTCAATTCATGGCGAAAAAATTAGACATACAGCACTCAGCAATGACATGAAACTGGCCAA\n") - f.write("ACCAATCCTACACATCCAATCTCATATATGAAATGTAAAAAAATGAAACTATATATAATGTTTACGATGA\n") - f.write("AATCAGCGGGAGGCAGTTGAAAGCAGAGTGTTTCAAGGACGCAGAAATTCCAGCACAAGGAAAGACTGAG\n") - f.write("GCCCTTGCCTTCAAGACTCCGGAGCTGCTGCTGGTGGCTTCAGAAGCGGTTGAAGAGCCTTCACAACAAT\n") - f.write("GCTCATATTTGGCCGGAATTCAGATTCATATTGCACACACAGTGCTGCAACGGCTGCCAGCTTCGCGACC\n") - f.write("CCCTTAGCAGGATAATCCTTTAGCTTTGGATCAACACATTGTTTAACTTTGTCTTCGCTCAATCTTGGAG\n") - f.write("TAGCCCAAGTAACAAGACTCTGCTGTCCACGAGGCATTGTATGATCAAAAGGTTTCCTCCCGGGCAGAAA\n") - f.write("TTCTAGTAGAACCACTCCCAAGCTGTACACATCACTCTTCTGTGTCAATTGG\n") - f.write("\n") - f.write(">gi|226791756|gb|GO545988.1|GO545988 Mdas9007J16_e521.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_194589.2| calmodulin-binding protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAGATTATAACTCAATATATTTTCAAGAGAAGGAAGGATACTTC\n") - f.write("AACATTTTTCGTATTCTAATGTATTCACTTCTTTGTATCATTTCAAAATACATATATATAACTTACAAAC\n") - f.write("CACTTTCTGATTCTATCATACATGGTTTACAAGGTGCAACAAATCGAGGTGGTCATCGAAAGGGTTCGAT\n") - f.write("CGGCGCATGTTCTTCAAAAAAAGCTGCTGCCTCAAAGCACTCGGCTGTTTCTAGCGTTGATGCCCTCGCA\n") - f.write("TCAACTTTGTACAGCAGCCCCAGATTGTACCAAGCAGAGGGGTTTCCTCTGTCAAGTCGTAGTGCATCCA\n") - f.write("TGAGAAAGCTTCTAACGACTGGTAGAGATTGGCCACCGAACTGTCTGAGTATACAGGCAGTGGATATCAA\n") - f.write("GCTTGGGACGTGGGTAGGTTCGACATCTAATGCCTTCCTGAATGATTCCAAAGCTTCTTGCTGGAGACCC\n") - f.write("TTGGCTTCGTAGAGTAAACCTGTAGAGTGCCATCTGGAAGCAGAATGAGGATTGATGCTCTGGGATTTTG\n") - f.write("AAAGGCAGACCTCAGCATCCCGCCATTGGGACAAGCTTGTATATAAATTAGCTAAAT\n") - f.write("\n") - f.write(">gi|226791728|gb|GO545987.1|GO545987 Mdas9007C14_e495.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566740.1| expressed protein [Arabidopsis thaliana] dbj|BAB01857.1| dbj|BAA85220.1 gene_id:MYM9.15 similar to unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("CATGCTAATCATACATGATCTAGTACAACATTTCAAAACAAGGGTTCTCAAATATACATTCATACCCAAA\n") - f.write("ACACCCCCATCACAATACACCTTTAACATTTAACAGATTTGAATGAAATCAGCAGTTCCATTCTCTCCAA\n") - f.write("ACTAGGGTTCCACATCCTGTAATTATATCAAGTTTCCATGTCAATTACCTCTTGCACATCTTGTGATGAC\n") - f.write("CTCACACCCTCTGTTGTAAGGATTCGCCGCCGCAGCGTGACAATTGTAATAAGAAGCCCCTGGTTTTCCA\n") - f.write("CAGGGAACCAAGTCCCTGTTGAGAGTCCCATAACTTATGTACTTCTTCTGCATTGCCAGAATTCTCCTGC\n") - f.write("TGCTCTCTGACTCCATCTCTGGCTCTGTCAAGCACTCCCCAATCTTCTTGCTGCAGACGCTTCTTCCCCC\n") - f.write("CATGGCAGCCTCGATTTCGCTTCCTTTGAGTGGATGATTCAGGTCAAGAACTGAAACCCCATTGCAGATT\n") - f.write("GAGAAGTGGATGTGGATT\n") - f.write("\n") - f.write(">gi|226791727|gb|GO545986.1|GO545986 Mdas9007D21_e498.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAACTTTGAAGACATACTCAATAATATCAGTCAAACTAGGCAAAGT\n") - f.write("GAACACCTAAAGCTCTACCTTGAAAATAACCTGATTATCTATCTACATCAAGACAGGCAACAAACAGACC\n") - f.write("CGAAAGACGATGAAAGAGTAGAAGTGTCATTGTAAATTCCAGAATTATAAAAAGGTCGTACCCAGTGCAC\n") - f.write("AAGGCTCCCGCTTTACGCAAGGTCTGGGAGAGGTGAATGTCGGCTAGCCTTACCCCCATTTATGGAGAGG\n") - f.write("CTGCTCCCCAGTCTCGAACCCGAGACCTACCGCTCATGCGCGAAGGCACTTGTCATTGTAAATTCCAGAA\n") - f.write("TTATGAGGAAA\n") - f.write("\n") - f.write(">gi|226791726|gb|GO545985.1|GO545985 Mdas9007A14_e487.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_199600.1| NADH dehydrogenase 10.5K chain-related protein [Arabidopsis thaliana] dbj|BAB11336.1| NADH dehydrogenase 10.5K chain-like protein [Arabidopsis thaliana] gb|AAL38780.1| putative NADH dehydrogenase 10.5K chain [Arabidopsis thaliana], mRNA sequence\n") - f.write("AATTTGTTCTTAATGGAAGATGGAAAATACATGAATTATTCAAACTACAACACACGCATTACTGCGTAAG\n") - f.write("CAACCCAAATAATCATCTTACACAAAAAACGCCTGATCTAAATAAAGGGCAGGCGATCAAAGGAATAAAT\n") - f.write("TTCCCGTGAAGGTAAATTTATTTCATTTCACACTGTCGATTATCAGGCTTTTAAAGACTCCCCAACTTTA\n") - f.write("ACAAGTTCCTCTAGTGCCTTCGAAATCTGTGGCTCTGTTAAACCTTCCAATCGAACGCCCCTCTCAACAC\n") - f.write("CCATGTCATATCTAGCCCACAACTGAGGTTCAATCCCTCTGCATTCACGAATCAAGATGGGCAATTTGGG\n") - f.write("GTTCGCACTCTTCAAATCCTTGTAATTCTTCTCCACAAATGTTCTGGTGGATGCGCTTGAAGGGGACGAT\n") - f.write("TGGCAAAGCAAAACCCTAATCTCCTTCAAGTTCTGAGATAGCTTCCCTCTCCATGCCATTTTCTCCCTCC\n") - f.write("CCCTCTCTCTCTCTGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791725|gb|GO545984.1|GO545984 Mdas9007K14_e525.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTATATAAAAAGCAAAGAGAGACATACAAAAAAATTATGAAGGAAAAAAAAAACAAGTGCTTGGTCCAT\n") - f.write("GAAATCGTTCGTTCATATAATTCTTGTACCACTGAACTGTCCCCTCTTCCACCGGCGCTTCGGCCTAACT\n") - f.write("TCGGATATAAAAGTTCCAAGGGGAGCACAACCCGATGATCGTATTGTGACACAAGGCCAACCGACAATAA\n") - f.write("CAAAAAGGCAGCTGGCATAAGGCCAATTCCTTCTAGCAGGAATGAAACAACAAAAAGGCAGCTGGCATAA\n") - f.write("TGCCAATTCCTTCTAGCAGGAACGAAAACACAACAACAAATGGCGACCAAAACAAATGAAACCTAAATTC\n") - f.write("TCAACTGTGCACAACCATAAACGCTTCCTTTGCACCGTGTCATTGGAGCAGCCTGGCGCCAAGTTGGTCT\n") - f.write("TTCACCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791724|gb|GO545983.1|GO545983 Mdas9007A17_e488.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTACAATTAAAACATTCCAATTTCTTCACTAAAATGCAACACTTTA\n") - f.write("CATGAGAACAAGCTAGGAAACCATAAAAATGAAAAAAGAAAAGTGAAAGAAAAGGAGACTCTTAGAACTA\n") - f.write("CTTAGAGATCTGCCTAAAGCATATTATAAGACATATTCGATCCAATTGACAGGGCTACGGGCGTTACAAT\n") - f.write("CGTTTTACTTTATCACCACATATCCGA\n") - f.write("\n") - f.write(">gi|226791723|gb|GO545982.1|GO545982 Mdas9007P05_e547.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ATACTAATGGGGCAGGAAAAACCACCTTTTATCCTTTTAACCATTTAAAAACGGCATTCATGCAAATAAC\n") - f.write("TCCAGTATTGATACAATCAAATGCGATTCCGGCAACGGAAGTTGAAAATTCAAAAGCCGAAACTGCTCGT\n") - f.write("TGTCCCTTCACTAAACAAAAAAAATCAATTGTCGTCCTCCTTTAACTCAAAAACTATAATAAACATTGAT\n") - f.write("TTGAGTCCTGGTAAATACAAATGGGAATTCAAGTGTGACCGCTACAGAACAAACATTCTGGTTTCCACAA\n") - f.write("CCTTCTCCTCCTGCCGAA\n") - f.write("\n") - f.write(">gi|226791722|gb|GO545981.1|GO545981 Mdas9007F21_e505.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179548.1| senescence-associated protein- related [Arabidopsis thaliana] pir|E84578 probable senescence-associated protein 5 [imported] - Arabidopsis thaliana gb|AAD10165.1| putative senescence-associated protein 5 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGAAAACTTAGTTTCCTACTAGAATTTCACTGCCTGTCAATCATCTAT\n") - f.write("CCATCCATAAAGTCCAGATAGAAAAAGAACATACGAATATGTACACTGACTACACTAGTCACAAACAAAG\n") - f.write("ACTCATCGAAAGTCATCAAAAGATAAGAAATTGAAAACAAACAGACGGTTTGTTGTGTTTGGATACTGGT\n") - f.write("TAAGCCCGACCCTGCTTGTTCCGGCGGAAGAGTTCCTCCGTTTGGGCGTTCTTGAAGGCGCTACAGGCGA\n") - f.write("CGAGATAGACGCAGATGAGGATCACCACAGCCACAATAAGGATGACATTGACCCTCCTCCATTCTTTCCT\n") - f.write("CAGGTTCCCCAAAAGTCCAGCCCTGCAGGAATTGCAGTTGTAGCACAAGAGGTTTTGGTCATTGTTCCAT\n") - f.write("ATCAAGCAGTCCGGGTCAGCTCCTGGGTTCACTGGGTTTATCCACAGTGTTGGATTCACATAGTTGTATC\n") - f.write("CACACATTGTTGGAGGTTCACAACATCCTGACTGAAGGGGAGAGATGTGAGCATAGAGGAACTGATCAGC\n") - f.write("TGACATGTATTGTTGTGTAAGCTTANGGCAAGTATCAGACTCAGCCAAACAAGTCCTTATTTTCTGCCAA\n") - f.write("GTCGAAGAGTAAGTAACATAGTCCCTCAGCCACTTGGAAAACCCTTTCAGCCGGT\n") - f.write("\n") - f.write(">gi|226791460|gb|GO545771.1|GO545771 Mdas9004H11_e284.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAG16977.1|AF184076_1 ACC synthase [Prunus armeniaca], mRNA sequence\n") - f.write("GAATGAATGAACAATATTTCAACTGTGCGATTTACAGGTTTCGGAAATTTTCCGAATTCGTTCCATAACA\n") - f.write("ACCGGAATATCTTTTTCAGTCAACGTTGTAAAACAAAACCGAAACCATCCGGGTTCAATACAATGACATG\n") - f.write("ATGAACCGGGAGTTACATTTAGCTTAGCTACATTCAACAACCTATCCCAGAGCTCAAGCTCCCCTTTCTC\n") - f.write("GCTGTAAGAGCGGATTAACCCGCTCATGTCAGCCCAACAGCTGAAACCCCCATTGCTCTTTGTGCACTCA\n") - f.write("ATGCCCAATTGCTTCAAACCTGTCACAAATTTTAGGTACATTGCACGGAGCCTTTCCCTACTAGTATCAA\n") - f.write("TGAACTTCCGGATAAATTTGGTGTCTGAAAGCATAGAGATGAGCAACCGTTGGGATGGGGAGGAAATGGA\n") - f.write("CGAGAACCTTGTCAACTTTTTAGCGGCAGCCAGAACATTCTTGTTATAGGAGTAGATAGCGCCAGCCCTA\n") - f.write("AAACCTGGAAGAGAGAGGTCTTTCGATAGACCATATACTATATGAACTCTGTTCTGGTCCAGATCTTCCA\n") - f.write("ATTCAACAATTTCTGCCATGCTTACAAACTCTTCACTAC\n") - f.write("\n") - f.write(">gi|226791459|gb|GO545770.1|GO545770 Mdas9004C19_e267.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S68805 pectin acetylesterase (EC 3.1.1.-) precursor - mung bean emb|CAA67728.1| pectinacetylesterase precursor [Vigna radiata], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTCTTATTGAATTTTTACCTTCAATTTACACAATCACACTCCTAGAAT\n") - f.write("AACTTTATTCGCAACACCATACAAGATGCCCGCTACCACTTTCAAATCAAAGCTCAAAAGAATAAATATT\n") - f.write("ACCCAGAACCATAAGTACGTAGGCCATTACATCAATAGGGTTTAGGTCATATAGCTCATAAAAACCATAT\n") - f.write("TTTCGACATAATGAAATTAATCTTCCTGATTGTTTGAGTCAAATTCACGGTTTTTGCAAGTGGGATTGCA\n") - f.write("CGGGTAAGGGCAATCAAACTTTTTGAACGCAGTGCGGTCGTAATACCAGTCTCCAACTGCCTTTGCAATT\n") - f.write("GTCGTCTTGCTCAACATAGGAGAGTCAGCTGCCAGCCATGTCTCCTGCGTTCCAATTTGGCAGTGGGCAA\n") - f.write("AGCAAGAGTCTATGAACGCTCCATGAGATGAAGAAATCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791458|gb|GO545769.1|GO545769 Mdas9003H06_e209.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("GTTCAATCAATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACACTACAAACAAAAGTACA\n") - f.write("AAACAATTCCGAGCTCTCACTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACCGG\n") - f.write("GTCGGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAAAGAATCCA\n") - f.write("AACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGT\n") - f.write("CATCGGCAAGGCCCAACGGGTCGAAGCTTCCTCCGGGGTAAAGAGGGTCGGTCACCTCTCCGAGGGGTCC\n") - f.write("GCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTC\n") - f.write("TGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCT\n") - f.write("TGAACCACACGGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCTGGGAAAACGCATCCAAGAGC\n") - f.write("TCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCACGGTTCTTGGCGAAGGTCTCTGGGTCAGCT\n") - f.write("GAGAGTCCGGCGGTGTCCCAGCCGTAGTCACCGGGGA\n") - f.write("\n") - f.write(">gi|226791457|gb|GO545768.1|GO545768 Mdas9003G16_e204.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF86906.1|AF223358_1 triose phosphate/phosphate translocator precursor [Mesembryanthemum crystallinum], mRNA sequence\n") - f.write("TTTTTTTTTTAACAAAAAACATGATAGAGAAGTAATTAAAACATTATCTAGAATCTCATGAGACCATTAC\n") - f.write("AAATTAGAATGTCTTCGTACTCTCAATCAATGGGGAAAAAAAAAGGGCAGGGGGGGGGGGCGGCGGAGGA\n") - f.write("GGAAAAGAAACAAACTATGACATAGATAACAGATACTCAATTTGCAATTTCTTCTGAAGGGAATTTACAA\n") - f.write("AATTTACAATGCATGGTTCCCTCCATGTCCGTTCTTCGTTCCGTCTCATGCCGCTTTTCCTTGTCGTTTC\n") - f.write("TCTTCTTCTATCTTGGCCTTGAGGTAAGAGTAGATTGCCACTCCTGCAATTGCAATGGCAGTTCCAATAC\n") - f.write("CGGTTTGTGTTGAAATCTTGTTACCAAAGATCACGATCGAGAAGCCAATCACAAACACACGCTTCAGCAC\n") - f.write("GTTTCCAACTGCGTGCGTAAGAGGCGCCACTCTCTCCAGGGTGTTGGTGGCCAACTGGTTATAGAGATGG\n") - f.write("TAAAACAATCCAACCCAGAAGAGGTCGGTGACGAACTTGACAAGTCCTACTTTAGCAATTGCATCATTGA\n") - f.write("AGCCATACTTGATCAGTTGAGGTCCCTCTAAGATGAGAGCGGGTGGAATGCAGACAATGAGTGCAATGAT\n") - f.write("TGAAATATAAGCATAGAGATTTGTACTATCCATATCAGTCATGGCTTTCTTTGAATAGATACTCCTGTAA\n") - f.write("GTGAAGGAGATA\n") - f.write("\n") - f.write(">gi|226791456|gb|GO545767.1|GO545767 Mdas9003G14_e203.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD40837.1| OSJNBa0086B14.9 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTAACAACAAACTAAACTAGATTAGACGAAATATTGTTCAATAGTGAG\n") - f.write("GCTGCAGACAACCAAATGAACAAAAAAACGCAAATTAAACACATCTAGGTCCTTCATATTCTACGAAACA\n") - f.write("AACCAACCAAAAGCAGCAGCCGCAGATCTTAAAAGGAGTTTTGCCTATAACCATAATATCTGACCACATC\n") - f.write("TTGTCCCCAACCCTAACCTCCTATATCATCCTATCACAAAAAAACACCACCTTCTGTCCGCAAAAGCATT\n") - f.write("ATACATATCAGTCTTCAATCCCGTCTGCAGCCACCCCACAATTAACCCCGCTCCATTGCAAGGCAGGCGG\n") - f.write("GTTGCTTAGGCACGCTCACCCCTGATCCTCCTGGCAAGCTGGATATCCTTCGGCATGATGGTAACCCGCT\n") - f.write("TGGCATGGATAGCGCAAAGGTTGGTGTCCTCAAACAGACCCACCAGGTAAGCCTCAGCAGCCTCCTGCAG\n") - f.write("TGCCAGCACTGCATGGCTCTGGAAACGCAGATCAGTCTTGAAGTCCTGAGCAATTTCACGAACAAGCCTC\n") - f.write("TGGAATGGCAACTTCCTGATCAACAGCTCAGTA\n") - f.write("\n") - f.write(">gi|226791455|gb|GO545766.1|GO545766 Mdas9004B19_e261.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F86339 protein F2D10.18 [imported] - Arabidopsis thaliana gb|AAF80615.1|AC069251_8 F2D10.18 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTATAACGAAGGCAAACTGAAATTCATTGAACATAAGGAGGATCATTAAGTACAGAAATGACGA\n") - f.write("CATTGGAATCGCGGGGAGAAGACGATCCTGAAACTGAATCCGATTTTGTTTTTGTGTTTTCCTAAAAACT\n") - f.write("AACCCCTAAAACAAAAGGTAGAGAGCCAGCAACTTATCCCATAGTGAAGAAAAGGTGCAGGCAGGCCTTT\n") - f.write("CAATTATCTTCTAAGCAACCCTACACATATCGCTTCTCCCCCTCCATTCAATTCCCGTTGCTCTACTCAT\n") - f.write("CGTCGTCTTCCTCCTCGCCGCTCTCGTCCTCATCCTCATCATCATCATCATTTACCTCAGACTTGGACTT\n") - f.write("GTCAGACTCTTCTTCGTCAGCTTCATTAGGTCCTTCAGCTAATTGCTTGTTGTATGCCTGAATGTTCTTG\n") - f.write("TTATACTCAACCTTCCTCTTATCTGCCTTGGCTTGATAAGGAGCTTTCTCAGCATCTGACAACGATTTCC\n") - f.write("ATTTCTCACCGCCAGCCTTACCGACAGCAGCAACCGACTTGTTGTTTGGATGATCCTTCTTGTACTTCTC\n") - f.write("TCTGAACTCCTCCATGAAGACGAAGAAGGCACTCGCAGGCCTCTTCGGCTTGTTCGGATCCTTTCCGGCT\n") - f.write("TTCTTCGCCGGCTTCTTGCTCGCTCCG\n") - f.write("\n") - f.write(">gi|226791454|gb|GO545765.1|GO545765 Mdas9003J01_e215.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAAGGAAAAACGGGGGCCGGGGCACCCCGGCCAATTTAATTTTTTTTTTTTGGGAAAAAATTGGGCGGG\n") - f.write("ATAAAACCCCCGCAAAACCCCCCCCCCTTTTTTTAAAAACCCCCCAAATTTCCAGTAATTTTAAAACCCC\n") - f.write("CCTTTCCATTTTCCCCCCCGAAAAGGGGGCCAAACCCAAAAAAAAAAAAAAAAAGGCCCCCCCAAAAGGA\n") - f.write("ACCCCCAAAAAAACCCCAAACCACCCCCCGAAAAACTTCTGCCCCAACCCCCCCCCCCCAAAAAAAACCC\n") - f.write("CCCCCCCCCCCGGAAAATCCCCCCAC\n") - f.write("\n") - f.write(">gi|226791448|gb|GO545764.1|GO545764 Mdas9003P03_e242.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD28640.2| geranylgeranyl hydrogenase [Glycine max], mRNA sequence\n") - f.write("AACGTATTATTAGTTTAAGATACTATTACAATGATATTTTGAAGGAGAAATTTTACAACGATTCTAAAAC\n") - f.write("AATGACGGACATAGAAATTTATATATGCTAGATCTCATTACACAAACTTGGAATTTCCACTCAAATCTGT\n") - f.write("TGAATTCAAAGAGTTCATTCCTCGTTACATGAGGAAAAACAAAAAATTACACAAACAACAAGGCTTCCTC\n") - f.write("CTTTCATACAGTAATTTTCTCCATCTCCCTCCTGAGTGCATTAGCCCTAACCAAGCTCCCAATGGTATTC\n") - f.write("ACAGCCAACTTCAAATCCTCCCACGGATTCCCCGGCACCACCCTCTTGTACAAGTAGCTATCGAACGTCA\n") - f.write("TCTTCTGCACGTACTCATCCGCACACATCTCCACGAACGCTTCCCTCGCGGGGTTCGACCTATAGAACAC\n") - f.write("CTTCTGCAACACATCCAACACCTTGTAAGTAGGCCAATAGGTCTTGTCCCACTTCTCCAAGTACGTCCTC\n") - f.write("AAGTCCGCCTCATTCACCATCCTCTTCCCATTCTCCGACCCCTCAACTATCGCCTCGGCACACATCCTGC\n") - f.write("CACTCTTTGCTGCAAAGTAGATGCCTTCACCAGAACACTTTGTTACGTACCCTGCTGCATCACCAACGAG\n") - f.write("TGCTACTCTGCCCGCCAACCTTCGTGGGCCGGG\n") - f.write("\n") - f.write(">gi|226791447|gb|GO545763.1|GO545763 Mdas9004C18_e266.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL49750.1|AF452012_1 aquaporin-like protein [Petunia x hybrida], mRNA sequence\n") - f.write("TTTTTTTTTAGCGTAAAAAGGTAGATTAAGGTAGAGAGAGGAGAGAAGACATTGTAATCATAAAAAGAAA\n") - f.write("ACACCACTACTCATGAACAATAATTAATGAACATAATTAAAGTTAAGTAATTAGATTATAAATAGAGAAC\n") - f.write("CCAGAAAGATTGAAAGATCATCATCCATCCTCTCAATACACACACTAACAAACAGAGAACAAAATATCAA\n") - f.write("CAGAACATTAATGTAGCTTTCTTTTCTTCAATCTTTGTTTTAGTTGGTTGGGTTGCTGCGGAAGGATCCC\n") - f.write("AACGCCTTGAGCGCCGCCGCCCTCAGAATGTACTGGTGGTACGCCGCTGCAGCCAGTGCTCCCACAAATG\n") - f.write("GTCCGACCCAGAAGATCCAGTGGTCATCCCAGATTTTATCGTTGTTGTAGATCACAGCAGCGCCGAAACT\n") - f.write("CCTTGCTGGGTTGATTCCAGTTCCAGTAATGGGGATTGTTGCGAGGTGCACAATAAACACAGCAAACCCA\n") - f.write("ATGGGCAGTGGAGCCAAAACAGGGACGTGGGAGTCGCGTGCGCTCCTCTTGGGGTCGGTGGCCGAGAAGA\n") - f.write("CGGTGTAGACGAGGACGAAGGTGCCGATGATCTCAGCTCCCAGAGCTGTGCCCTTGCTGTAGCCACTAGC\n") - f.write("CACAGAGTTGGCGCCGCCGCCGA\n") - f.write("\n") - f.write(">gi|226791446|gb|GO545762.1|GO545762 Mdas9003B18_e180.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTCTTTAATAACTCATTTATTAAGTACCAAAAAAAATACAAGGGCCGTT\n") - f.write("TATTATATTTTCCTTTGCAAGGCCTAATGCAAAGGGCGAATAATGAAGTTTTCAAACTAGCAGATAGATG\n") - f.write("AGCTTCTGGAAAATTATATGAAGCTCAGTTTATTGTAAGTAAGATTCACGATAGTTTCCATTTCGCTTCC\n") - f.write("GTTGAACAGCCTTGGAAGAAGTTGCGGAGGCAGCAATTCGAAGGTTTTTGAATGGCACGCTTATGCATAC\n") - f.write("ACGTCTAAGCCCCAAGTCTTGGAAGGTAGACTGGTACGATACTTCCTGTCGATACTGTAGATGAGCTGCA\n") - f.write("TGTCTTCATCGCTCAGCTGGAATTCAAGAACCTCCAAATTCTCTTTCAATCGCTGAATTTTCGATGATTT\n") - f.write("TGGAATCACTGCTGTTTTCCTCTGAATTCCCCACCTCAGACAGATTTGTGCCACGCTCTTTCCGTATTTC\n") - f.write("TTAGCCACATCATTGAGAACTGGATCATCCAAAGGTGAA\n") - f.write("\n") - f.write(">gi|226791445|gb|GO545761.1|GO545761 Mdas9003B06_e177.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P16059|PSBP_PEA Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving system of photosystem II) (OEC 23 kDa subunit) (23 kDa thylakoid membrane protein) pir|JS0771 photosystem II oxygen-evolving comp, mRNA sequence\n") - f.write("TTTTAGAGAGCTCAAAGACAATTCACAATCTTAAGGTAATTTACATTACACAAACCCTCTCAAATAAATT\n") - f.write("CTTATGCAACACTGAAAGAACTTGCAGTGCTCTCTACAAACTTCCTTGCTCCTTTGAACCACCTCTTGTC\n") - f.write("TCCGGCTTGTGCCTTTAGAATGTAGAGCTTGCCGTCTTTCACGGTGGCTGTGATAATCTGGTGCTTGCCT\n") - f.write("CCTTCATCTCCGTCGGCTGTCCTTGTCAACACAGATACCTAGTAGTACTGCTTTCCGTCAATCACTCGAC\n") - f.write("TACAACTCTCCAATATGTTGGCTGTGGCCACGGCACCCGGGTCGAAACCACCCTCGGATTCATTCTTGCC\n") - f.write("AAAGTAGGATTGTTTGCCTAGCAAGTAGTCCACCTTCGCGAGGAATTCCTCGGGGGAGCCATAGTCGGCG\n") - f.write("ATGGATTTCATGTCGGTTAAGGTGATTGTGACGGACACATTGCTGTTGCTGTCGAAGTTGTCCTCGTACC\n") - f.write("TAAGAACTTGACCATGGAAC\n") - f.write("\n") - f.write(">gi|226791444|gb|GO545760.1|GO545760 Mdas9011H23_e848.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_680161.1| No apical meristem (NAM) protein family [Arabidopsis thaliana] emb|CAC35884.1| ATAF2 protein [Arabidopsis thaliana] gb|AAL87335.1| unknown protein [Arabidopsis thaliana] gb|AAM91696.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("CAGAAATGGCACTTTACGGAGAGAAAGAATGGTATTTCTTTTCGCCAAGGGACAGAAAATATCCAAACGG\n") - f.write("TTCAAGGCCGAACCGGGCAGCCGGAACCGGGTACTGGAAGGCGACCGGGGCTGACAAGCACATTGGAAAA\n") - f.write("CCCAAGGCACTCGGGATTAAAAAGGCACTCGTGTTCTACGCTGGTAAAGCCCCCAAAGGAATCAAAACCA\n") - f.write("ATTGGATCATGCACGAGTACCGCCTCGCCAATGTCGACCGGTCCGCCGCCGCTGCCAAGAAAAATCAAAA\n") - f.write("CCTGAGGGTACGTCCGTCTTTCCATTACCCTTTTTCTCTTTTACCATTATACCCTTGGACCCACACACGT\n") - f.write("CATTGACCGTGGACCATATTTTGTAATTTGACTAAAATATAAATGCATTTATTATTTCGACGGTCAGCTC\n") - f.write("AGATGTGCAATCTAAAAGAAAGAATATCATATCTAATTATATTTTACATATTATAAGATGAATGTATTAA\n") - f.write("GTAAATTCATGTACCTTTTTCGGTCTCTCAAATTTTGATCATGTCATCAATGCCTCTTAAGAATGCATGT\n") - f.write("TGTAACTTCTGGTAGATTAAATTAGAATATCGCTTTCGAAAAATAAATGAATCCGGCTTCAAATATTTTA\n") - f.write("ATCTCAATTTTGTTTAATTACTCAGAGTGCTTATCGTTCTAAATTGATGTTTATGTAATGCAGCTTGATG\n") - f.write("ATTGGGTACTATGCCGCATATACAACAAG\n") - f.write("\n") - f.write(">gi|226791443|gb|GO545759.1|GO545759 Mdas9011M20_e875.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAATTAAAGAATTATAAAAGATCAATACATAGAGAAATAAGAGAGGGACATATATATTGTCACATATACT\n") - f.write("GGCTAGATATATATTTATCTAGCTAGCTACTTGACAGTTATTTGTACGTAATTACTTGACAATTAAAAGA\n") - f.write("AGAAGAAGCAAAGAAAAGTGAACAAGACAAAGATGGAAGTAAGACCATGAGGGTGGAAGTGCATTCTCAA\n") - f.write("ATGAACCGATTTAGAAAAATAAGGTGGCGGGGGACTGTAAGGATTTACAGGATAAAGGCTTGGTGGTACT\n") - f.write("ATAGAGGGCGCAAATGGAGGCCGATTCGGGATTAATGAGGGAACATCTGCCGCGGGAGGAGAGGACGAGG\n") - f.write("ATCCGCAAGTGTCTTGACACGGAGGCCTCACAGGTGGTGGTGGTTGAGGTTGAGGGTGGGTGGTGGACAT\n") - f.write("TCACGGAGAGCTGGTGGTGGTGAAGAAGGAGGCGCAGGAGGTGGTGGGCATTCAATGATAACCGGTGGTG\n") - f.write("GCGGCAATGGTGGTGGTGAAGAAGGAGTCGCAGGAGGTGGTGGGCATTCAATGATAACTGGTGGTGGTGG\n") - f.write("CGATGGTGGAGGTAGAGATGGCGCGGGGCATGGGTTGGGGCACTCATTGCA\n") - f.write("\n") - f.write(">gi|226791435|gb|GO545758.1|GO545758 Mdas9011H02_e843.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n") - f.write("CCACTAGGGACGACCGGATCGGTGTTTGCACCGGAATCTTCAAGCCTGATAATGTGTCCCAGGAAGATGT\n") - f.write("TGTCAAGATTGTTGACACATTCCCCGGTCAATCCATTGATTTCTTCGGTGCCCTAAGGGCTCGAGTTTAT\n") - f.write("GACGATGAAGTGAGGAAGTGGATTTCCGGTGTTGGAATTGACGGGATTGGGAAGAAGCTTGTGAACTCAA\n") - f.write("AAGAAGGTCCCCCGACTTTCGATCAACCTAAGATGACTCTGGAGAAGCTCCTTCACTACGGACAAATGCT\n") - f.write("TGTTCAGGAGCAGGACAATGTGAAGAGAGTCCAACTGGCTGACAAGTACTTGGCCGATGCAGCCCTTGGA\n") - f.write("GATGCAAACCAGGACTCCATTAACCGAGGAGAATTCTATGGAAAGGCAGCCCAACAAGTTAATGTACCAG\n") - f.write("TCCCAGAAGGCTGCACTGATCGAACAGCTGCAAACTTCAACCCAGCAGCAAGGAGTGACGACGGTAGCTG\n") - f.write("TCAGTACGAGTAATTGGAGCTGAAGAAAATAAATATTCTGTTTGCTGGGTTATTGATATTTTCTTTGTAA\n") - f.write("TTTGCGCTTGTATTTCTATGGAAATTCTTGCAATTATTTTGTTTTAATTATTAAACAAGCTATTGATACT\n") - f.write("CCGGCTATTGAACAGTCGATAAGAACATAATGTTATGTTGTTGAGAATATGTTGTCATTGTCGCAAACAA\n") - f.write("AACTTCACAACATGTTATCAATACATTCATG\n") - f.write("\n") - f.write(">gi|226791434|gb|GO545757.1|GO545757 Mdas9011N23_e879.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T02946 hypothetical protein 3 - common tobacco chloroplast gb|AAA84680.1| unknown protein prf|1102209C ORF 3, mRNA sequence\n") - f.write("TTTTTTTTCAAGAATTCTTCTTACTTTAATACATAATACATAGGTCATCGATTCAGCATTGGATAAAAAA\n") - f.write("GATAAAACGTGGGATGAAATACCCATTTTTTCCAATCAAATAACGGATTCAAATCATTTTATCGACATGA\n") - f.write("GTGTTTTATATCGAAAAAAAATTCCAACTATTTGTTTTGAAACCATTTCTGTCTTAACTTATTAACTAAC\n") - f.write("ATAGTAGTAGAAAGAATACCATGCTGCATCTGAACTTCAAACGGTTTAGCTTTAACCCTGTTAATGGTTT\n") - f.write("ACATTATTGGTTGATAGAGAATCAAAGTAGATTTACCAATGAATCGCGAAATGCTATGGTTCTTCAATTT\n") - f.write("TTTTTTCAGAAGAAATTCGCGGAATCATGCACCTTTTTTTTTCGCGTTATAACGAAAAAATGCAGTTGGT\n") - f.write("CGTATCCAGCCTATTCTTGAAATAAACAACTCGCACACACTCCCTTTCCAAAAAAAATCAACACACCAAG\n") - f.write("CACTACGCTTAGATTTATTAGATTTGTTGCTAAAATATCGGTATTAAACCCGAAACTCCCGGCGGATGGC\n") - f.write("CAATAACCCAAGGAAAGGAAAGAATCGGTTACATTTTTCATATGATATCCTCTTTCTTATAGATAGACTA\n") - f.write("ATTATTTTATTTATATTATTTTTGTATTATTTTTATTATGAATTTCCCTATTTCTAAATAGAATATACTA\n") - f.write("AATAGAGTCAAAAAATA\n") - f.write("\n") - f.write(">gi|226791433|gb|GO545756.1|GO545756 Mdas9011C24_e824.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566564.1| expressed protein [Arabidopsis thaliana] dbj|BAA94980.1| gb|AAF26101.1 gene_id:K14A17.9 similar to unknown protein [Arabidopsis thaliana] gb|AAK55691.1|AF378888_1 AT3g17020/K14A17_14 [Arabidopsis thaliana] gb|AAK91493.1| AT3g17020, mRNA sequence\n") - f.write("TTTTCCGGTAAGCGAATCACCATCTCGGACTACCAGTTGAATTCACATGTATACGGTAGCAAATGCATGT\n") - f.write("AACGTAGCGATATACGCACATCAAATTTGTCCAACTTCAACATACCGCAACAAACAGTTGAAACCTTAAT\n") - f.write("TTAACTAGATCTTATTAAGATAAAAACTAGATCTTGTGCAAACTAAAAGGCTCAGTTGCAGGTAAGGAAG\n") - f.write("CAATTGACGCATTGCACTTATTTACCCAGCACGCATTGAGGACAAAGGATTTAGCTGGCATGGGACTCAG\n") - f.write("AACTAGTCTTGACGACAGTAACTGGGCACGAAGCATTATTTACGATATGGTTGCTGACACTGCCCATTAT\n") - f.write("AACCCTCTTAAGCTTGCCAAGGCCTCTGTTTCCAATAACAAGGAAGCTCAAGGGGGTCTTGTCAATTGCC\n") - f.write("TCGAGAATCTTCTCACGGGCATCGCCCCAGTAGATCTTCATCACCACCGTAACCTCTTTCTGCGTCGCAG\n") - f.write("TGTCGGCGATGTCGATGGTTTCAGCGTCAGGCGTCACTCCATATTTCTTCATGATGGTGGGATCAGAAAA\n") - f.write("CTCCTTCACAGGAATCAAAGGTGAACCGGTGACGCCCCACAGCTGCATCTCTCCCTGCTCGTAGTTCTCT\n") - f.write("TCAGGCCG\n") - f.write("\n") - f.write(">gi|226791432|gb|GO545755.1|GO545755 Mdas9011N11_e878.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGGAGGTAGAAGGGACTTGCAGACGAGAGAGAAGGACTTTTCTGGTAAATGGGGTCGTCGTCTAGGT\n") - f.write("GGTCAAGGACGGCGTGGAAGATCTCGTCGGTGAAGAATATCGAATGGGGTTGTTCATGGCGGCGGTGAGG\n") - f.write("CTGAGCTTTTTTCATGGGAGTGAGTTTCCTGCCTGAGTCGATAAGAGTTTGAAGGCGACAAACTAAATTA\n") - f.write("ACAGAAAACGGTGGATTTGGGGGAGACGGAAGGATATCCAGAATGTCAAATTACGATAATGTCCTTGTTG\n") - f.write("ACCATCGACTCTATTCTTTCTTATCAGGGGAAGTAAGCATACGCGAAACAAGAAATTTTTAGTTGTGACG\n") - f.write("GAAATACAATTGATATATTACGAGTTTTAATACGAATTATGAAAAATTTTACTTTTTAAATTATTAACTT\n") - f.write("TTTAACATATATATTTCACCGTTTGTTTAGTGACGTGATGTACCATCCGATATACCGATAATGGAAAATT\n") - f.write("TGAGCTCCAACACATAGAACGAAAAAGTCCATCATAATTAATTAACAAATTCGTATTTAGTGAGTTGAAC\n") - f.write("CTTTTACTTATAAATAATAAAAAAAAAGAAATATCGAAGAGATTGTAACGTAAATGTCAAGGTTACGCAT\n") - f.write("\n") - f.write(">gi|226791431|gb|GO545754.1|GO545754 Mdas9011D03_e825.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27878.1|AF139466_1 chlorophyll a/b binding protein CP29 [Vigna radiata], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTATATCAACCATGTAGTCATTTAGCAAGTAGGAAAAGCTCACATGCCA\n") - f.write("TTGCATACACTAATCCTTTGATCCCATCACAATCTTTACAAGCTTAAGCAGTACATATCATGATTCAGAT\n") - f.write("AATTAATCATGGTCTACTGATTAAAAAACCAAACATGATATGCACATAAAGATACTTCTCTAAGAAGAGA\n") - f.write("AGGCGTCAATAATGGTGGTGTGGAGCGGGTCACTCAAATGGGTAGCCCAGTTGTTAAGTGGTCCCTTCCC\n") - f.write("GGTGACGGCGGCTTGCACGGCAAACCCCAGAAACGCAACCATGGCGAGGCGGGCGTGCTTGATTTCGGCC\n") - f.write("AGCTGAAGAGTGGCCTTCTTTTCCGGGTCAGCAGCAAGGCCCAACGGGTCGAAGAACTTGCCACCCGGGT\n") - f.write("ACAACCTCTTTTCCGGGTCGAGCTCGGCGTTCCTCTGGAACTCGATGTAGCCAATCACTAGAACTTCGAT\n") - f.write("CCAGATCAACGTGGTTAGTGAGAAAGGGAAGTGGTTGACCCAAGTAGGACGACCCTTCGATGAGCTCCAC\n") - f.write("CTTTCCGGCGTCTTGCCATGTGATCCCGGTGACGGACTCGACAGTGAGAGCACCGAGCGTGGCGAGCATG\n") - f.write("GCCCACCTTCCATGAATCAGCTCGCACTCCCTAAACCTCTG\n") - f.write("\n") - f.write(">gi|226791430|gb|GO545753.1|GO545753 Mdas9011D18_e828.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CAAAAAATCCCCCCTGAATTTTTGCCTGTCAGGAAGGGGCAAAAATAATTTCA\n") - f.write("\n") - f.write(">gi|226791429|gb|GO545752.1|GO545752 Mdas9003E01_e190.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n") - f.write("TTTAAATAAGGATATAATTTATTTCATGAATTTCTCAATAAACATCATCCTGAATCCGTTAAAACACCAA\n") - f.write("ATTCGAAAACAAAAGAGATTGCCTCGAAAAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGGTCTTGA\n") - f.write("AACCCTAATCAAGGACAAACTTAAACAAACCACCGAAACCCTTGGCTAAGAGCCACAATGGTACGTACAA\n") - f.write("CAACAATATTAATTACGACGAAGAAACATGATGAAACATGAACAACAACAACAACAACAACAACTTAGTA\n") - f.write("GCCTGCAGGCTTGTAGGCGATGAAACTGATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATACGG\n") - f.write("ATGAAGGCGTTGGGATAGGCCTTCTTGGCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGCATC\n") - f.write("CGAACATGGGCAGCTTCCACATTGTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791423|gb|GO545751.1|GO545751 Mdas9003F15_e199.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46293|RS16_GOSHI 40S RIBOSOMAL PROTEIN S16 pir|S41193 ribosomal protein S16 protein - upland cotton emb|CAA53567.1| RS16 protein, 40S subunit [Gossypium hirsutum], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTAGCAAAATAAACTAGTAATTAATTGAAGCATGTCATACTTAATATGGTAACCATT\n") - f.write("CAATATCCAACATACTCAAAAACAACAACAAAGTCTCGATGATCAAAATTCTGGAAAATTATAAAATACC\n") - f.write("CATTTAACTTCCAACTTCTTAAAACAAAGTCAATAACCCTTAAACCATAAACCGAAACGAAGAAGCTAAA\n") - f.write("CCTGTCCATCTTTCGCCTTCCATTTGCCCCAAATCAACGGTAAGACTTCTGGAATCTAGCACGAGCACCA\n") - f.write("CGACCGCCGAACTTCTTGGGCTCGCAGCGCCTCGGATCAGCAACAAGGAGGGTCCTGTCATACCTGACCA\n") - f.write("GAATGTCCTTAATCTCCTTCTTGCTCTGCTCATCCACATATTTCTGGTAAAAAGCGACGAGAGCTTTGGC\n") - f.write("GATGCTCTGGCGGATGGCGTAGATCTGGGAGATGTGACCGCCTCCCTTGACGCGGATGCGCATGTCGACA\n") - f.write("CCGGCGAAGCGCTGTCGTCCGAGGAGTAGGATGGGTTCGTAGGCCTTGAAGCGGAGGATCTCGGGCTCGA\n") - f.write("CGAGCTCGATTGGGCAGCCATTGATCTTGATGAGGCCACGGCCGCGCTTGCAGTATGTGACAGCGACAGC\n") - f.write("GGTCTTCTTGCGGCCAAAACACTGCACTGACTCGATTGCGGGAGTCGCCATTGCTA\n") - f.write("\n") - f.write(">gi|226791422|gb|GO545750.1|GO545750 Mdas9011M01_e870.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB40974.1| isopentenyl diphosphate isomerase 2 [Nicotiana tabacum], mRNA sequence\n") - f.write("TTTTTTCGGTCAAGAAAAAACTGAAAACGCCTTACGAGTCCAAACTTATTGGAACAGGAAAAAAACACCA\n") - f.write("ACTATAATAAAACCACAATCAAAGTTTCCCAGCAGACTCGATTTAAGTCAACCTGTGGATGGTTTTCATG\n") - f.write("TCAGCAGCTTCCTTGATGGTGTTTTTCTCAACATGGTCCCACCACTTGAACAAGAAGTTGTCCACCACGA\n") - f.write("GCCTGAACCAAGGCGACAGCTTCAGACCTTCCTCCCCGGCATCTGCCTTCCTCAACAGCTCTTTCAGCTG\n") - f.write("CTCCTGGTTTACGTACTTGATATCAGCTACCTCGTCAGGGTTCGGATGCACATTAACATCACGTACAGTG\n") - f.write("AAGAGAAGGTAATCAAGTTCATGTTCTCCCCACTTGCCATCAGAAGGTGCCTTGTACAGCATGCGACCCA\n") - f.write("ACGGGATAAACTGATCAACTGGCACATCTTCAGCAGGAATACCGAGTTCATCCAAAAGCTTCCTTTGAGC\n") - f.write("AGCATTTCTTACCCCAAGAGAGTTCTCATCAATAAGCTCGGATTCACGATACAGCGGATGGCTGCAACAG\n") - f.write("GTGTTTGTCCACACAAGTGGAAAT\n") - f.write("\n") - f.write(">gi|226791421|gb|GO545749.1|GO545749 Mdas9003A08_e171.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_180375.1| glycosyltransferase family [Arabidopsis thaliana] pir|E84680 probable glucosyltransferase [imported] - Arabidopsis thaliana gb|AAC98458.1| putative glucosyltransferase [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTATGTTAATTGAGAGGTTGCTTAATTAACATTCCCAAATAATTGGAGTTGTGCAACAAACGTGCATAA\n") - f.write("TAGAGTTGCGGAACCAAAGGAAAAAGCGCACATATAAATTCTAGATGTGTTACATTTCTAGTATTTCGGC\n") - f.write("CTTTTACATCGCTAATGAAGCGTCTTATGGCAGCCAGTCAATGAGATGATGAAGAAGAAACCACATGATG\n") - f.write("GCAATATGGAAGTCACATTTCGTGTCTGAAATTTTTTTCCTTCACATTTACTAATGAATTGAGATAAGTT\n") - f.write("CTTTTGTGATGACCCATTTAGAGCCACTGCATCCTCCAATGTTTGTGTTGCTTTCATGACCTTCTTCTGC\n") - f.write("AAACCGTCACCCGATTTTCCACATATCAGAACGGTTGATCTTCTCTGCTACCTCCACCCTTCTAACTGGT\n") - f.write("TTAACCCGATCACAAAGATTGAGTCCAATGCCCCAATCATCAACTACTAGTTTCCTATTAGTGATTTGGT\n") - f.write("CAGCCACTAGAGGAAAACATAGCATGGGAACACCACACCGCATACTTTCCAGTATAGAATTCCATCCACA\n") - f.write("ATGCGTTAAGAACCCTCCTACTGCTGGATGTGAAAGCACCTNCATCTGAGAGCACCATGGCACCATCAAC\n") - f.write("CCTCTATCTTT\n") - f.write("\n") - f.write(">gi|226791420|gb|GO545748.1|GO545748 Mdas9003F11_e196.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q42954|KPYC_TOBAC Pyruvate kinase, cytosolic isozyme pir|S41379 pyruvate kinase (EC 2.7.1.40), cytosolic - common tobacco emb|CAA82628.1| pyruvate kinase [Nicotiana tabacum], mRNA sequence\n") - f.write("ATGCATTGTTCAGCAAACGATCCTATTAGTAAACGTATTGCATAAAGTCCCATATCGCAATATCGGCAAA\n") - f.write("TTATGTAGCTATCAAAGCCTGCCCATCACATACACTGATGACGGCGGTAAATGTAAATGTTTTCGCATCC\n") - f.write("AAAAACACATATTAAACGAGCCAAGTCAAAATCATAAGCATTGTCATTGGCTAATTTTGAAAACGCCAAA\n") - f.write("AAGGAAAGGATGAACATCACTTCACGGTCAAAATCTTGATCACTGATGCAGTTCCATCACGGTGCAAAGC\n") - f.write("CACAACAGCATCTCCGTTCTTGCAAAGCCCCTTTGTCTTGGCATGTTGAAGGGCAAAGTCCAGTGCTTCT\n") - f.write("TCGGTCGTCTCTGCATGAAAGGCCCTAAAAAATCCCGCGCTTAAAACTGGAACCAACCCACGGAAAATCA\n") - f.write("AACTATCCTTGCTGGAGCTTCATCACTGCATGACCAGTCAAATGAATCTGTCTTGATCTCGGGGACAACA\n") - f.write("ACAGACAGTATAGGCATGCCAGGTCTGTACTTGGCCACCAGCTTTGCAGTACTTCCTCCTCTGGTTAGGA\n") - f.write("CCAATATAAGAGCTGCTTTGGACGAGTTG\n") - f.write("\n") - f.write(">gi|226791419|gb|GO545747.1|GO545747 Mdas9003E06_e191.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P24922|IF52_NICPL Eukaryotic translation initiation factor 5A-2 (eIF-5A) (eIF-4D) pir|S21059 translation initiation factor eIF-5A.2 [similarity] - curled-leaved tobacco emb|CAA45104.1| eukaryotic initiation factor 5A (2) [Nicotiana plumbaginifo, mRNA sequence\n") - f.write("TAGCAGAAACTAAGAGAAAACCCAAGGGGGACAGAGAAGCTCGGTCATCAACTTCGGAGGCAGAGAGATG\n") - f.write("TCGGACGAGGAGCACCAGTTCGAATCCAAGGCCGACGCCGGCGCATCTAAGACCTATCCCCAGCAGGCTG\n") - f.write("GTACCATCCGCAAGAATGGCTACATCGTCATCAAGGCCAGACCTTGCAAGGTTGTTGAAGTCTCCACCTC\n") - f.write("CCAAACTGGAAAGCACGGTCACGCTAAGTGCCACTTTGTGGCAATTGATATTTTCAATGGAAAGAAGCTT\n") - f.write("GAAGATATTGTTCCTTCGTCCCACAATTGTGATGTTCCCCATGTCAGCCGTACTGACTACCAGCTGATTG\n") - f.write("ATATCTCTGAGGATGGCTTTGTGAGTCTTTTGACTGAAAATGGAAACACCAAGGATGATCTGAGGCTTCC\n") - f.write("CACTGACGACAGTCTGCTTACCCAGATCAAGGACGGGTTTAATGATGGAAAGGATCTTGTGGTGACCGTC\n") - f.write("ATGTCTGCCATGGGTGAGGAGCACATCTGTGCCCTCACGGACATTGGTCCGAAGAATTAAGTATGATGCT\n") - f.write("GTATCAGTAGCTCTAGCTGATGGCACGACCTTCTTTGCTTT\n") - f.write("\n") - f.write(">gi|226791411|gb|GO545746.1|GO545746 Mdas9011O12_e881.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q41229|PSE2_NICSY Photosystem I reaction center subunit IV B, chloroplast precursor (PSI-E B) pir|T16963 photosystem I chain PSI-E, isoform b - wood tobacco gb|AAB31705.1| photosystem I subunit PSI-E [Nicotiana sylvestris], mRNA sequence\n") - f.write("CTAGAGTGACCAACAGCAGCACAGAAATCTCACACATGGCTAGCTGTGGCATGGCATCAGCTGCCTCAGG\n") - f.write("CTTTGTGGTAGCACCAAACGTTGCAACCACCAACTCAGGCTCAGCTTCCAGCCGGAGTAGCATGCTGTTT\n") - f.write("TTCCCTTCAAAACCCAACACCAACACCAGAAGCAATGCCAGGTTTGTGATCAGGGCAGCTGAAGAAGCCG\n") - f.write("CTGCGCCTCCGGCCGCCACCACGACTGCACCAGAGGGGGCAGCTACCCCTAAGCCTAAGCCACCACCAAT\n") - f.write("TGGACCCAAGAGAGGCACTAAGGTGAAGATTCTTAGGAGGGAATCCTACTGGTTCAAAGGCATTGGATCT\n") - f.write("GTTGTGGCTGTGGATCAGGATCCGAATACCCGTTACCCTGTCGTGGTCCGATTCAACAAAGTTAACTATG\n") - f.write("CCAATGTGTCCACAAATAACTATGCTTTGGACGAGATTGAAGAAGTTAAATGAGTTTGTAGTAGCACTGT\n") - f.write("AAATTGTAATCTTAATTAAATTGTCCTTCTCTCAGTTTCTTCCTTACTTGTTGGTGCCCTTTATTTGTGT\n") - f.write("ATCAAAACCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791410|gb|GO545745.1|GO545745 Mdas9011J12_e853.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q43517|FER1_LYCES Ferredoxin I, chloroplast precursor pir|T07175 ferredoxin [2Fe-2S] I precursor, chloroplast - tomato emb|CAA99756.1| ferredoxin-I [Lycopersicon esculentum], mRNA sequence\n") - f.write("TTTTTTTTCAACAGAGAGAGATTCATACAAGGGTGAGTTTACAAGATACAATGATCTCCATACCACAAAT\n") - f.write("GAGAGTACAAAAACATTAAGCAACTCATATAATTAGAAACAAGACAACCTTAACCCGAAACAAACTAAAG\n") - f.write("CCAGATCCAACCAGCCAGCAGCCATCAAAACATGACATCATCATGAGAAAGCTCAAAAGCACTTAACCAG\n") - f.write("TAAGCTCCTCTTCCTTGTGGGTCTCAAGTGTGACGTCAGACGACGGATAAGCCACACAAGTGAGCACAAA\n") - f.write("TCCACCGTCCATCTGCTCATCATCCAAAAAGCTCTGGTCCGACTGATCCACACCCCCACTCACAACTTTG\n") - f.write("CCGGCGCACGAGGAGCAAGACCCTGCCCTGCATGAGTAGGGAAGGTCAATCCCGGCCTCCTCCGCCGCGT\n") - f.write("CGAGAATGTACACGTCGTCGGGGCACTCAAACTCTTGTGGCCCTTCTGGTGTGAGCAGCTTCACCTTGTA\n") - f.write("GGCAGCCATCGCCACACGCCCTCCGCGGTTGGCCTTGAGCCCGAAAAGGGCCTGACCGACGTTGGGGGAT\n") - f.write("AACCGCAGGCTGGTCATCGGCTGGCCGCGGATGAAGGAGGTGCTGACCATGGTGCCTGAGAGAGCTGTGG\n") - f.write("CTGCCATGTTTGTTGGTTTGCTTTGGTTGCAAGGCTTTTTCCTCGTGCCG\n") - f.write("\n") - f.write(">gi|226791409|gb|GO545744.1|GO545744 Mdas9011C19_e823.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|G86459 Hypothetical 55.6 kDa protein - Arabidopsis thaliana gb|AAG26075.1|AC069299_1 hypothetical protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTCTAATAATATCAATATATTACGTGAAGAAAAAACCTTACATACGATACGACATATTATTATTAACA\n") - f.write("CACCACTGTAAATCCATTTCATAATTCATTTTCCTTTTTATTGTCCTCACGAAAACTAAGCCATCAGTCA\n") - f.write("CGTGGCATTATTTCCCACCGAAACCTTATTGCTAGGGTTTTGCCTCATTACTTGCAGAGATCTAGTGGAG\n") - f.write("CACCACAGAGACAATCATTCCCCAGAAACGCCGAAGCACCAAACTTGGTGGCCGGAAGCGGTCCGCAAAG\n") - f.write("ATGATTGTGGCTGACGTTCAGTCTCTCCAGCCCTGAAACTCCACTCGGCACCTTCCCGAAAACCAAATTC\n") - f.write("CTCGACAAGTCCAAATACTTCAACGTCTTCACAATCCTCAACTTCTCCAAATCAAACTTCAACTTATTCC\n") - f.write("CAGAAGCCCAAAACCCCACCAAGAAATCGGTCCTGTTCAGCAGCCCGACTGGACTCCCCGAAATCTCGTT\n") - f.write("CTCTGATAAATCGATGTAATCGTAGAAATACGTCTCCGCCGGCTTCCAGTCGTCCAATTTCAACTTGATC\n") - f.write("CCACACTTTGCGAGCTTCAGAGAGTAGATGATCGGCGACGACGTCACCCATTTTGGAATTTGCTTCAGAT\n") - f.write("GGAAGCTGTTGTACGACAAATCCAGGGACTCGATGCCT\n") - f.write("\n") - f.write(">gi|226791408|gb|GO545743.1|GO545743 Mdas9003D02_e186.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F96755 hypothetical protein F3N23.22 [imported] - Arabidopsis thaliana gb|AAD55649.1|AC008017_22 Hypothetical protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTAAGAACAAAATTGCTTCACATTTCTGCCATCTCTTACATTAAATGT\n") - f.write("GAATTTAAACAATCTCAAGGAAAGTAAATACTCTCCAATACTATACATCTACCTCATTGCGACTTCTTGA\n") - f.write("CATTACCAAACGTCATCCTCTCTCCAGAAATGCTCCTCAAGAGCTGTTTAGAACACATGTTCTCAGCTGT\n") - f.write("TGTCGCGTTTTTCACACGGTTGGCTTTTACCCAAGCAGGTTCCTCGGGAACAAAGCGGGAGAATCCAAAT\n") - f.write("TTGATCAACAAGAGAACATGTTCCATAACCAGAATTGCAGCCAGGCCAGGCTCTATCTTCCATTTGCCCT\n") - f.write("CTTCATCATATAACCATACAAGAAGTGCGCAGTTGGTGCATATAGACATAACTACAAGAAACTGAAATAT\n") - f.write("GTTAAGCCAAGCTCCAATTGTTGTGGAAAAGCGTGGAGTTGGTCTGCGCAACATGGCAAGAAGCTTCAAT\n") - f.write("GCATCCGCCCTAATTTCAGTGATGTTGTTCAAAATTGCAAAGGCAAAAGCAAGGGGGAATGCACAAGCAA\n") - f.write("ACATCATGATCATTCCAAACTGCAATGCCACCTCAAGAAAGTCATCAAACAGCCCATCTTCCAGTTCCAT\n") - f.write("GCCAATGCTAGCGGAATATGAAGGCTTCAGGTACTCTTTCTCTACCCTAGAAGCAAACCGAATCTTCCCT\n") - f.write("GTCGTTGAACCTTTTTCACACTTTTT\n") - f.write("\n") - f.write(">gi|226791407|gb|GO545742.1|GO545742 Mdas9003A06_e170.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("GGAAACCCTAGCTTGGTCCATGCACAGAGCATCTTGGCCATCTGGGCTACCCAAGTGGTGTTGATGGGCG\n") - f.write("CAGTTGAGGGATACAGAATTGCCGGCGGACCCCTCGGAGAGGTGACCGACCCTCTTTACCCCGGAGGAAG\n") - f.write("CTTCGACCCGTTGGGCCTTGCCGATGACCCAGAAGCCTTTGCTGAGCTCAAGGTGAAGGAGCTCAAGAAT\n") - f.write("GGAAGGTTGGCCATGTTCTCCATGTTTGGATTCTTTGTCCAGGCCATCGTCACCGGAAAGGGACCATTGG\n") - f.write("AGAACCTTGCCGACCACCTTGCCGACCCGGTCGCCAACAATGCCTGGAACTATGCCACAAACTTCGTTCC\n") - f.write("CGGAAAGTGAGAGCTCGGAATTGTTTTGTACTTTTGTTTGTAGTGTTGTCGGTGATGTAAATTTGGTACC\n") - f.write("AAGTAATGGACAACAATTGAT\n") - f.write("\n") - f.write(">gi|226791406|gb|GO545741.1|GO545741 Mdas9011L22_e869.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T17007 major allergen Mal d1 - apple tree emb|CAA96537.1| major allergen Mal d1 [Malus x domestica], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTGGACATTAAACTTTTTATTATTATAGTAATTTTATTCAAACAAAGGTAGCAAT\n") - f.write("ACCCTTAGTAAGTTAGTATTTTTCCAACTAAAGCATCACTGAATGAAAAAAACATAAGAAACTTGAACTT\n") - f.write("ATGCCATGAAGACAACAAGGGTAACACACAAATTACATGTATCGATAACATCAGATTTAGTTGTAGGCAT\n") - f.write("CAGGGTTGGCCACGAGGTAGGCTTCAAGAAGCTTGAAGAGACCGGAAGCCTTCTCTTTGCCAGCCTTAAC\n") - f.write("ATGCTCTTCCTTGATCTCAACATCACCCTTAGCATGGTAGTGGCTAGTGGTTTTGATGATGGATCCTCCA\n") - f.write("TCAGGAGATGCGATCAATTTGGTCTCATAAGTGATCTTCTCAAGCTTGTCAGACAAGGTATCTCCTTCAA\n") - f.write("TCATAGAGTAACTGTATGTAAAGTTGTCTTTGTCAATCCCATTGACCCTTTGCTTAACATACCCGTATTG\n") - f.write("GCTGCCTTCACCAAAGGTAACTTTCTTGATGGTTCCAACACCTCCATCGCCTTCGATGATTTCAGTGCTT\n") - f.write("TTAATTGCTTGTGGAGCAATCTTCGGGATGAGGTTATCGCCATCAAGGATAAAAGCCTTGAACAATCTAG\n") - f.write("GTGCAGGGATGACAGAGGTGAACTCGGTTTCATATGTGAAAACACCCATGATGAACTTTGGATTTGGAAA\n") - f.write("ATGA\n") - f.write("\n") - f.write(">gi|226791399|gb|GO545740.1|GO545740 Mdas9003F16_e200.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGGATCTGAACCATGTAACCTCTTAATTTCAGACACATATTGTAGCAC\n") - f.write("ATAGTTCAAATTATTGTTGTCCAATACTTGGTACCAAATTTACATCACCGACAACAATACAAACGAAAGT\n") - f.write("ACAAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTGGCGA\n") - f.write("CTGGGTCAGCGAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAAAGAA\n") - f.write("TCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGCTTCT\n") - f.write("GGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTACGCCGGGGTAAAGGGGGTCGGTCACCTCTCCGAGGG\n") - f.write("GTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCAAGAT\n") - f.write("GCTCTGTGCATGGACCAAGCTAGGGTTTCCCAGGTAGTCGAGACCGCCCTCGCTGAA\n") - f.write("\n") - f.write(">gi|226791398|gb|GO545739.1|GO545739 Mdas9011K09_e860.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P10708|CB12_LYCES Chlorophyll A-B binding protein 7, chloroplast precursor (LHCI type II CAB-7) pir|S07408 chlorophyll a/b-binding protein type II (cab-7) - tomato emb|CAA32197.1| chlorophyll a/b-binding protein [Lycopersicon esculentum] gb|AA, mRNA sequence\n") - f.write("ATAAGTTTGTAGGTCACCAGCTGATTTCATACATATTGGAACGAAGGTTCCAAAGAGATTTTTGTACACA\n") - f.write("AGCACATCAAATTACAAGTTTTTAGTCCTACAAATTTCCCTTGGAACAACACAATACTTCTCAGCCTCTT\n") - f.write("TTCCCGGATCGATGACAACGTTGCTCCTTCTCCTCCCGCACTTGAAAGCCCCAGTTAGAATTCTCCTTCG\n") - f.write("TTCCTCACTTGGGGGAGAAAGAAGCGAAAATGGTGGCATGGCCGGGATCAGCGAGGTGAGCGAAGAGGTT\n") - f.write("GTCGATGGGGCCAGTCCCAGTGTAAATGTGTTGAAACCAAGCCCCCATCACAGCCAACATAGCTAGCCTT\n") - f.write("CCGTTCTTAATCTCCTTTGTCCTCAACTCCTTGATCTTCTCAGGCGAGCCGCTTCCCCATCCAAGTGGGT\n") - f.write("CGAACCAGAGCCCTCCCGGGTACCCTACATCTGTCCCGGTGAGCTTGTTGTTGGGGAAGATTGGGTCGGT\n") - f.write("GTTAACGGAGCCGGGCTTGAGGATGTCGGCCCATCTCCTCCCCTCGGCCCACCCGATCAAAACAAGCTCA\n") - f.write("ACGACGAAGAGAGTGGTGGTGTCTGTGAAGTACTCTTGCTCTCCGGCTGTGTACCATGACGGGGTGTTTA\n") - f.write("GAATG\n") - f.write("\n") - f.write(">gi|226791397|gb|GO545738.1|GO545738 Mdas9011D09_e826.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_196073.1| beta-ketoacyl-CoA synthase family [Arabidopsis thaliana] pir|T48449 fatty acid elongase-like protein - Arabidopsis thaliana emb|CAB85559.1| fatty acid elongase-like protein [Arabidopsis thaliana] dbj|BAC41850.1| putative fatty ac, mRNA sequence\n") - f.write("TTCTAAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACACACATGGTGGATCCTGA\n") - f.write("TGGCAACGTGTTTGCTGGCTCTTTTCTATGGTTTCTCCTGCCTCTGTAAGTTACTTCTCAGAAGGAGAGA\n") - f.write("CCAGGCATGCTATCTGCTGGCCTACGAGTGCCACATGCCACCAGACGACCTGAAGCTCAGCACTGATTCA\n") - f.write("TGCGTGAAAATCGTCTTGCGGAACAGGAATCTAGGACTGGAAGAATTCAGGTTTCTCTTGAAAACTATTA\n") - f.write("CCCATTCGGGCATTGGCGAGGAAACTTACTGCGCAAGAAACATCATCCAAGGCCGACAAGAAACTGCAAC\n") - f.write("CCTAGAAGATGAACTTGCGGAGATGGATGGCATCATCTTTGACGTGCTGGACAAGCTTTTCGCTCGGGCT\n") - f.write("ACCTCAATTTCTCCGTCGCAAATCGACATTCTTGTCGTCAATGTGTCGATGTTCTCCCCTGCACCCTCCC\n") - f.write("TATCTTCACGTATAGTGAATCGTTACTAGATGAGGGACGACATCAAGAGCTTCAACCTCTCGGGAATGGG\n") - f.write("CTGCAGTGCGACCCTCATTGCCATTGACGTTGTACAACACTTGTTCAAGTCTCACAAGAATGCGAATGCC\n") - f.write("ATCGTTGTAAGCACGGACTCGTTGGCTCCTCATTGGTATTGCGGCGTAGAAAAATCCA\n") - f.write("\n") - f.write(">gi|226791396|gb|GO545737.1|GO545737 Mdas9011H05_e844.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P09756|CB23_SOYBN Chlorophyll A-B binding protein 3, chloroplast precursor (LHCII type I CAB-3) (LHCP) pir|S01962 chlorophyll a/b-binding protein 3 precursor - soybean emb|CAA31419.1| chlorophyll a/b binding preprotein (AA - 32 to 231) [Glycine, mRNA sequence\n") - f.write("TTCTATCTGTTGTTGTCCATTACTTGGTACCGAATTTACATCAGCGCGACAACACTACCACAAAAGTACA\n") - f.write("AAACCGTTCCCAGCTCTCACTTTCCGGGAGACGAAGTTTGTGGCATAGCTTCGCAGCTTTGATTGGCGAT\n") - f.write("CGGGTCCGCCCGGTGGTCCGCAAGGTTCTCCCCTGGTCCCTTTCCGGTGACCATGGCCTGGACCAGGAAT\n") - f.write("CCACCACATGGAGAACTTGGCCTACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCATAGGCTTCT\n") - f.write("GGGTCATCGGCTACGGCCAGCGGGTCGAATCTTCCTCCGGGGTAAAGAGGGTCGGTCACCTCTCCCAGGG\n") - f.write("GTCCGCCGGCCAGTCTGGATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGAT\n") - f.write("GCTCTGTGCATGGACCGTCCTGGGGTTTCCCTTGTAGTCTAGACCGCCCTCGCTGAAGATCTGGGCTCCG\n") - f.write("GCCTTGAACCACACTGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCTGG\n") - f.write("\n") - f.write(">gi|226791395|gb|GO545736.1|GO545736 Mdas9011E17_e832.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA80688.1| chlorophyll a/b-binding protein, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTAGTTCAAATCAATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACA\n") - f.write("CTACAAACAAAAGTACAAAACAATTCCGAGCTCTCACTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAG\n") - f.write("GCATTGTTGGCGACCGGGTCGGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGG\n") - f.write("CCTGGACAAAGAATCCAAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTC\n") - f.write("AGCAAAGGCTTCTGGGTCATCGGCAAGGCCCAACGGGTCGAAGCTTCCTCCGGGGTAAAGAGGGTCGGTC\n") - f.write("ACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCC\n") - f.write("AGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAA\n") - f.write("GATCTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCTGGG\n") - f.write("AAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGGAGTGGATCACTTCGAGCTCACGGTTCTTGGGC\n") - f.write("GAAGGTCTCTGGGTCAGCTGAGAGTCCGGGCGGTGTCCCAGCCGTAGT\n") - f.write("\n") - f.write(">gi|226791388|gb|GO545735.1|GO545735 Mdas9011K14_e861.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTGAGAAGATGAGTACCACTGGAACTGGCTTTAGCAACCACGCTTTCACCATGCCCGGCGGTCTCCAAG\n") - f.write("TAAATGAGCAAACTAGCAAGAACAACACCCCATGCAACTTCCAGATGCCTCTGCACTACCCAAGGTACCA\n") - f.write("GAAGAGTGACTATGAGAGCATGCCTGAATGGAAACTGGACTGCCTTATGAAGCAGTACGGCCTCCCACTC\n") - f.write("ATTGGGGATGTCAACCAGAAGAGGAAGTTTGCCATGGGAGCCTTCCTTTGGCCTTCACAATACGAATGAG\n") - f.write("AAACCCTAGCTAGTAGCTTAATTGCTACGATTTCTAATAATATTCTACATATATATGGTATTACAAAAGA\n") - f.write("CTACTGGCATGCATGTATATAGTGAAATAATATTAATTGCTTTTTAGTAGTATCCCTTATTTAAGTACTG\n") - f.write("TCTATCTGTATTCAGCAGTGTATTACTGTGTACTTTTGCTATTAATGGAATCAAAATAAGGGTTGTAATA\n") - f.write("TAAGGTATGTGTTATCTATTGTATTAACCCGTTGTTTATGTCTAAAAAAAAAAAAAAAAAACTCGCCTCG\n") - f.write("TGCCGAA\n") - f.write("\n") - f.write(">gi|226791387|gb|GO545734.1|GO545734 Mdas9011L02_e866.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564644.1| senescence-associated protein -related [Arabidopsis thaliana] dbj|BAC43242.1| unknown protein [Arabidopsis thaliana] gb|AAO42971.1| At1g53885 [Arabidopsis thaliana], mRNA sequence\n") - f.write("CCAATTACCACTCATTCCATTAATTTTTCTCCTGCTTTGCTTTTTTGCAGTGTCAATTAACAAGAGAATG\n") - f.write("AAAAAGATCAAAAGAGAAATTAAACTATATATATATATATATGCATATGTCTAAAGTACAAATATCTTTC\n") - f.write("TTTGATGTCTGGTTTTCTCCTGTTGCAGATGTACATCTTCAAAAACATTAGTGTTGCGAGAGCCACGCCT\n") - f.write("ACTAGTGTTAGCATTACTACTCTTAGTAAGGCTGCAACGATATAGGCCACGCCTATAGGATGTTATCATT\n") - f.write("TGCTTGGTAGAAGCCTCTAATTCCTTCATGTCATCAATAACAATCTGTCTGTTCCTGCACTCTATGCTGC\n") - f.write("AAAAACCTAAATCACCTCTGTACATGTAGACCTCTCTATCAAGGCTTAATCCCTTGGTGCATAAGTGACA\n") - f.write("TGTTTTAAGAAAGCAAGAGAATTGCTCGAGGGAGCTGCAGGTTGTGGATTGGCTCAGTCTTAATGCAGAT\n") - f.write("TTCTCAATGATATTTGTCTTATTTCTTTGTGAATTCTGTACAAGGATTCCCAATCCAACAGCCACTGAGC\n") - f.write("TCCCATGGCTGGTTTTATCACTGATGCCCAGCTTATGGGCAGCTGGC\n") - f.write("\n") - f.write(">gi|226791386|gb|GO545733.1|GO545733 Mdas9003B21_e181.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TAAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGTTTACATACAAGCAGGTAGCTTAAAGATCATCTA\n") - f.write("TTGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAAGCCCAGGCATTGTTGG\n") - f.write("TAACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAA\n") - f.write("GAAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCC\n") - f.write("TCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAA\n") - f.write("GGGGTCCTCCGGCAATGCGGTAACCCTCAACAGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAG\n") - f.write("AATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCT\n") - f.write("CCGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGC\n") - f.write("CCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACG\n") - f.write("\n") - f.write(">gi|226791385|gb|GO545732.1|GO545732 Mdas9011O24_e884.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P09755|CB22_SOYBN Chlorophyll A-B binding protein 2, chloroplast precursor (LHCII type I CAB-2) (LHCP) pir|S01961 chlorophyll a/b-binding protein 2 precursor - soybean emb|CAA31418.1| chlorophyll a/b binding preprotein (AA -33 to 223) [Glycine, mRNA sequence\n") - f.write("TTTTTTTTTAGTTCAAATCAATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACACTACAA\n") - f.write("ACAAAAGTACAAAACAATTCCGAGCTCTCACTTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAGGCATT\n") - f.write("GTTGGCGACCGGGTCGGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTTCCGGTGACGATGGCCTG\n") - f.write("GACAAAGAATCCAAACATGGAGAACATGGCCAACCTTCCATTTCTTGAGCTCCTTCACCTTGAGCTCAGC\n") - f.write("AAAGGCTTCTGGGTCATCGGCAAGGCCCAACGGGTCGAAGCTTTCCTCCGGGGTAAAGAGGGTCGGTCAC\n") - f.write("CTTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCA\n") - f.write("GATGGCCAAGAAGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAA\n") - f.write("AACTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACTTGACACC\n") - f.write("\n") - f.write(">gi|226791384|gb|GO545731.1|GO545731 Mdas9003F01_e195.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTCGAGTTGAAATGAACTTACTATTGACCATAAATTGAGACAACCAAGAATCACAA\n") - f.write("TCAAGTACATCACAATCAAGTACAAATACGGGCTTCCAACTGGAACCCGAGTTCTAAAACCCTCACAAAC\n") - f.write("ATTTCAGCAGACAGCACAAACCCATTCTTAGCATAGAGCATTAAGTATAGTCTTATCGTCAATAACACCA\n") - f.write("AGAACAAACCCATCATTACCATCTTTTCTATACACCACGAATGACAAAAAACCCGACCAAGCAAGCTAAC\n") - f.write("ACATCAAGCGACTACTATGACGATGGAGGCAGTGAGGAAGGCGACGAACGAATGAAGATGATGAGGAAAT\n") - f.write("ACATCATAGTGGCTTTGGTGAATAAACACCATTTGAAATAATACTCAAAACTTCTCATATAACTCCATAA\n") - f.write("CACTGGGCAATTCAAAGCATAGCATGGTCAAAACTAAGGCTCCACAATTATCTTTCCGGTAGCATGGCCA\n") - f.write("TCCATGGCTTTAGCCCAAG\n") - f.write("\n") - f.write(">gi|226791383|gb|GO545730.1|GO545730 Mdas9003A22_e175.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAAAATATATATTTTTAAAGAGGACTGAACCCAGTCAAAGCTCCGGCTAGGCCCTCAAGCCCAAATTAT\n") - f.write("ATTACTTGAAAAAACATAAAACGGGTGGGGCAAAGTGTAAACCCCGACAATCAAAAGTAAAATCATATAC\n") - f.write("AACCACTCTAAGCAAAACTCCATGAAATTTCAACCTTCAACAAATCATCTTCAATAATTTCATGATCACA\n") - f.write("AAACTCCTCACCAACATTTTGCAACCCTTCACCAACATTTTGTAAATGGAGGACCGGCTTTGAATGAATT\n") - f.write("AATTTAATTCATAAACTGTTACTGTTTGACAAAAGGCTTCTGCAGGTTCCCAAGTAAAATCACTCCTCCG\n") - f.write("GTGAATCTCCAAAAAAGTCAAAGTTTGCATATGCATTTTGAAAGTCTTCTTCAGCTATGTACCTGCTTTT\n") - f.write("TGGTTACTACAATATACTTCAGCAACTTTGGCTACTGCAAGGCCCATGCCGATGTCCTCCACCACAACAC\n") - f.write("AATTGTTTGCAGCTTGAATTTT\n") - f.write("\n") - f.write(">gi|226791382|gb|GO545729.1|GO545729 Mdas9011K15_e862.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P09756|CB23_SOYBN Chlorophyll A-B binding protein 3, chloroplast precursor (LHCII type I CAB-3) (LHCP) pir|S01962 chlorophyll a/b-binding protein 3 precursor - soybean emb|CAA31419.1| chlorophyll a/b binding preprotein (AA - 32 to 231) [Glycine, mRNA sequence\n") - f.write("TCGAGATTTGTTTTGCAATGGCAGCTTCCATGGCTCTCTCTTCCCCAACCTTCGCCGGCAAAGCCGTGCA\n") - f.write("ACTTTCCCCGGGAGCCACCGAGCTTTTTGGAAACGGAAGAGTGTCCATGAGGAAAACTGCTACCAAAAAA\n") - f.write("GTCTCCTCTGGCAGCCCATGGTACGGCCCTGACAGAGTCAAGTACTTGGGGCCATTCACCGGTGAGCCCC\n") - f.write("CAAGCTACCTCACCGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCCGGACTCTCAGCTGACCCAGA\n") - f.write("GACCTTCGCCAAGAACCGTGAGCTCGAAGTGATCCACTCCAGATGGGCCATGCTCGGAGCTCTTGGATGC\n") - f.write("GTTTTCCCAGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAAGCCGTGTGGTTCAAGGCCGGAGCCC\n") - f.write("AGATCTTCAGCGAGGGCGGTCTCGACTACTTGGGAAACCCTAGCTTGGTCCATGCACAGAGCATCTTGGC\n") - f.write("CATCTGGGCTACCCAAGTGGTGTTGATGGGCGCAGTTGAGGGATACAGAATTGCCGGCGGCCCCCTCGGA\n") - f.write("GAGGTGACCGACCCACTTTACCCCGGCGGAAGCTTCGACCCATTGGGTCTTGCCGACGA\n") - f.write("\n") - f.write(">gi|226791376|gb|GO545728.1|GO545728 Mdas9003B15_e179.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566796.2| glyceraldehyde 3-phosphate dehydrogenase A subunit (GapA) [Arabidopsis thaliana] sp|P25856|G3PA_ARATH Glyceraldehyde 3-phosphate dehydrogenase A, chloroplast precursor (NADP-dependent glyceraldehydephosphate dehydrogenase subunit A), mRNA sequence\n") - f.write("TTTTTTACAAGATTCTCATTATTAATCAGAAAAGAAGAATAAAAGAAAAAGAAAGAAAAGTAGAAATTAT\n") - f.write("AAACGCAGAACGGTAAAAGAAAACCAAAAAACATGGATCTGGCCGCCGGGAATGACAAGTTGGAGGAGGA\n") - f.write("GGAGGAGCTAATTTGAATTTTGAAATGATGATCACTTCCAGTTGTTGGCGACAATGTCAGCCAAATCAAC\n") - f.write("AACCCTTTGGGAGTAACCCCACTCGTTGTCGTACCAAGCAATGACCTTGACCATGTCATCGCCCATTACC\n") - f.write("ATTGTCAATGAAGAGTCGACTGTGGAGGAGACATCTGTGCACCTAAAGTCGACTGAGACAAGGGGCTCGT\n") - f.write("CACAAACAGAAAGGATACCTGCAAGCTCCTTCTCGGCGCTGTCTCTGAAAGCAGCGTTCACCTCTTCTGC\n") - f.write("AAAGGTCTTCTTAGTTACTTGGACAACAAGGTCCACCACCGACACGTTTGGGGTGGGCACACGCAGGGCA\n") - f.write("ATGCCATTTAGCTTGCCCTTCAGACTTGGAAGGACTAGGGCCACGGCCTTTGCTGCACCAGTGGAGGTGG\n") - f.write("GAACGATGTTGAGAGCAGCAGCCCGT\n") - f.write("\n") - f.write(">gi|226791375|gb|GO545727.1|GO545727 Mdas9011E16_e831.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|EAA30389.1| hypothetical protein [Neurospora crassa], mRNA sequence\n") - f.write("TTTCATCATCATCATCGTCATCTATCATTAATACTAACTGAAGTGAAGAATTTATATACATGTATGATTC\n") - f.write("CGATGTTCGGAGAATTGTGTCTTTGTATTTCTGCAATTCATATCTCCAAATATTTGCTGTGTTTCCTTAG\n") - f.write("AGTTTCTGCATAGCAACGATGTCAGATGATTGGACGAAATCTTCGAAACCCTCAATCTCTTCTTGTAATT\n") - f.write("CGGATAGACCAACTTTGTCATCTTCGATGACTAAATTGATTTGAAGCTTCTTGATACCAAAGCCGACAGG\n") - f.write("TACTTGTTTGGATGCTCCCCAAACGAGACCATCTTTCTCGATTCCTCGAACAGAAGCTTCAAGAGCTTTC\n") - f.write("ATATCAGTTTCATCATCCCAAGGCTTGACGTACATCGTGACAACAGACTTGGCAGCAGGCTTAACTTTGC\n") - f.write("CTTCTTTCTTCTTTTTATATTCAGCAAGCCGCTCATTTCGTAACTTCTCAGCTTCAGCGTCTTCCTCTTC\n") - f.write("GTCATCACTTCCGAAAAGGTCTATGTCGTCGTCTTCCTCCTCTTTTTTGACATCTTTTGCGAGGTTCAAG\n") - f.write("GTAACATCGGAGGCTTCAGGTCCATAAATCGAGTATTCAACTGAAGCATCACCGGGAATGCTAGAGAATT\n") - f.write("CATTGGCGTATGAACCAATATGCTTGTACCATCTAGCTGCGCTGGGGAACTTCTCTGTATCTGGGGCTGA\n") - f.write("TTGAAGGGCTTTAAATG\n") - f.write("\n") - f.write(">gi|226791374|gb|GO545726.1|GO545726 Mdas9011F11_e837.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCCTCACCATCCGTCGCAAGCGGCTGAGCTTGGTGGACAACTGGGTGGTGTACGACGGAGAAACCGAGGT\n") - f.write("GAATCCGCGGTTCTGCGCGACGAAGCACGTGAACATCCTCAAGAACAAGTGCTTGGCGCACATGACCTCA\n") - f.write("GCCAACAGCTGCAAAGGTAGTGGCTCGTCGAAAAACTACGACAACAAGAACGCGGTGTTTTATCAGATGG\n") - f.write("AAGGGTCGTACGCGACGCGGTGCTGCGCGGTGTACGACAGCAAAAGGAGGAGGGTGGCCGAGATCAAGAT\n") - f.write("GAAGGAGGCAGTGGGCGGAGTGGCGTTGGGAGTCGACGTCTTCCGCCTCATCGTGCAGCCCGATATGGAC\n") - f.write("ACGGCGGTGGCCATGTCCCTCGTCATCTTGCTTGACCAGATGTACGGGACGTCGAGGCGGTAAAAAGTTC\n") - f.write("AAATTCCTTTTACTTCGTCACCCACCTTTTTCCCCTTGGTGGATTCACATCTCCTCCTCCTCTATAAATT\n") - f.write("CTATGTTCCAAATCTCTCTTTTTTGGTTTGATCTCGTCGATCTCTTGTTGTCTCTCCGATAATCCCACTT\n") - f.write("GCGTTTATCTTTTTTCTTTTTCTTTCCTTTTTTTCTTCTTCTTTTAAATCGGAAAAAATCAATGAAGCTT\n") - f.write("GGTTTTTTCCTTTTATATAAAAAAACCAGCTTCTTTAAGTGGGATGTATATATGACTTGGAAAAAACAAA\n") - f.write("GTTTA\n") - f.write("\n") - f.write(">gi|226791373|gb|GO545725.1|GO545725 Mdas9011P03_e885.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|JQ0956 myb-related protein 306 - garden snapdragon gb|AAB23528.1| Myb oncoprotein homolog {clone 306} [Antirrhinum majus=snapdragons, J1:522, flowers, Peptide, 316 aa], mRNA sequence\n") - f.write("TTTTTTCCAGAGCAAAAGCAGATACGTAAGTATGGATATACTTTAATTAATTTACACTTTTCTGTTTTTT\n") - f.write("GATTAAGGTGGTTTTATCTTTCTGCTTAGGCTAGTTGACAAAATAAAAGGAGTACTACAAGGATGGCTAG\n") - f.write("CTAGCTACAAAGCTCAAAAGCCTAATTCCAAAGAAATTAAACAAAAGAAACCCTAATTAAGTACTCGATC\n") - f.write("ATCTTTTGTTTTAAACAAAAGAAACCCTATTTATAGTACTTGATCTTGTTTTTTTTTTGTTTTTTTTTTC\n") - f.write("AAAACAAGCCTGCACCATTCTCCAATGATATGTTGATTAGGTCTTCGTGGGCATGAGGTGCAGCATCGTC\n") - f.write("AAGGAGCCACTTCTCCAGCAATGAGAGAGGGACTTGTCCCTCCAAATTGGGCTTGCTCTCATCCTGAAAC\n") - f.write("AGACAGCTTGCCTGATCTGCTATGAAATTTGCATTGTTCTCATCCACTGACATGGACTGAGACACATCCG\n") - f.write("ATGGGGATGAGTTGAAGCTGAACAACGAATCGAAAGCCTGATCCGGCGTGGTGGTTGCGCTGTGCGCCCC\n") - f.write("TTCACTAGAAGTGCTCATTGAACGACCTCTAGTAGTTGCAGTAGCGCCACCTTTGTTGTCGTTGTCGTTG\n") - f.write("TTGTTGTTTGTTGTGAAGGAAT\n") - f.write("\n") - f.write(">gi|226791372|gb|GO545724.1|GO545724 Mdas9011K16_e863.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB56850.1| catalase [Prunus persica], mRNA sequence\n") - f.write("TGACTACTTCCCATCAAGGTTTGATCCTGTTCGCCATGCTGAGACCTTCCCAATTCCTTCTAATATTTTC\n") - f.write("ACTGGAAAGCGTGAGAAGTGCGTCATTGAGAAGGAGAACAACTTCAAGCAACCTGGAGAGAGATACAGAT\n") - f.write("CTTGGGCACCCGACAGGCAAGAGCGATTCCTCCACCGATGGGTTGATGTCCTATCCGAACCTCGTGTCAC\n") - f.write("CCATGAAATTCGCAGCATTTGGATCTCATACTGGTCTCAGGCTGACCGATCCTTTGGTCAAAAACTGGCG\n") - f.write("TCTCGTCTTAACGTGAGGCCGAGCATTTGAGGGCGATGCCAATGCAAGATGTTTGAGTATCGTGATACTG\n") - f.write("TCATACTAAATTTCGCATGTAAGTGACACGTAGCCTCAATGTAATAAGTCCGAATCGTTCGTACTATGCA\n") - f.write("ACTCCAATGTAATCCCTGTTTGGTGCCAATTATCTCCTGTTAATGGATGTGATCTGGTTGCTGTTCGGGG\n") - f.write("TTGGCGGTGTTGTCTGAGGCGGCGATGCTCGGTGATGGATGACGTTTCCGGTGGCTGGCTTGGATCTCTG\n") - f.write("TCGGTGGAGGAGAT\n") - f.write("\n") - f.write(">gi|226791371|gb|GO545723.1|GO545723 Mdas9011M03_e871.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD28640.2| geranylgeranyl hydrogenase [Glycine max], mRNA sequence\n") - f.write("AGATACTATTACAATGATATTTTGAAGGAGAAATTTTACAACGATTCTAAAACAATGACGGACATAGAAA\n") - f.write("TTTATATATGCTAGATCTCATTACACAAACTTGGAATTTCCACTCAAATCTGTTGAATTCAAAGAGTTCA\n") - f.write("TTCCTCGTTACATGAGGAAAAACAAAAAATTACACAAACAACAAGGCTTCCTCCTTTCATACAGTAATTT\n") - f.write("TCTCCATCTCCCTCCTGAGTGCATTAGCCCTAACCAAGCTCCCAATGGTATTCACAGCCAACTTCAAATC\n") - f.write("CTCCCACGGATTCCCCGGCACCACCCTCTTGTACAAGTAGCTATCGAACGTCATCTTCTGCACGTACTCA\n") - f.write("TCCGCACACATCTCCACGAACGCTTCCCTCGCGGGGTTCGACCTATAGAACACCTTCTGCAACACATCCA\n") - f.write("ACACCTTGTAAGTAGGCCAATAGGTCTTGTCCCACTTCTCCAAGTACGTCCTCAAGTCCGCCTCATTCAC\n") - f.write("CATCCTCTTCCCATTCTCCGACCCCTCAACTATCGCCTCGGCACACATCCTGCCACTCTTTGCTGCAAAG\n") - f.write("TAGATGCCTTCACCAGAACACTTTGTTACGTACCCTGCTGCATCACCAACGAGTGCTACTCTGCCCGCC\n") - f.write("\n") - f.write(">gi|226791370|gb|GO545722.1|GO545722 Mdas9011K05_e859.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD33072.1|AF149251_1 secretory peroxidase [Nicotiana tabacum], mRNA sequence\n") - f.write("AGAAAACCATGGCTTCTTCTTCTTCTTCCAGAATTCTCTTCTTCTTCTTTGCTTTGCTTTCTCTCTCAGC\n") - f.write("AGTTTCTTGCTTTGCTGAGAGCAATGAGCAGGATCCAGGTCTTGTCGTGGACTTCTACAGGGACACGTGT\n") - f.write("CCTCAGGCTGAAGAGGTCATCAGAGAACAAGTTAAGCTTCTCTACAAGCGCCACAAGAACACCGCCTTCT\n") - f.write("CTTGGCTCAGAAACATCTTTCATGACTGTGCTGTCCAGTCATGTGATGCATCTCTGCTGCTGGACTCAAC\n") - f.write("AAGGAGATCGTTGTCTGAGAAGGAGATGGACAGGAGCTTCGGTATGAGAAACTTTAGGTACATTGAAGAG\n") - f.write("ATTAAAGAAGCTTTGGAGAGGGAGTGCCCTGGTGTTGTTTCCTGCTCAGATATTCTTGTCTTGTCTGCAA\n") - f.write("GAGAGGGTGTTGTTAGGCTAGGAGGCCCATTCATTCCTCTTAAAACTGGAAGAAGAGATGGAAGGAGAAG\n") - f.write("CAGAGCTGAGATCCTTGAGCAATACCTTCCTGACCACAATGAGAGCATGTCCGTTGTCCTTGAGAAGTTT\n") - f.write("GCTGACATGGGCATTGACACCCCCGGTGTGGTCGCCCTTCTAGGAGCTCACAGCGTTGGAAGAACACACT\n") - f.write("GTGTGAAGCTGGTGCACCGGTTGTACCCAGAGGTTGACCCTCAGCTCAACCCTGATCATGTCCCTCACAT\n") - f.write("GCTCAAGAAGTGCCCTGATGCTATCCCCGACCCCAAAG\n") - f.write("\n") - f.write(">gi|226791242|gb|GO545980.1|GO545980 Mdas9008A15_e557.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F86339 protein F2D10.18 [imported] - Arabidopsis thaliana gb|AAF80615.1|AC069251_8 F2D10.18 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGACTAATCGATGATTAAATGCTTAATTGAAAATAAGTCACACACT\n") - f.write("AACTTGCATAATAAGAAACTAACGAAAGCGTTATGTTACGAAAGCAAACTGAAATTCATTGAACATAAGG\n") - f.write("AGGATCATTAATTACAAACACAACGAGTTGGGAATCAAGGGGAGCAGACAATCTTCAAACTTAATCCGAT\n") - f.write("TTTCGTTTGTGTTTTTCCTAAATCTAATCCCTAAAAGCAAAAGTAGAGAGCCAGCAACTTATCCATAGTG\n") - f.write("AACACGAAGTGCAGGCAGGCCTTTCAATTATCCTCTAAGCAACCCTACACACATTGCCTCTCCCCCTCCA\n") - f.write("TTTCGATTCCCCTACTCTCTACTCATCGTCATCTTCCTCCTCGCCGCTCTCATCCTCGTCTTCATCATCG\n") - f.write("TCATTTACCTCAGACTTGGACTTGTCAGACTCTTCTTCATCAGCTTCGTTATTTCCATCAGCTAATTGCT\n") - f.write("TGTTGTATGCCTGAATGTTCTTGTTATATTCTACCTTCCGCTTGTCTGCCTTGGCTTGATAGGGAGCTTT\n") - f.write("CTCGGCATCTGACAACGATTTCCATTTATCGCCAC\n") - f.write("\n") - f.write(">gi|226791241|gb|GO545979.1|GO545979 Mdas9007P01_e546.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD29671.1|AF126402_1 major allergen Mal d 1 [Malus x domestica] emb|CAD10375.1| allergen Mal d 1 [Malus x domestica], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGATTAAAAAGTAATTTCATTATATTTATAGAAGATAATACAC\n") - f.write("TCCGTTCAGTCTGCAACTTTTTTCCAAACAAAGACATCAATAGCAACAAGAAGATCATCACAACCATAAC\n") - f.write("ACTTATTTTTCAAGCCCAAACTGCCCAAACCATGGTTATTACTTTTGGCTGACGTGAAAAAAACATACAA\n") - f.write("AGAAAAGCCACACAACCTTCGACTGACCATATAGTAACGGTAACACCCAAAACACCATAGATACTTATGA\n") - f.write("TTAATTTAGTTGTATGCGTCGGGGTGGTCCTTAAGGTAGCTCTCAATAAGTTTGAACAAACCATGGGCCT\n") - f.write("TCTCTTTTCCAGCCTTGACGTGCTCTTCCTTGATTTCAATGTTTCCCTTGGTGTGGTAATGACTGATGCT\n") - f.write("CTTGATGGTGGAACCACTTCCACATGCCACCAACTTGGTCTCGTAAGATATTTTCTCGATGGTGTCTGTC\n") - f.write("AAAGCATCTCCTTCAATCAAAGTGTAGGAGTATGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791240|gb|GO545978.1|GO545978 Mdas9007L15_e532.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAG13395.1|AF283006_1 cold acclimation protein WCOR413-like protein [Oryza sativa (japonica cultivar-group)] gb|AAP50941.1| putative cold acclimation protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGACTAGTTCTCTCTTTCTAGTAACTCTGTTCCTGTCTTCCCCTGTCCCTGTTCCTCTAGATGGCAA\n") - f.write("AAAAACAGAGCTACTTGAAGATGATGACTGAATCTGATGCCGCCGATTTGATCAGCAGCGATTTCAAAGA\n") - f.write("GCTCGGCGCTGCTGCTAAGAAGCTCGCCGGCCACGCCGTCCGCCTCGGCAGCTTGGGATTCGGAACTGCT\n") - f.write("TTTCTCAAATGGGTTGCTTCGTTTGCTGCAATCTATCTGTTGATCTTGGATCGAACAAACTGGAAATCGA\n") - f.write("ACATTCTTACAGGGCTATTGATCCCCTACATTTTCTTTACCCTTCCTTCAATATTGTTCAACATCTTCAG\n") - f.write("GGGAGAGATTGGAAAATGGATTGCTCTCGTTGGTGTTGTCTTACGGCTTTTCTTCCCTAAACGTTTCCCA\n") - f.write("GAGTGGCTGGAATTGCCCGCAGCGTTGATTCTTCTTATAGTGGTTGCTCCTAGTTTATTTGCGAACACTC\n") - f.write("TGAGAGGCGACTGGATTGGTGTTGTAATATGCCTTCTCATCGCCGGTTATTTGCTGCAAGAACACATCCG\n") - f.write("GGCAGCTGGTGGGTTCAGAGACGCTTTCACCAAAGCTGGTGGAATATCGAA\n") - f.write("\n") - f.write(">gi|226791239|gb|GO545977.1|GO545977 Mdas9007P21_e554.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T09642 hypothetical protein precursor - alfalfa gb|AAB41813.1| unknown protein [Medicago sativa], mRNA sequence\n") - f.write("CATAGCCCACATTCAATATTACTTAAATCTGAAAACTTAAATAGCTTTCTGGTTGAAAATATAGCACTGC\n") - f.write("AGTCTGCAAACTTAAATAACAGTAACACATCTGCCCTCAGCAACGGCCAAATTTACAAAATGTCCGAATC\n") - f.write("ATATTACCCGTTGCACAATCTCTATAATGATGTTCTAGTCTTATGATGATTTAACCAAAAAAACTAGCAT\n") - f.write("TTAAGCAACAGGGGAGACCTTAACTTCATCTAGGATAGGGCCACAAAGAGCTCCATAGTCCTTGGTGTGG\n") - f.write("TAAAAGGAGCTGAAAAACGTGATTCTGGTCCTGATTGAAACCGCTTTGAAACTGAAACTGGCCTTCTTGA\n") - f.write("ACCCGCCTTTTCCTTTGGAGGCGAAGGGAACTTTGAGCGTGTCCTTGCCGGCAAATGCTTCAACCATCAT\n") - f.write("TGATCCTTGGCAGCCGTTTCTTGCATCACCGACGGTGAATGAGAGGCTGTAGAGCTTGTTGGGAACTGTT\n") - f.write("CTAATAATCTGGGCTATGGCGCTTTCTCTCCCCGCAACAAGCTCAACTGCGCCCTTTCCGACTGGAACAT\n") - f.write("TGAAGTGATTGGAATCG\n") - f.write("\n") - f.write(">gi|226791238|gb|GO545976.1|GO545976 Mdas9007C05_e494.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27880.2|AF139468_1 photosystem I reaction center subunit III [Vigna radiata], mRNA sequence\n") - f.write("CACAAGCATTTGGTACATTAATTCCAAGTAATTTTACAAATTATACAAAAAAATTAAAAACAAATAAAAA\n") - f.write("AAAAAACCTCAAACGTCCTTGGCAACAAGTTCACCATTCACTAACTCTCTGTAAGCACCCACAGGCCAGC\n") - f.write("TAAACCCTCTGAAAACCAAGCTAGTACCCAAAGGCACATCAATGATGATCTCCTTCTGTGTCGGCTTCTT\n") - f.write("ATCATCCCTAAGGGCAATCAAGTACCTCCTCCCAACCCACCCAATCCACCCAGCAATGTACAGGAACAAA\n") - f.write("ATACCAGGCGTGATAAACTCACCCCAGTGCCTCGGGTCACCGCTGACAATCAAAGGGGGGAGCCCATCCA\n") - f.write("ACCCACAAAGCAAACCCTGCTTGCCATAGTTGGAAAACCCCCTCTGAGTCTTCTCTATGGGGGCCTTGAT\n") - f.write("GGCTAGGGCGGGTGCACTGTCGGGTGCATAAAGCTTCAGTGAGGACTCGAGTTTTTTGATCTGCTGCTTC\n") - f.write("TCACGCTTGGCAAACTGCTTGGAGTCTTTGCATGGGGTGAGTCCCGAGATGTCACCAACTGCAGGCATGG\n") - f.write("GGGCCGAG\n") - f.write("\n") - f.write(">gi|226791237|gb|GO545975.1|GO545975 Mdas9007N06_e540.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|A85097 neutral invertase like protein [imported] - Arabidopsis thaliana emb|CAB78074.1| neutral invertase like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("GTTTATAGTTTATATTATTTTCAAATTAAAAACTCATTTGATAATACTAAACAAAAAGTATCTTCATCAC\n") - f.write("TTGATCTAACGCACATTTGAAAAAAAAAAAAGTATATGTGTTTAAATGCTTAATGTTCCACATTCCCACC\n") - f.write("AAATATTGACATACCCAAAGTGTTCGCATACAAAATCGAAATTAAAAGGTCCATGAAGCAAATCTTTTAA\n") - f.write("TAAGGGGTTTCATTTGCTCGTCCTCCTCCAATGCTATCATGCCCAAATGAAACGGGTCTTCCAGCATCAT\n") - f.write("CTTCGCCACCAAGTACCCCGCGATCGACCATGTCTGGTACTTCCGTGCCTGCTTCCCCATGAACCTCCCT\n") - f.write("AGCTTCCCATCATAGTACTCCGGCCACCCATCTTTCGACAACCGGCTTTCCGCCAGCTCGATCGCACGCC\n") - f.write("TTGCAATCTGTGGCCGGCCGGTCTTTATGCATGCCGCGGTTAACAACCACAGCAGTACTGGCCAAGAGCC\n") - f.write("TCCATTGTGGTAACTCCATCTAGTATTCTTTGGATCACAGCCAGTAACAATCCTCCACTCATGACTTTCA\n") - f.write("AATGCCGGATAGCAAATCTTCAAC\n") - f.write("\n") - f.write(">gi|226791217|gb|GO545974.1|GO545974 Mdas9007J24_e522.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T06386 probable malate dehydrogenase (EC 1.1.1.37) - garden pea gb|AAC28106.1| nodule-enhanced malate dehydrogenase [Pisum sativum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTGCAATTGAAAAGTATGAATTCACATTCTTCGAATTTATTTTC\n") - f.write("GCATCAGAAGCTAGCCCTTGCATACACGCAAGATAGAAATACATGATATTCCTAAAAACTCATGATCGAC\n") - f.write("CAGCCAAGTTATTTCAAAACTGTCACTACAAGTTTCCGCCCGCAGAAGAAGGCTTCTATTCTTCAATCTA\n") - f.write("CAACAATAGAAGCAACTCTGTATTTCTTCCGAAAATAGCTTCAACATAGAACACTGAAAGGATACCGACT\n") - f.write("TCATTCTACAAAACTGAAAGTACTGATGCATTGCTAAATCTGCTAAAAAATATCTGTAAAGCATTCATTA\n") - f.write("GAATGAGGTAATAGAAGCTTCTGATAATAGCGACCTAAGCAGTCACGGTCTGCTTGTTGGCAAAAGCAAT\n") - f.write("ACCCTTCTCAATGCTGGCTTTCAGTTCCGGCTTGAGTGCTTCCAACGCCTTTTGCTCATATTATGTCAAA\n") - f.write("CCTTGGAGGTCAGACGGTATGAAAGCTTCAATTCCATTCCTTCCAAGCTTAACCCTTGATGCAAAGAATG\n") - f.write("GAAGCTCGGTCAG\n") - f.write("\n") - f.write(">gi|226791216|gb|GO545973.1|GO545973 Mdas9008C01_e568.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46280|EFT2_SOYBN ELONGATION FACTOR TU, CHLOROPLAST PRECURSOR (EF-TU) pir|S60659 translation elongation factor EF-Tu precursor, chloroplast - soybean emb|CAA61444.1| EF-Tu protein [Glycine max], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTGATGAAACCTACAAGATATATAACATTTCAAGGTGGAAATTGC\n") - f.write("TTCCAAATGTCAAAAACCCGATAAAAATTGAAGCTGAGAGAGTTCAAGTTGGGCACCAAATTGCCAAAAC\n") - f.write("AAGTTGAGACCACCCCATAATTTGTATTTTCTATCACTCAATAATGGATTGAATAACACCAGCTCCAACA\n") - f.write("GTCTTCCCTCCTTCTCTGATGGCAAACCTCATCCCCTGCTCGCACGCCACCGGAACAATCAGCTCGACCA\n") - f.write("CAATCTTAACGCGATTGCCAGGCATCACCATCTTCGACTCCTCATCCTTATCGTTCATAATCGAAGTCAC\n") - f.write("CTTCCCGGTGACATCAGTAGTCCTCATGTAAAACTGCGGCCTGTAACCCGAAAAGAACGGTGAATGCCTT\n") - f.write("CCCCCCTCTTCCTTCTTCAACACATACACAATCGCCTCGAATTTGGTATGCGGGGTAATAGTCCCGGGTT\n") - f.write("TGGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791215|gb|GO545972.1|GO545972 Mdas9008B06_e562.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_186898.1| pentatricopeptide (PPR) repeat-containing protein [Arabidopsis thaliana] gb|AAF32456.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCGAACAAACGCTCTGCTACATTATCCTCGTGAAAGACATTACAA\n") - f.write("GATACAGTCTAACAAAGCCTAAGCAGCCACCGCCGTGGGAGCAGCACGTTCTCCAGATTTTGCAGAATAA\n") - f.write("AATAGATCCAACACATCAGCATGGTTGCGGATGTAGCCTGGACATTTGGAAAGGAAATTCTGTGCTTCAC\n") - f.write("TGTGCCGTCCAGCCTTGAAATAAGCTTCAAATACATTGAGGAAGACGGTGGTAGATGGAAACCTCCTTGA\n") - f.write("AGTCATCGCCTTCAGGAAAGCTAAAGCATCTTCACCTGTTCCAGACTTTGATACATACTCAACGAATGGA\n") - f.write("TCAATAAAAGGAGGGAATCCATGATTTTTCATCATACCCAGAATATTCAGAGCATCCTTGAATCCACCCT\n") - f.write("GAACCAATAACTTACTTATCAACAACTTGTATGTGGTATGCCATGGCTTGAGTTGCCCTTCATTGACCGA\n") - f.write("ATCATTGAGTAACTTGTATGCATCTATCGCACTGTTTTTTCTGCAATATGCATCTACTAATATATCAAAA\n") - f.write("GCATAACCAGCAGAGGCAGC\n") - f.write("\n") - f.write(">gi|226791214|gb|GO545971.1|GO545971 Mdas9007I09_e517.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566842.1| pectinesterase family [Arabidopsis thaliana] dbj|BAB01985.1| pectin methylesterase-like protein [Arabidopsis thaliana] gb|AAL49785.1| putative pectinesterase [Arabidopsis thaliana] gb|AAM20211.1| putative pectinesterase [Arabidops, mRNA sequence\n") - f.write("TCCAGTATTTTTTTTTTTTTTTTTTTTAAGGTCCAAAGGGAAAGGGGTTTTTTCATCACAAGAAAAGTAC\n") - f.write("CCACATTAACCATCCATGTTGCAGGCCAAAGATGAATACACATAACACAACAAGTTGATCTATATTATCC\n") - f.write("TGGACAAACCTAAAAGCCAAATCAAACGAATTCTTCAGCACAAGCAATTACATCTGATAAACGCTAAAAG\n") - f.write("TGACCGTGTAACGCCTCTTGCACCTTGAGAACACAGGATTTGAAATAGCTATGTTGCATATCTTATGCTT\n") - f.write("TCGTCGTAAAATGTTTTCAATATACTCGACTATCTTTGTTGGGATCATTCCCATGTTTTTAACTCCTAGG\n") - f.write("CAGAATACGGTATTCTTAGGGCCATTCTCTGAGCAAGCCAAGGCCTTCCTGGATCAGGATCAATGAAACG\n") - f.write("ATGCTGGAGGAACTGGTCTGCTTCCTCATCTACCAGCTCTCTTGCCCATGTCACCCGTTTTGATGGGCAA\n") - f.write("CTACCCGGTCCAAAATACCTGTATTCATAAAAGCAAGCAGTTCGTTCATTCTCTGTTTTACCCCAATTAT\n") - f.write("TCCATCCTAC\n") - f.write("\n") - f.write(">gi|226791213|gb|GO545970.1|GO545970 Mdas9008B18_e567.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P24226|HISX_BRAOC Histidinol dehydrogenase, chloroplast precursor (HDH) pir|A39358 histidinol dehydrogenase (EC 1.1.1.23) precursor, chloroplast [validated] - cabbage gb|AAA32991.1| histidinol dehydrogenase, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGCTTTTTTAGAATTCACTTGCATTTTCATAAAGATTAGTTTCAAAA\n") - f.write("ACACTTCCAAATGAACCCCAACGTTTATTGAAATTTGGGGAAAAAGAAGGAAAAAGGAATGCTTCAAAAG\n") - f.write("AAAGAAAACATTACCAACCTAGAACAAAGTTTAATGGTATTCCACCCACCAGTTTTGCTCTATAGTACAA\n") - f.write("CGATCAAAATTCAACCACCGCAGATTTTTCAATAGTAGCTGGTACATCCCCAAAAACGGCAATTTGCCCC\n") - f.write("AAAGGGGAGAACAAATTTGGCAAATGCTCTTGCTGCGAAAATCACCTTATGTTAGGACCTGCCGGGCTTC\n") - f.write("GATATCCTTAAGTCTAAGGGTTACAGCTCTCTTGTGCGCCTCTAGTCCCTCAACTTCGGCCATGGTAGCC\n") - f.write("ACATATGGGCCGAGCTTTTGCAAACCTTCCTCTGTCAAAGACTGCACTGTCATGTACTTGAGAAATGAGT\n") - f.write("CCAA\n") - f.write("\n") - f.write(">gi|226791191|gb|GO545969.1|GO545969 Mdas9007G16_e507.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191183.1| copper homeostasis factor (copper chaperone) (CCH) [Arabidopsis thaliana] pir|T47741 copper homeostasis factor [imported] - Arabidopsis thaliana gb|AAC33510.1| copper homeostasis factor [Arabidopsis thaliana] emb|CAB87423.1| copp, mRNA sequence\n") - f.write("CAACACACTGACTCTCTTCCATTTATTTATACAGGAATCATACAACAAGTTCAAAGAAAAACATTGGGGG\n") - f.write("TTTACAAACAAGTAAAAGTTTAACGAGGACTTAATAGTCTATGACGTTGGGGTTCACCGATGAAACACAT\n") - f.write("ATTAAACGACATTGAATAGGCAAAACACTAAGCTAAGCAGCACCCACAGTTTCTGCAGGCTTTGCTTCCG\n") - f.write("GTTCTGCTGGTGCCGGTGCTTCTGCTTCCCAATAAGCAGTTTTCTTGCCAGTTTTGGAAACAGTTTGCAG\n") - f.write("CACTGTCTCGGGTGGTAAATTGCTTTTCACTGTCACCTTCTGAGCGTCAAAATCTATGTCATATGATTCT\n") - f.write("ACACCTTCAAGTTTGCCAAAAACCCGTTTGACGGCCCCAACACAGCCTTGACACGACATACCAACCTTGA\n") - f.write("GGACCGTAGTAGTCTGTGACGCCATGTTAGGGTATTTGGGATTTCAAGAAAACTGAGGAAAAATTGAGAA\n") - f.write("ATTTTGTTATGGATTTGATTGGATGCTGTTGTGCATCTGGTCAAACCCAAATGGTCCTTTTATAACAGAG\n") - f.write("AATAAAAA\n") - f.write("\n") - f.write(">gi|226791190|gb|GO545968.1|GO545968 Mdas9008E01_e576.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564534.1| chorismate synthase (5-enolpyruvylshikimate-3-phosphate phospholyase), putative [Arabidopsis thaliana] gb|AAL09759.1| At1g48850/T24P22_3 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTCAATTGAATGAAATTTATTCAGTTTCAAAGTCTAAAACACATAATTCTGGGATTAACAGTACCTCCCC\n") - f.write("CGGATAAAAAAAAACCTTGTTTCACATATTTAAAAAAAATAACTGCAGTAATGATAATAAATAATAATTT\n") - f.write("TATTGGCTCGGAATTACTTCTACAGATTGAATGATTGAAAAAACTTATTTTTGAAAAAAAATGGTCCACA\n") - f.write("CACCTCACATATATTCCAGTCTGACAGCGTCTCACTAATTCTAACTTGCCGTTTCACACCAAACATGCGT\n") - f.write("TTCATGACGATGAATTTTCACTGTCCGAAACAAAACATAAATAATGCTATAAAACGTTTGTCAACCTTCA\n") - f.write("AATGTGCACACCAGCTGCCTCCGCTGCTTCAACCACTTGCGGCGGCACAGGGTCTTGTAAGTCAACCATT\n") - f.write("GGCTGTGGCACAAGGTCTTGTAAGTCGGGATTGATAGGAAACATGTGACACTGTGCAAAATCTGCCATTA\n") - f.write("GTTGGTCCACCAACGCA\n") - f.write("\n") - f.write(">gi|226791189|gb|GO545967.1|GO545967 Mdas9008H24_e600.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAB87573.1| chlorophyll a/b binding protein of LHCII type I precursor [Panax ginseng], mRNA sequence\n") - f.write("ATCCCCAATGTTTACTATGGCTCTCTCATCCCCATTCACTGGGAAGGCCATTCCTCTTAACACACAGACA\n") - f.write("GAGTTCACAGCTGTCCAAGGAAATGGTAGGGTTTCTATGAGGAAGACGGGCAAAAAGCCTGCTGTCTCAT\n") - f.write("CAGGGAGCCCCTGGTACGGCCCTGATCGTGTCAAGTACCTCGGACCATTCTCCGGTGAGGCTCCATCTTA\n") - f.write("CCTAACCGGTGAATTCCCCGGTGACTACGGGAGGGACACTGCTGGGCTATCAACAGACCCCGAAACCTTT\n") - f.write("GCCAAGAACCGTGAACTTGAAGTCATTCACTCAAGATGGGCAATGCTTGGAGCTTTGGGC\n") - f.write("\n") - f.write(">gi|226791188|gb|GO545966.1|GO545966 Mdas9008H20_e599.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T51178 actin ACT2 [imported] - Striga asiatica gb|AAC49652.1| actin [Striga asiatica], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTAGTCAATGATCACTGTGAACACAAATATATTCAGCAAAATTACAGATAATCCA\n") - f.write("GCGGCAAACCTACAAAGTCATCGTCCAGACATTTTAAGTAACATAAAGCGAAATAAAAACGGACAACAAA\n") - f.write("ACCAGAGAGCAAGAATGCAAGCAGCATTTTCTTTCCATTATCATCACTCCGCCTATCGTTGATTGTTCTC\n") - f.write("AGAAGCATTTCCTGTGCACGATTGAGGGACCGGATTCATCGTACTCAGCTTTGGCAATCCACATCTGCTG\n") - f.write("GAAGGTACTGAGGGAAGCTAAGATAGAGCCTCCGATCCAGACACTGTACTTTCTCTCTGGTGGGGCAACC\n") - f.write("ACCTTGATCTTCATGCTGCTTGGGGCCAATGCAGTAATTTCCTTGCTCATTCGGTCAGCAATTCCAGGGA\n") - f.write("ACATGGTTGAACCACCACTAAGAACAATGTTGCCATACAAATCCTTCCTGATATCGACATCGCATTTCAT\n") - f.write("TATGGAATTGTAAGTGGTCTCATGAATACCAGCAGCCTCCATTCCGATCATGGATGGTTGGAAGAGGACT\n") - f.write("TCTGGGCA\n") - f.write("\n") - f.write(">gi|226791187|gb|GO545965.1|GO545965 Mdas9008F01_e585.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172184.1| mitochondrial carrier protein family [Arabidopsis thaliana] gb|AAM98208.1| mitochondrial carrier protein, putative [Arabidopsis thaliana] gb|AAP42736.1| At1g07030 [Arabidopsis thaliana], mRNA sequence\n") - f.write("CGATTTTCCTATTCGAACTCATTTTCCTGATTTTGAATCGCTTATTTTTTTTTTCGACAATTTTCTCCGC\n") - f.write("GAAGTTTGAACCCCATCTTGTACTACACCATTCACCATGGCGATTGACGCCTCCCCTGCATTCCAAACCG\n") - f.write("TCACTCAACCCCACGACTTCCGGCCAGAAATATCAGCATCCCCCTCCTCCGCCCATGACGGCCTAGAGTT\n") - f.write("CTGGCAGTTCATGATTGCCGGCTCCATAGCGGGCCTAGTTGAGCACATGGCTATGTTCCCAGTTGACACG\n") - f.write("CTCAAAACCCGCATGCAGATTTTTGGCGGGTCCTGTTCCGTTCAACCTATTGGCGTTAGACGGGCCCTTG\n") - f.write("GCTCGATTCTGAAGCTCGAAGGCCCCGCAGGGCTCTACCGCGGCATCGGCGCAATGGGGCTCGGAGCAGG\n") - f.write("ACCTGCCCATGCA\n") - f.write("\n") - f.write(">gi|226791167|gb|GO545964.1|GO545964 Mdas9008H06_e596.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565841.1| hydrolase, alpha/beta fold family [Arabidopsis thaliana] pir|H84778 hypothetical protein At2g36290 [imported] - Arabidopsis thaliana gb|AAD21437.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTACCAGCAACAATCCTAGTTTCACACAATTATTTCTCAAATCCAACTTTCAAAATTCAATCCCTAA\n") - f.write("GAAGCAACTGCATTATGATGCAACAATCTATAAACAGAGTTGGCCGGTACAAGATCTATCATACATACCA\n") - f.write("AACTGACTAACTGAAATTCAGTAACTCCGTATTGGAGAAATGCACAGAAAAGTTCACCCCGAGGTAGCTC\n") - f.write("GTTACGTAAGAGGAAATGTTTACTATCCGTCGGTTAAAAGTGCCTTGACAATGGTCTCGCACATCCCATC\n") - f.write("AGCAAGTGGCAACAAATGTCCAGCACCTGGTATCTCATGATAGTGGATCCATGGAAGCTGTTCAGCAATG\n") - f.write("TAGCGTTGCAGTAAAACGGGTACCATGCGATCTTCATCTCCATGCCACACGTGGACAGAAGCTTCATTGT\n") - f.write("TAGGGAATGGGTTTTCCAGTTCCAGAGGACTGAATTCCCAGGTCCCAAATCCAACATTCATGTCACGGTA\n") - f.write("AATGGACTCAAATTCTCCCTGCTGTCGTACCTGTCCCGCATATGGTTCTCTTTTTTGAAGCTTGGGCAGG\n") - f.write("ATTTCTTTGTCTTGGTCAGAAAGACAATCTATACTTCGAGCCAGAACACTTGAACCAGGAAACCATTTTT\n") - f.write("GAGTGTTCCAGA\n") - f.write("\n") - f.write(">gi|226791166|gb|GO545963.1|GO545963 Mdas9008P12_e635.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TAAAACACCAAATTCTAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGA\n") - f.write("CAGAGGTCTTGAAAGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACCAGA\n") - f.write("CTCATAGAGCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCT\n") - f.write("GCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAAGCTCCCTCTCCGGAATCGAACCCTAATTCTCCGTCA\n") - f.write("CCCGTCACCACCATGGTAGGCCACTATCCTACCATCGAAAGTTGATAGGGCAGATATTTGAATGATGCGT\n") - f.write("CGCCAGCACGATGGCTGT\n") - f.write("\n") - f.write(">gi|226791165|gb|GO545962.1|GO545962 Mdas9008K24_e611.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GCGTTTCAGACGTATAGTTGATTGCTTCAGAACAGACATATCTCAATGAGATAGAAGACGGAGAGCAGAC\n") - f.write("CAAGAGCGTAATGGTGGAGGTTAACGGTCTGTCCCTTCCTGTTGGGAAGAACTTTGCCATGTCTTGGCAA\n") - f.write("ATGGGGATCAAGGCTTGATTTGCTATACGATATGTGCCCTTTATTTTGAGCTAGCTAGTTTTGGTCCTCT\n") - f.write("AATTTACTTGTTCTGCAGCCATTCGGGCGGAAATAGTTGATGTCTTTAGAGTTATTATCGCGGTT\n") - f.write("\n") - f.write(">gi|226791164|gb|GO545961.1|GO545961 Mdas9008E17_e582.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566086.1| expressed protein [Arabidopsis thaliana] pir|T02683 hypothetical protein At2g46820 [imported] - Arabidopsis thaliana gb|AAC33500.1| expressed protein [Arabidopsis thaliana] gb|AAL38332.1| unknown protein [Arabidopsis thaliana] g, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGTACGTAAGTGTACTTTTATCATTTATTTCTATAATAAAATATCG\n") - f.write("GAAGCATCGCGATATGAATTACAAGGAGCTAACAGGGAAACAAATGACAGTAGTACTAGTTACATATATC\n") - f.write("TCGCAGACAAAGTACATACATAACATTAAGTATAACTTTGGTCAGAATATGCTTCTGCAAACAACATGAA\n") - f.write("GAATGTTCACTTCTTTTGCGGACAATGCTGCGAGATATTTACGTATGTAGATAGAAGCTTCAAAAACCGG\n") - f.write("CCACGATTTCATCTCATCTCAGCAGCAATACTTTTCGGTTTGTTCTAGCTGCTGCCGATTATATCTTTGT\n") - f.write("ATGTGCCCTTAATCTTCTGTGTCAAGGCTTCTCTGTCTGGTTTGAAAACAAGGTTCTTGTATGCAAACCA\n") - f.write("CCCAGTGTAACCAATTCCTACAAGCTCAAGAACACCAGGGACTAAAGGAAGCCTATCAATTGCCGAGATC\n") - f.write("ATTCCACTGAAGCCCCATACTGCAACAGCAACAGCTACTGCAAGTGAAGACACTGCATATTTATCTTCCA\n") - f.write("CTTTCTCCCAAGCTTCTTGAACTGTCTTCACAATCTCTGGGGGCTCAGCTGTTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791163|gb|GO545960.1|GO545960 Mdas9008H07_e597.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO42863.1| At2g36290 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTACCATCTACAATCCTAGTTTCACACAATTATTTCTCAAATCCAACTTTCAAAATTCAATCCCTAA\n") - f.write("GAAGCAACTGCATTATGATGCAACAATCTATAAACAGAGTTGGCCGGTACAAGATCTATCATACATACCA\n") - f.write("AACTGACTAACTGAAATTCAGTAACTCCGTATTGGAGAAATGCACAGAAAAGTTCACCCCGAGGTAGCTC\n") - f.write("GTTACGTAAGAGGAAATGTTTACTATCCGTCGGTTAAAAGTGCCTTGACAATGGTCTCGCACATCCCATC\n") - f.write("AGCAAGTGGCAACAAATGTCCAGCACCTGGTATCTCATGATAGTGGATCCATGGAAGCTGTTCAGCAATG\n") - f.write("TAGCGTTGCAGTAAAACGGGTACCATGCGATCTTCATCTCCATGCCACACGTGGACAGAAGCTTCATTGT\n") - f.write("TAGGGAATGGGTTTTCCAGTTCCAGAGGACTGAATTCCCAGGTCCCAAATCCAACATTCATGTCACGGTA\n") - f.write("AATGGA\n") - f.write("\n") - f.write(">gi|226791162|gb|GO545959.1|GO545959 Mdas9008O13_e631.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TGCAGAACGACTTAGGAAGAGAAGGATGGGAACTCAACGTTTGCCCTCGTTAAACCTCTAAACAAAACAT\n") - f.write("CGAAGTCGTGCATTATATCAAATGATTGGAAACCGTGGTGTATTCGGTAGAAAATAAAACTGGTATGGAT\n") - f.write("TATCCAGCAAACTGCATATTGCTCCACCTGCAGATTAGCGATCAGAGAGTCGAAACAGTTCAGAGAAACA\n") - f.write("GGATAAACGATGAGAAAGTTGAGCTCTGGATCGAAAAATGTCGAGTACTATATATATATTCCCAAGTTGT\n") - f.write("TTTTGGTTGTGCAGATTGGATTGCAAGGTGCTGGCGATCAAAGCTTGTACAATGCCATAATTTAATTTGT\n") - f.write("TGTATTTCGGATTTGAGTTTGTCTTATTTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791161|gb|GO545958.1|GO545958 Mdas9008F17_e591.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_173322.1| peptide transporter -related [Arabidopsis thaliana] pir|G86322 hypothetical protein F6A14.2 - Arabidopsis thaliana gb|AAF27093.1|AC011809_2 Similar to peptide transport proteins [Arabidopsis thaliana] gb|AAL49811.1| putative pept, mRNA sequence\n") - f.write("TCGAGTCCCTTTTTTTTTTTTTTTTATAATAATAATAATTATTATTATTATTGAAATCTCTAACATCTAA\n") - f.write("TACTAAAACAGGTTGATTCGATTTGATTGGATTTTATTTGCATATATACAGAGCCATGTTTAAGCATTTG\n") - f.write("TTGAACCTAACTGCACCTGATCAGTATCATATGGCTTCTCTTCAACGTTCACATTTGTGGCCTTGTAATG\n") - f.write("ATAACGTTGCGCACAAAACAGAAAGTAGGCAAAAGTCAGAACCCCAATCCCAGCCAATAGGAAGTAAAAG\n") - f.write("TACTCCAATCTCCCAGCATTGAGGTCAT\n") - f.write("\n") - f.write(">gi|226791141|gb|GO545957.1|GO545957 Mdas9008O11_e630.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAAATGAATAGTATCATGATTGATTTTTTTGTGTAAAAATGTGGTTT\n") - f.write("TTCGTTAAAGTGAACAGTACCGTGAGCTTTTCGTTAAAGTTCCCCATAATATTTGAACTTGATCATGGAT\n") - f.write("AAAAGTCAAAACAATCACCATATGAAGGAGCAATTGCAGTAACCCTAGTTCTCAAGATAACCGAATTTAA\n") - f.write("CTGACAAACTGCATCTCTATGCTTTGAAATTCTAACATACGAACTAAATTAAATCTTTTCGGTTTATATT\n") - f.write("TTTCCGAAAATTCCTACTATTTGGGCTCCAATGGTGACTTGTCTATAATCCAGAACCTGTTTTTCTTCGT\n") - f.write("AATATATGGCTGCAACTTCCACATCCTGTTGTTTTTGCTGCGCCGGAATCCAGAATTCAGATACCCAGAT\n") - f.write("ATACTTGTAAGAAGTTGCATATCGGTTAGCAGCTAAAGACTACACTCTGTGTCCATATAGGAGGATCAAG\n") - f.write("AAAAGCCTGTTGTCTAGTCTGTGTGATCACGGAAGCGGATGATTTTGTTGATGAAGGATCTCTCACGGCG\n") - f.write("GTATATAACAAACGACGACATGCAGAAGCAAGCAAC\n") - f.write("\n") - f.write(">gi|226791140|gb|GO545956.1|GO545956 Mdas9008G12_e593.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P14278|CB24_LYCES Chlorophyll A-B binding protein 4, chloroplast precursor (LHCII type I CAB-4) (LHCP) pir|S10857 chlorophyll a/b-binding protein precursor - tomato gb|AAA34141.1| chlorophyll a/b-binding protein precursor, mRNA sequence\n") - f.write("TTTTATATTACTAAGGAGCTTGGGAGTTTTTTACTGCATACAGCGGTTTCAATACAAGCAGTTTCTAGTA\n") - f.write("AAATTGCATCAGAACTAATGGAGTCCACAACAAGAGAACCTCAACACAAGCAGTAAGTTCGGGTAATGTT\n") - f.write("ACAGATGAACGGCCATGGCTTGAGGTTTCTTCACTTTCCAGGGACGAAGTTGGTGGCGTAAGCCCATGCG\n") - f.write("TTGATGGCCACTGGGTCATCGATGTGGTCG\n") - f.write("\n") - f.write(">gi|226791139|gb|GO545955.1|GO545955 Mdas9008E21_e584.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTCATGAACATTAAATACTTGATGGGCACTGACAAAGTGCCAGAAAATACAACTAGAGACCCATATCTTG\n") - f.write("GTTACACCAGTTAATGATAAAGAAATGAAAATTCAATTCATACCCCCTGAAAAACATCTGTTTTCCTTTT\n") - f.write("ACCTTAGGAACAACTTCTGCATCCATCACACAACCACAAAGATCAACACACCCAAAAACAGTAAACACTA\n") - f.write("TCGAACTAACGGGATTAAGCTTCAAACTCCATGCCAGAAACGGGCAATCTCCTTATATCGCCGCTCCTGG\n") - f.write("ATTTGACGAAAGATAATTAGTGGAATTATCCCAGGTTAATGGTTCTGCTGTACCCAAGCTTCGCCACCTT\n") - f.write("CCCTCATGCACCGAAGGTAAACTAAAACTTAACCTCCCTTTTGCTCTATCCCCACCCGGAAAAATCGAGC\n") - f.write("TCCAACACCTTTGTTGGATTCTGCACTGAGAGTATAAAGATTCATTCAGGCCCAAGTGAACCCTCTGAAT\n") - f.write("AATTATGCTCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791138|gb|GO545954.1|GO545954 Mdas9008L04_e613.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTCCTTTTTTTTTTTTTTTAAATTAAGATATTTTAATGAACATGTATAACCAAATTTTTTATGCC\n") - f.write("AGGTAATATCTTACAGAAACAAAAGAAAATAATTTTCTTTTGTTCAATTCACAGTTTTCTTTTCCTTTTC\n") - f.write("TTTGCTTTCTGTCGAGTTTTACAACCTAATATGCACATCTGCGTGTCTAACACGTAAAAGGAAACAAAAC\n") - f.write("CCCATTTTACGCATGCAGCGGTCCCCGGCATGCCGCCAGAAACGTTTCTACAAAGCCGAAAGGGACTCGG\n") - f.write("TTCGCCACGAAACATCTGCAACGCCGCCCACCGGGTAATCAAACAAACCGTCTAAAGCCAGGTACTCCAC\n") - f.write("CCCACCAATATAATTGTTATTAGCAAATTCAGAGTCGCCACCGATTCCGAAGTCGAACGAGTCGTAACTC\n") - f.write("GGAATCATGTCGTTCTCGAACCCTACCATGCCATCCAATTCAACGGCCTCGGAGCCACTCGTGGTGAAAT\n") - f.write("CAGCAGCCTCGATTTTTCCCTCCTCACTTGCTCCATTGGTCGGTGGAAAACCAAGC\n") - f.write("\n") - f.write(">gi|226791137|gb|GO545953.1|GO545953 Mdas9008K16_e608.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P29677|MPPA_SOLTU Mitochondrial processing peptidase alpha subunit, mitochondrial precursor (Alpha-MPP) (Ubiquinol-cytochrome C reductase subunit II) pir|S23558 ubiquinol-cytochrome-c reductase (EC 1.10.2.2) alpha chain precursor - potato emb|C, mRNA sequence\n") - f.write("TCGAGTTTTCTTTTTTTTTTTTTTTTTTGCCAAAACAAATCCTGGTATATGTAATTTGGATCAAATTAAT\n") - f.write("CCTTTCAAAATTTTATTTCGACAATTGCCAACAACGGCGAATAGCTCGGAAGCCGTGAGTAGTCATGCGA\n") - f.write("TTCAAAAAATTACAGCCAGCAGGAGGCATCCTCTCATTTTGCTTGGAACCTGCTGCTAATTGAGTCGTAA\n") - f.write("CCGGGTACATGTACAACATTGCCATATGTTGCCATTGTTAGCGGTGAAGAAATAATCTTCTGCGCGATTG\n") - f.write("TAGTAATATCTTTCAAGCTCACTTCTTCTACCGTCTTCAAGAAGTGCTCCACAGGTTTCCTCTCTCCGTA\n") - f.write("TGTCAAAACCTGCCTTCCTATATCCTCTGAATGCAATCATTCTAGATTCTAGAT\n") - f.write("\n") - f.write(">gi|226791136|gb|GO545952.1|GO545952 Mdas9008O15_e632.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_190817.1| expressed protein [Arabidopsis thaliana] pir|T08450 hypothetical protein F22O6.130 - Arabidopsis thaliana emb|CAB43425.1| putative protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTCTTTTTTTTTTTTTTAAATAAATAAAACAAAGAAAATTATGAAAATTAAACCGACCACCAAT\n") - f.write("CTGTAACAGGAAAATCATGGATCATAATGTACATGTAGTTATACATAAAAGGAAAATCTTTTAATCTCCA\n") - f.write("ACCCTAAGAACTAAAAACATACTAAACAAAAAAAAGTTTCGAAAGAAGCAAACAGACACTTCAAAAGAAA\n") - f.write("AAACCATCAAACTATTTTTTGTTCCTTCCTCCCATTTTTTCACACCTCTTGAATTTTGAAAACAATGCGC\n") - f.write("CTATCGACAGATTCAAGAAGACCAATGTCATCAATCGATTGATACTCGGAACTATCATCGTCATCAAAGG\n") - f.write("AAATGTTCAAATCGAGAGACACACAAGGGCTTGTTTCCTCCAAAGCAGCAATATCCCTATTATCTTCTTC\n") - f.write("ATTTAGCCCTTCTGATAATTTTTGCTTGATAGGAGGAGAGCAAGCTCTTGATCTCGAGCTGAAGCTTTCG\n") - f.write("CAGCTCAAAATAATGATAGCATCTCCAAGACCAACTTCTTCGCCACTTGAATTGGTTATTCGTCCTCGTT\n") - f.write("CAATTGCTCTCTTAAACCCCATTTGAGAGCAGTAGTCCGCCTCG\n") - f.write("\n") - f.write(">gi|226791114|gb|GO545951.1|GO545951 Mdas9008H13_e598.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_190146.1| senescence-associated protein family [Arabidopsis thaliana] pir|T47500 hypothetical protein F9K21.180 - Arabidopsis thaliana emb|CAB75489.1| putative protein [Arabidopsis thaliana] gb|AAK62405.1|AF386960_1 putative protein [Arabi, mRNA sequence\n") - f.write("TCGTGCCGCAATCATGGTGGTTTCTCTTGCTGGGTTCGCGGGTGCGTGCTACAGGAACACCTTCCTCATG\n") - f.write("TGGGTGTACCTGTTCGTCATGTTCTTCGTCATCGCCGCCCTCATCGGCTTCATTATCTTCGCCTACGCCG\n") - f.write("TCACTGACAAGGGCTCCGGGAGGTCGTTGACGAATAAGGGTTACAAGGACTACTACCTGCAGGACTATTC\n") - f.write("CGGCTGGCTGAAGGACCGCGTGGCGGATAATGGCTACTGGAGGAAGATTGCGTCTTGTGTGAGGGACTCA\n") - f.write("AAAGCTTGTCAAAAGATCGGGAGGAGTGTGAATGGTGTGCCTGAGACTGCTGACATGTTTTACAGCAGAA\n") - f.write("AGCTCAACTCTATCCAGTCTGGCTGCTGCAAGCCACCTACAGAATGTGGATATAGCTATGTGAACGAGAC\n") - f.write("CGTCTGGACCACCGGAGCAGGTTTTTCCGGGACCAGTACGGACTGCACACTGTGGAGCAATGACCAACAG\n") - f.write("CAAA\n") - f.write("\n") - f.write(">gi|226791113|gb|GO545950.1|GO545950 Mdas9008I03_e601.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27882.2|AF139470_1 chlorophyll a/b-binding protein CP24 precursor [Vigna radiata], mRNA sequence\n") - f.write("CCGTTGTTAACGGCATTTAAGTACCAATTAAATTGAAAAGGATAAAAAAAAATTGGGTAATTATTTATAT\n") - f.write("CTACATATTGAAAAGTAAATGCCAAATGGTTTACAACCCAAGGGCACCAAGGGGCGTCTTTCCTTGCCCA\n") - f.write("CCTTCAAAGTAAAAAATGAGCATACCCACCATACCAAGCCTTGCATGCTTAATCTCACCCAGTTTCAGTC\n") - f.write("TCTCCAACTTTTCCCTGTCTGGAACGTAAACCCCGTCCTGAATGGACCCGGCAAACCCCAAGGGGTCAAA\n") - f.write("AAACTTGCCACCCGGGTACCCTTGCTCTCCGGGGGAGTTGGCAAATTTCTCCAAGGTCTTGGACCAAGGT\n") - f.write("GTGGCCCACTCAACGGACTGGGACTCAGGGTTGTAAAAGTCCACCCATCTCTTGCTTTCCACCCATCCCA\n") - f.write("TGACCAAAACCTGAATGCCAAGCAGTG\n") - f.write("\n") - f.write(">gi|226791112|gb|GO545949.1|GO545949 Mdas9008K19_e610.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTGTTCTCGGAGTCTACAAACTTGGATTCAAGAGCAAACTACGACAATACACAACGTCAATGCATGACCG\n") - f.write("ATCTGGTAAATAGTAGAAGATCCAAAATAAAGCTGTAATGTTGGCAGACGAAGACATGTTTTACTCGAAG\n") - f.write("AACAAGAGGTTTGTACCAAAACAATTAGTAACTGATTGCACAGCCATACCCCATTTGATCGAAGAGAAAT\n") - f.write("GAGATGTACACATCGCACGCAACACCTTCTCACTATAAAAGGGGTTCGTCGTCACCGTCATCTTCCATAT\n") - f.write("TATAATCATCTTCATCATCATCAACATCAAAACCCTTATAATAATCATCATCACTAAAGTCCTCCTCCTC\n") - f.write("TTGTTCCTCCTCCTCTTCATTTTCATCTTCATCCTCACCTTCACCTTCTTTCTTTTCTTTTGTATCATTT\n") - f.write("TGGCCCTGACGCTGCTCGAGCTTTTCAAATAAATCCAACTTCTCCAGCCCTGAGTTAGGATTCCATCGAA\n") - f.write("CTCTCTTTCGACCTGGCTGCTGCACCCTTGAACCTCCGGTCAGTTCTTGAGGAAATCCCTTGAGCTCCAA\n") - f.write("TATACTAAAAAGAGAACCGCGTCTTATNCGTGGTTTTTGGCTTTGTTCTGTCAGAATATCTTTCTACATC\n") - f.write("TTCGTTTTGCCTCTCATTCGA\n") - f.write("\n") - f.write(">gi|226791111|gb|GO545948.1|GO545948 Mdas9008L16_e618.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_178536.1| GDSL-motif lipase/hydrolase protein [Arabidopsis thaliana] pir|A84459 probable GDSL-motif lipase/hydrolase [imported] - Arabidopsis thaliana gb|AAD25823.1| putative GDSL-motif lipase/hydrolase [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTAAACCATTCAAATTCATAACTTATACCCAAACGCTGCCACAAATGTACTTTCACACAACATA\n") - f.write("TAATTGTTGTCTTGGGTCACTCAGAAATGGGTACAGGAATACGTACTAATATCACAGGCACCATAGGTCC\n") - f.write("ACAAGATCCTAGGCTTAATTCCATTTTTCTGCAAACAACATATTCTTCTACCAACACAGCATCGCGTAGA\n") - f.write("ATACATATATGATGACAAAGCATATATATGGCGCGTACATTTCTCTTGAATTTGAAGCTAATCAAAGGAA\n") - f.write("CTGGGCAAGTACTTTTTTCACCACATAATCAGAGATTATACGGTTTGCTTTTTCAGTAGGATGAAAGGCA\n") - f.write("TCCCAGAAAATGTATTTGCTTGCGTCTGTGCAAGTGAGCAAGTTGTTTCGATTGCATGCGTAGCCCATTT\n") - f.write("CAAACATTCCACTGGCACAACACGCCGCCGATGACACCTCGAATCCATAAAAAGAAGGCCTTCTTATCAT\n") - f.write("ATGCAGGAAAATGTAATATGGGTTTGAAAAAACCAATTTGATCCCAGGAAGCTGTTTATTCAGATTTGTA\n") - f.write("GTCAAGGTCTTCAGCTTGCCATTGAACTCTAAAGCCACA\n") - f.write("\n") - f.write(">gi|226791110|gb|GO545947.1|GO545947 Mdas9008K18_e609.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568487.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTACCTGCTAATTCGATATTCATACGCTAATGTGGTTTTAACGAGAACAACAACATTGCATTATCT\n") - f.write("GCTAATGCTACATAACGAGAACCTTTACAACTGTGGTCTGTGCAGCAATTCCTAATTCCTTGACTAAAAC\n") - f.write("TGAAGTTTCATGCCCTTTATACACGACACTCGACAGTACAATGATTTCATCGCTTTGAGAACACCACCAA\n") - f.write("GATCAACATGGACATAGACATCATGATTTTGAAACCGGAGGTTTCCCAAAAGTTTTGTCTTTCAGCAGCT\n") - f.write("GCAGCTCCACCACCACCCCGCTGTAACTGATCTTTGAGCTCTTTCAGAGCCTTGTCTCTCCGCTCACCCA\n") - f.write("TCCTTTGAAGCTTTCGTGTTTGAGCACGAGCTTCCTGGAGACAAAACTCTAATTTCAAGACCCTCTTTTT\n") - f.write("CAGTTCCTGATCAACGCGTCGTTGTTTCTCCAACTGTGATTCAAACTCCTTAGTTTTGAGCTTCCAATGA\n") - f.write("GCAGACATTACCCTGATTTCATCTT\n") - f.write("\n") - f.write(">gi|226791109|gb|GO545946.1|GO545946 Mdas9008E19_e583.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM64550.1| unknown [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGCACCCGTTTTCTCAACATTTCTGTTACATCTCTCACTTTGCTCTTCCTAAGGAGAGCTGAGATGGAG\n") - f.write("GATTGCAACAGAGGCCAAGACTATTTCTCTGCCCAAGACCATGAGTCAGCAGCTACCAACAAATATGGAG\n") - f.write("GACTTGCGCCAAAGAAGAAGCCTTTGATTTCAAAGGATCATGAACGTGCCTTCTTTGATTCAGCAGATTG\n") - f.write("GGCACTATGCAAGCAAGGTGCAGGGGTGAATCCGAAATCAACAGCAGCAGTGGAGACCTTACAACCAAAG\n") - f.write("CTCCAGAGAACTCCACACCAGCAGCTCCCCCCAAGGAGACCTGCTTGTACATCTGGCCATGAATGATATG\n") - f.write("CAGCCTCGGAGCATAGAGTCGTCGAGGGCTCAAAGTAGTTTGTTGTTTGAGAGGATTAATGTTGATGACA\n") - f.write("AAGCTATATATATAACAAGCATCGGAATTGGCTGAATGTAATAATTGTCAGTTAGTCTTTTTTTTATTTT\n") - f.write("TTATTTTTTTATTTTTAATAAG\n") - f.write("\n") - f.write(">gi|226791108|gb|GO545945.1|GO545945 Mdas9008K07_e607.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTTTTTTTAATAATAAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCG\n") - f.write("ATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAG\n") - f.write("ACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCAC\n") - f.write("AATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAG\n") - f.write("CGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTA\n") - f.write("GGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTC\n") - f.write("CACATTGTCCAGTACCTTCCATCTTAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCT\n") - f.write("CCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCA\n") - f.write("\n") - f.write(">gi|226791089|gb|GO545944.1|GO545944 Mdas9008O06_e627.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_199223.1| casein kinase, putative [Arabidopsis thaliana] dbj|BAB10977.1| casein kinase I [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTGACTATGTGTTTCAGAGAAGTAAGTTGCAGTAGACACCGGATGCCTCTGCTTCCATAACTGCACCTG\n") - f.write("CTACCCCTGCAGCTTTACCCCCTGGACCATCTGCGTAAACATCAGACAGACCTACAGCATCGGGACGAGA\n") - f.write("TTTTCTAGAAAGACTCTCATGTGCGTTAGAGGCATTTTCTATAAGGAATAGTTCTGGTCATGGTTATGGC\n") - f.write("GATCACTCCAGACATAGGTCGACCGATGATGCGCCATCGTCCAAAGACGTCCAAACTGATTCAGAAAGGG\n") - f.write("CTCGTAGTTCATCTACAAGTGGCAGTAGTTCAAGGAGGCCAGTCATATCAAGCAGCCGGCCAAGCTCATC\n") - f.write("TGGTGAGCCCAGCGAGAGTCGGTCAAGCCGGCTGGTCTCAAGTAGTGGCCGCCTGTCCACCACCCAAAGG\n") - f.write("GTTCAACCTGGGTATGAACCCAGAACATCTTTCACCCGAGCATCCGCTGCAAGAGGTGGCCGTGATGACA\n") - f.write("CACTTCGGAGCTTTGAACTCCTTTCAATCGGCACAGGAAAGAGGAAGTAAGGTCTCAAGATT\n") - f.write("\n") - f.write(">gi|226791088|gb|GO545943.1|GO545943 Mdas9008F07_e588.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CCTCAAAATACTAGAGCTAGACAAAGATAAACAACACGATAGAGAAACTTCTGCTTTACATGTACATTGA\n") - f.write("CATTTGCATGTGCAAAGCTCTCTTTCCTCCTTTCCTTTCTTTTCTTCCTCACCTTTCGAATCTTTCTCCT\n") - f.write("AAATTAAGGAGATTGTTGTTTTGTTGTTAGTGGTTGCCATCATCATCACATTGAAATCAACTTTAGTTAA\n") - f.write("TACTAGCCTCCTGCACGCGCTCACGGGCGTGCGGAAGGCCCTTTTGTAATTAAGGCATTCTACGTGCGAC\n") - f.write("TTAAATAATTTAAATGATAACAAAAGAGCGGTTGCTCTCTGATCTAATTGCAGACACAATCTGCAGAACC\n") - f.write("GTCTTCTATGGGATTTGAACTTGTGAAGTGTGAGGTGGAGACCTCTATTACAAAAATGTTACAACAGTAG\n") - f.write("ACAAAAAAGGCCAAAAATACCAAAAGCCGCACCTCCTATACTCCATGTGTGGACTCCAATTTTCAATCAC\n") - f.write("AATTCAAAATTCAAGAGGCCTGTACAGTGTTCAGATGTAGCAATCCTATGCAATCGGCCAAATGATGTGT\n") - f.write("GTCCTCTCAAAGATCTGGTTTGAGAGAGTGGGACACCATCGG\n") - f.write("\n") - f.write(">gi|226791087|gb|GO545942.1|GO545942 Mdas9008G21_e594.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM23005.1|AF502434_1 orcinol O-methyltransferase [Rosa hybrid cultivar] emb|CAD29459.1| orcinol O-methyltransferase [Rosa chinensis], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTAACAAAAAAGCACATCAATCCCAAACTGGTCCATAATCATATGGTATGCATTTT\n") - f.write("GACAGTACTTATTCAGCAATCAGCATCCACATAAATCATATATATCACATGGTTGCTTCTAACTTTCTAA\n") - f.write("AGAAAAACTTCAATGAGGGATCTCAAACCAAATATTGGTGTCACCTTGTAGCCGCTGAAACCAGCCTCCA\n") - f.write("GGAAGAGCTTTTTCCAGTCTTTCTCGCTCCTCTCTCTTCCAGTGACCACAACCATCATAAGCAGATCAAA\n") - f.write("CAAGAGCTTTGCTTCGGTTATTTCATGCTCATCTTTCTCTTCATTTATCACTATGTCTATGATTATAACT\n") - f.write("TTCCCTTGGCCATTGCTTGCAATTGCTTCCCTGCATTTCTTCAAAACCTTCAAGCATTCCTCATCGCTCA\n") - f.write("GAGCATGCAAAGTCAGCTTGAGGAAAACAGCATCCGCTGGAGGGATAACCTGGAACATGTCTCCTCCAAC\n") - f.write("AAACTTCAAATTCTCACTGTCTGGCAAATCAGCAACAACGTGTGGAAGTTCAAGAACTGTGCATTTCAGT\n") - f.write("TGAGGGAAAGCGTCACAGAGAATCCTAGCAACTTTTCCAGTCCCACCACCAACATCAACCAATGAACTCA\n") - f.write("AC\n") - f.write("\n") - f.write(">gi|226791086|gb|GO545941.1|GO545941 Mdas9008L07_e614.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T09544 phosphoprotein phosphatase (EC 3.1.3.16), catalytic beta chain - alfalfa emb|CAA05491.1| protein phosphatase 1, catalytic beta subunit [Medicago sativa], mRNA sequence\n") - f.write("TTTTTTTTTAACTAGAAGACCCAGAAAAATTTCCCGAATTTCATCACAGGCATCTGGCTGTTCTGACATT\n") - f.write("TTCCATGGCCTCGGAGAGACTAATAATTCATAGCAGCAAATTAGTGTACAAGGACGAAGAGAAGAAGATA\n") - f.write("CACAGCCTTCTACCTTCTAACCCAACTTTATACCATTCTGCATTATTTTCTAGTGATTACAGTGAAATTA\n") - f.write("AGTTGGCTCTCATGCTTCCCGATGGAACCCTTGGCTCGATCATGATACAAACCGGGCTTCGGCACCTTCC\n") - f.write("CTCTCCGCCAAATCAAACATCTTACCTGTGCATCATGGACCTGATTCCTGTAACAGTGTTCCCAGGCTTA\n") - f.write("GCTGTTGCTGTGCTCGCAAAAGCGCTAACTCCAGACGAAGTATTTCCAGGCTTAGCTGTAGTCATGCTCC\n") - f.write("CAAAATTGAATTTCGGCTTTTTATCTGCAGGTTTTAGTATTTGAAAAGAGCACATTAATGTCTCATCCAC\n") - f.write("ACTCATCATGGCACCGGCATTATCAAATTCCCCACAATAATTAGGTGCTGAAAATATCGTCACAAGTTGG\n") - f.write("CGGTTGGCAAATAACTCGTAGCCATCCTCCACAACCTGGTGAGCACGACAAACGAGATCCAAATCGTGCT\n") - f.write("TCTGAAGAAACTCCGTCACTGTGTCAAGACCAAATGTAAACGAAACTCCACGGTCGTTCCTTCCCCACCC\n") - f.write("TTGACATCTTTACT\n") - f.write("\n") - f.write(">gi|226791085|gb|GO545940.1|GO545940 Mdas9008I07_e602.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_176897.1| glyoxal oxidase (glx1) -related [Arabidopsis thaliana] gb|AAG00252.1|AC002130_17 F1N21.11 [Arabidopsis thaliana] gb|AAO22637.1| putative glyoxal oxidase (glx1) [Arabidopsis thaliana] gb|AAO42437.1| putative glyoxal oxidase (glx1), mRNA sequence\n") - f.write("GAAACAAAATATCAATTAATGCTTTACGGTTCTTATCCACATTTAATTCATCCACGAACTTTCTAACCAA\n") - f.write("AAATTAAAATCATACATCAAGACACCAGATGTATCCAGCGCGCAACACTTGGCACGCCCTGATTGACCGC\n") - f.write("AAATGCCATGTAATAACCCGGCGGAGCAACCATCCCATTCGGCGGCGCCACACAGCTAATCCTGTAACGC\n") - f.write("CCCTCACCGTCCGGCACCGACGGCGTAACGGCCAGTTTGACCAGCCGCTGACCCTGCGAAAACGAATGCG\n") - f.write("TGGCAAAAGGCGCGTTCCCCAAATTAACCTCCACAACCCCCACCACGGACAGCGGAACCGACACCGTAAC\n") - f.write("GTCAAAACTCTCGCCGTAGCGCACCGTTTCGGGTATCCCCTCGAAAATGGGTCGGAGATTCGCCCGGTCC\n") - f.write("GGACTCAAATACTCGGGCGAAAACGCTTCGATTCGTAACTCCGTGGGAAACTCGGCGTCGAATCTGTAGA\n") - f.write("AATAATGCGGATTGCTTCCGGCGATTAATACCCGTCCATCGGGTAAGAGATTCGCGGTGGAGTGGTACAA\n") - f.write("TCGGGGCACGGT\n") - f.write("\n") - f.write(">gi|226791084|gb|GO545939.1|GO545939 Mdas9008N11_e625.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGAGCAATGTCAGGTAAGTAATCAGGCAAGGGGTTCCGGGCAGTCAGTTCCTGAATGGAAGCTTGAT\n") - f.write("TCCAAGTGTTGACTGATTGCTCTCTTTCTCATTGTCTTGCAGGTAAGAACAAGGTCAAAGGAAAAGACAG\n") - f.write("GGAAAAAGCATGATATGGGATACTCTTGCTCTTGTGTGGCTTGTTTGCAGAGGTATTATCGGGAGGAAAA\n") - f.write("TAAGCTGAGTATTTCGAAAGACTCTGCTGAGAGTGCCCTCTCGAATGTGAAGAAAAGTTGAGCATTTTTT\n") - f.write("TTTATTTGCGGGTTTGCCTGGCCGTGGAGGATGGAGGTCGACATATATAGAAGTCTCCCTAACAACAAGT\n") - f.write("AGTAATGCTATTCCTTTACCCTTCTTGATCATAGCAATGTAGTAGGAGCTGCAAGCTTCACATGTTTTAA\n") - f.write("CTTTGTCAGAACGCTTTGAAAAAGTGGTATGTGGTATCTGGAAAGCTGATGTTGCGTATAAAGATTGCAG\n") - f.write("ACAAGCTTTATCCCAGGAAATCTGGCTCTCGAAGTTTGGAGAGCGGTGTCTCTTCGGTTTTCGAACAAGC\n") - f.write("AATCCTGTCGGGGATCTGGC\n") - f.write("\n") - f.write(">gi|226791083|gb|GO545938.1|GO545938 Mdas9008O18_e633.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCAAACACATATTGTAGCACATAGTTCAAATTATTGTTGTCCAAT\n") - f.write("ACTTGGTACCAAATTTACATCACCGACAACAATACAAACGAAAGTACAAGACAACTCCTGAGCTCTCACT\n") - f.write("TTCCGGGAACAAAGTTTGTGGCGTATTTCCAGGCATTGTTGGCGACTGGGTCAGCGAGGTGGTCGGCAAG\n") - f.write("GTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGAACAAAGAATCCAAACATGGAGAACATGGCCAAC\n") - f.write("CTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGCTTCTGGGTCGTCAGCAAGGCCCAAGGGGT\n") - f.write("CAAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTC\n") - f.write("AACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCAAAATGCTCTGTGCATGGACCAAGC\n") - f.write("\n") - f.write(">gi|226791063|gb|GO545937.1|GO545937 Mdas9008N16_e626.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n") - f.write("TTTTTTTCCTTTTTTTTTTTTTTTTTTTATTTTCTTTAATAACTCATTTATTAAGTACCAAAAAAAATAC\n") - f.write("AAGGGCCGTTTATTATATTTTCCTTTGCAAGGCCTAATGCAAAGGGCGAATAATGAAGTTTTCAAACTAA\n") - f.write("CAAATAAATGAGCTTCTGGAAAATTATATGAAGCTCAGTTTATTGTAAGTAAAATTCACGATAGTTTCCA\n") - f.write("TTTCGCTTCCGTTGAACAGCCTTGGAAAAAGTTGCGGAGGCAGCAATTCCAAGGTTTTTGAATGGCACGC\n") - f.write("TTATGCATACACGTCTAAGCCCCAAGTCTTGGAAGGTAAACTGGTACGATACTTCCTGTCAATACTGTAA\n") - f.write("ATGAGCTGCATGTCTTCATCCCTCAGCTGGAATTCAAGAACCTCCAAATTCTCTTTCAATCGCTGAATTT\n") - f.write("TCAATGATTTTGGAATCACTGCTGTTTTCCTCTGAATTCCCCACCTCAAACAGATTTGTGCCACGCTCTT\n") - f.write("TCCGTATTTCTTACCCACATCATTGAG\n") - f.write("\n") - f.write(">gi|226791062|gb|GO545936.1|GO545936 Mdas9008O07_e628.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_193170.1| casein kinase I (CKI1) [Arabidopsis thaliana] pir|C71405 probable casein kinase I - Arabidopsis thaliana emb|CAA55395.1| casein kinase I [Arabidopsis thaliana] emb|CAB10213.1| casein kinase I [Arabidopsis thaliana] emb|CAB78476., mRNA sequence\n") - f.write("TTTGACTATGTATTTGATTGGACTATATTGAAGTATCCGCAAATTGGCTCCAGTTCCAGAACACGACCAA\n") - f.write("GTACAAAACCAGCTTTAAACCCTGGACCATCTGCAGAAAGAACAGAAAGACCTACAGCAGTGGCACAAGA\n") - f.write("TTTTCGAGAAAGACTCTCAGGTGCAGTAGAGGCATTTTCTAGAAGGAATAGTTCTGGTCATGGTTATGGC\n") - f.write("GATCACTCCAGACATAGGTCGACCGATGATGCGCCATCGTCCAAAGACGTCCAAGCTGATTCAGAAAGGG\n") - f.write("CTCGTAGTTCATCTAGAAATGGCAGTAGTTCAAGGAGGCCAGTCATATCAAGCAGCCGGCCAAGCTCATC\n") - f.write("TGGTGAGCCCAGCGAGAGTCGGTCAAGCCGGCTGGTCTCAAGTAGTGGCCGCCTGTCCACCACCCAAAGG\n") - f.write("GTTCAACCTGGGTATGAACCCAAAACATCTTTCACCCGAGCATCCGCTGCAAGAGGTGGCCGTGATGACA\n") - f.write("CACTTCGGAGCTTTGAACTCCTTTCAATCGGCACAGGAAAGAGGAAGTAAGGTCTCAAGATTCCTTTTGT\n") - f.write("ATTATCTATCAAAGATATGTCTCGGCACTAAAATGGTTTTGGCACAGCTTACT\n") - f.write("\n") - f.write(">gi|226791061|gb|GO545935.1|GO545935 Mdas9008F10_e590.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n") - f.write("CTTGTATCCTTTTAGTTTTGCAATGGCTGCTTCCATGGCTCTCTCTTCCCCAACCTTCGCCGGCAAAGCC\n") - f.write("GTGCAACTTTCCCCGGGAGCCACCGAGCTTTTCGGAAACGGAAGAGTGTCCATGAGGAAAACTGCTACCA\n") - f.write("AACAAGTTTCCTCTGGCAGCCCTTGGTATGGCCCTGACAGAGTCAAGTACTTAGGCCCATTCTCCGGTGA\n") - f.write("GCCCCCAAGCTACCTCAAGGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCTGGACTCTC\n") - f.write("\n") - f.write(">gi|226791060|gb|GO545934.1|GO545934 Mdas9008M21_e622.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P19950|R141_MAIZE 40S RIBOSOMAL PROTEIN S14 (CLONE MCH1) pir|A30097 ribosomal protein S14 (clone MCH1) - maize, mRNA sequence\n") - f.write("TTTTTTTTCTTTTTTTTTTTTTTTTTTAGACCAAAAGATACTTCATTGCAGACCAGAATAACAGTATAAA\n") - f.write("TAACAAAACAAAACTTAAAAGAGTAGCAGAACTCTTTCCGAATTAATTGGAAATAAAACTTTCGAAAAAC\n") - f.write("ATAGTAAAAAACTAGAGAGTTTCGAAACCGAAAGTAACAGCGCCTAATTTCGAAGTAACATAATCCAACT\n") - f.write("GAGGCACAGCGACCACCCTGACAAGCAGTTCTGACCAGATAAGAGGTGCAAAGCTTACAGCCTCCTTCCT\n") - f.write("CTCCTTCCACCCTTTCTACGGGGGCTGTCAGTTGGAATTGGAGTCACATCCTCTATACGACCAATTCTCA\n") - f.write("TTCCAGAACGAGCAAGAGCACGGAGGGCAGACTGGGCACCTGGACCAGGTGTTTTTGTTTTGTTCCCGCC\n") - f.write("AGTGGCACGGAGCTTAATATGAAGTGCAGTAATGCCCAATTCCTTGCATCTCTGCGCAACATCCTGTGCT\n") - f.write("GCAAGCATAGCAGCATATGGGGAAGACTCGTCCCTGTCAGCCTTCACCTTCATACCACCGGTGATACGAA\n") - f.write("CAAGGGTTTCTCTTCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226791059|gb|GO545933.1|GO545933 Mdas9008I21_e603.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197053.1| UDP-glucose dehydrogenase-related protein [Arabidopsis thaliana] pir|T51527 UDP-glucose dehydrogenase-like protein - Arabidopsis thaliana emb|CAC01748.1| UDP-glucose dehydrogenase-like protein [Arabidopsis thaliana] gb|AAL07049.1, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTATAATTTCCTGGTTTCTGATTTTATTACATTAATCTAAGAGAA\n") - f.write("TAACAAATTGAGATATATTCCACTAAACTGAGGACAAACTCAGGAACCGTATTAAGGGTACTATTACAAG\n") - f.write("TAAAATATGACGCAACATAACCCCCAACTTTAAGAAAGGTGAAATAACAAATTAATACAAGAAGATAAAA\n") - f.write("ATAAGGACGAATTAAGCATCCACTCTCAGTAACAAACTTCGGAACTGATAGAACTTTTACGCACAAGGGG\n") - f.write("ATCGATCTTCAAATTACTGTGCTTCTCTCCTCATCATCAAGTCTTTACGCCACAGCGGGCATGTCCTTGA\n") - f.write("GCCACTCGTCCAGGGGCTTTCCAATCGAGTAAACAATGAACCCAATTTGCCTCAGCTTCTCAGCATCCAC\n") - f.write("CACGTTCCTTCCATCGAACACAAATGCAGGCTTCTGCATCTGATCATAAATCTGTTGGTAATCAAGACTC\n") - f.write("TTGAACTCATCCCACTCGGTCAGGATGCAGATTCCGTGAGCATCCTTTGTTGCCGCATAAGCATCCCAGG\n") - f.write("CTACACCAACTTGCTTCACAGCAGGGGGGCTCTGAGGTTGAAGATGAATG\n") - f.write("\n") - f.write(">gi|226790978|gb|GO545721.1|GO545721 Mdas9011D23_e829.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_568984.1| protease inhibitor/seed storage/lipid transfer protein (LTP) family [Arabidopsis thaliana] gb|AAL50083.1| AT5g64080/MHJ24_6 [Arabidopsis thaliana] gb|AAM10364.1| AT5g64080/MHJ24_6 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTGAGTTTTCACAATCCCACAAGAAAAAATGGGAGCAGCAACGACTCTGGTGGTGGTGATGGCGGTGCTG\n") - f.write("CTGTTTGGACTTGGGGACTGCGCGGCGCCGGCTCCTGCGGTGGACTGCTCGAGCCTGATCTTGAACATGG\n") - f.write("CGGACTGCTTGTCGTTTGTGTCGAATGGGAGCACGGACACGAAGCCTGCAGGGACTTGCTGCAGTGGCCT\n") - f.write("CAAGACTGTTCTCAAAGCCGACGCTTCCTGCCTCTGTGAGGCCTTCAAAAGCAGTGCTCAACTCGGCGTC\n") - f.write("GTTTTGAACATCACCAAGGCCATCTCCCTCCCCGCCGCTTGCAAAGTCTCCGCTCCGTCTGCCTCCAACT\n") - f.write("GTGGATTATCTCTCAGTCCTGCTGGTGCTCCTGGTGGAGCACCTACCTCGCCGGCACCTTCTCCAATGTC\n") - f.write("AGGTGCTGACATTGGTGGTGCACCAGCGTCGTCGACTACTGGAGGGAATGAGCAAACACCCGCTGCATCT\n") - f.write("CCTCAGGGAAGCTCAGGTTCTTTTATGCTCGCTAGTTCGGTTGGATCCCTACTTGTTGGTCTTGTAATTG\n") - f.write("CATCATTCCCTTGTTTCTGAGAGCCGAGTTTGGTGGTGCCATTTTTGTGAGTAGAGAGGGATGATGTGAT\n") - f.write("ATATGGCACTTATGTTTATTTTACCATTGGAGTTAGTTCATTCTGAG\n") - f.write("\n") - f.write(">gi|226790977|gb|GO545720.1|GO545720 Mdas9003B09_e178.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL38341.1| chlorophyll a/b-binding protein [Arabidopsis thaliana] gb|AAM47913.1| chlorophyll a/b-binding protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTGACAATTAAACAAAGGAGCTCGGTGGTTTTACTGGGTACAGCGATTTCAATACAAGCAGT\n") - f.write("TTCTAGTAAAATTAAATCGGAAACAGCCATGGATTTAGGTTTCTTCACTTTCCAGGGACAAAGTTGGTGG\n") - f.write("CGAAAGCCCATGCGTTGTTGGCCACTGGATCAGCAATGTGGTCAAAGAGGTTCTCGACTGGGCCCTTTCC\n") - f.write("TGTGACAATAGCCTGAACAAAGAATCCAAACATCGAGGTCATAGCCAGACGCCCGTTCTTAAGTTCCTTC\n") - f.write("ACCTTCAGTTCAGCAAAAGCTTCAGGATCATCAGCAAGTCCGAGTGGATCAAAGGCACCTCCTGGGTAAA\n") - f.write("GTGGGTCAAGTCCTTCGCCGAGTGGTCCTCCACCAACTCTGTATCCCTCAATGAATCCCATGAGCACAAC\n") - f.write("CTGGACAGCCCAGATAGCCAAGATGCTCTGAGCATGGATAAGGTTTGGGTTGCCAAGGTAGTCAAGGCCG\n") - f.write("CCCTCGGAGAAGATTTGAGATCCAGCCTTGAACCAAACTGCCTCGCCGAACTTGACCCCATTCTTTGACA\n") - f.write("AGATTTCTGGGAAGACGCATCCCAGTGCAC\n") - f.write("\n") - f.write(">gi|226790976|gb|GO545719.1|GO545719 Mdas9011H20_e847.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TAAAATTGTCCATTGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAGCTTAAAGATCATCTA\n") - f.write("TTGTACACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGGCCCAGGCATTGTTGG\n") - f.write("TAACAGGATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAA\n") - f.write("GAAGCCGAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCC\n") - f.write("TCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAA\n") - f.write("GGGGTCCTCCGGCGATGCGGTAACCCTCAACCGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAG\n") - f.write("AATGCTCTGTGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCT\n") - f.write("CCGGCTTTGAACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGC\n") - f.write("CCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTCTTGGCAAAGGTTTCGGG\n") - f.write("GTCTGCTGATAGCCCAGCAGTGTCCCACCCGT\n") - f.write("\n") - f.write(">gi|226790975|gb|GO545718.1|GO545718 Mdas9011M23_e876.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564094.1| coronatine-induced protein 1 (CORI1) [Arabidopsis thaliana] sp|O22527|CLH1_ARATH Chlorophyllase 1 (AtCLH1) (Chlorophyll-chlorophyllido hydrolase 1) (Chlase 1) (Coronatine-induced protein 1) (CORI1) pir|E86329 coronatine-induced pr, mRNA sequence\n") - f.write("TTTTTTTTTGCTAGTACATGATTAATGAATTAGAAAAATTGAGATGGTGCTAGTACATATCAACCCCCAA\n") - f.write("ATTTCAGTACTTGAGCACATGCATTTGATGACTGAGCTGTTTATTCGAAAGTAACAATCTAGGATCCGAA\n") - f.write("ATAACCCTCGAAGAAAGCCTGAAAATAATCACTGACATTAACCACTGATAGGCCTTATAACCCCCTCTTT\n") - f.write("ATGTGCTAATATGTGCAGCTAATGTCAGTGACTATTATCAAGACAACCTTGAGCTTGAACTTATGCTCTA\n") - f.write("ATGAACTCCACAGGTTCAAGCTTTGCAGGAGAACTATCAGGATCACCAACAATGGCAACCAAATCCCTAT\n") - f.write("CATCACCATTCAAATAAGCATTCAGAAACGCCACAACAATCCCACCCACAGTCTTCCTCATTAGCTCCCT\n") - f.write("CGGTCCTGTCCCGTTTTTACACATGCACCCCGACACTGCCCCAACCATGCCCTGTGGATCGTCGTCCAAC\n") - f.write("ATGTCCATGTGACCATAGTCCTTCACAACAAAATGTGCACATGGAGGCTTGCACTCATAGAAGAAATCCT\n") - f.write("TGTGGTTCACGCCATCTGGGGCACAAGGTTTTGACATGCAAGCATTTTTACCTTCCGGTCCCAGGCCAGC\n") - f.write("GCCGATCACTATGACTGGAATCGAGAGGTC\n") - f.write("\n") - f.write(">gi|226790974|gb|GO545717.1|GO545717 Mdas9003A11_e173.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T05875 hypothetical protein T29A15.190 - Arabidopsis thaliana emb|CAB38282.1| hypothetical protein [Arabidopsis thaliana] emb|CAB81420.1| hypothetical protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTTTGACGGAATTCTGCAGTTCAGTTGATCGAAAAAGAGAAATGATGAAG\n") - f.write("ACATTACGGGCGGAAATCATCCGGTCGTTGTTATGTTTAGCATCATTACAAGAACATTCAATTTGAATCC\n") - f.write("GAATTCACAAGCTGTTAGTTATGATAAGAAATCAATGGCAAGCACGCACGCACTCAATTTATGAACAAAA\n") - f.write("CACGCTCCTTTGAAGGAACTTTCTTTCATACCGCCACCGGTGTTTCACTCTTCTTCTTCTTCTTCTGCAA\n") - f.write("CCGATGGCAGCCCCTCTTTGAACCACGCGTAAAGTCCGCCTTCTAAGTGGAAGACATTCGTATAACCGTT\n") - f.write("GAGGACGAGCAAGTAGGCTGCTATCAGTGATCTTGACTGTTGGCCTTCTGGGAGATTTTGGGTCGGTCTC\n") - f.write("ATCGTACCGCCGGCGGCGCAAGCCACTATTATCTTTGCCTTCTTATCTAGCTGCGATCCCACACTTGATA\n") - f.write("TGAACTCAGGGTTCTCTTCTGTGCCGGCAAAGATGCCGAAAAACGCGAAAGCAGCACGGCGGGCAATGTC\n") - f.write("CCACGCTGTCCACTCCTTTATAAGCCTGTATATTTGCACGTTAA\n") - f.write("\n") - f.write(">gi|226790973|gb|GO545716.1|GO545716 Mdas9011F04_e835.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n") - f.write("ACCGGATCGGTGTTTGCACCGGAATCTTCAAGCCTGATAATGTGTCCCAGGAAGATGTTGTCAAGATTGT\n") - f.write("TGACACATTCCCCGGTCAATCCATTGATTTCTTCGGTGCCCTAAGGGCTCGAGTTTATGACGATGAAGTG\n") - f.write("AGGAAGTGGATTTCCGGTGTTGGAATTGACGGGATTGGGAAGAAGCTTGTGAACTCAAAAGAAGGTCCCC\n") - f.write("CGACTTTCGATCAACCTAAGATGACTCTGGAGAAGCTCCTTCACTACGGACAAATGCTTGTTCAGGAGCA\n") - f.write("GGACAATGTGAAGAGAGTCCAACTGGCTGACAAGTACTTGGCCGATGCAGCCCTTGGAGATGCAAACCAG\n") - f.write("GACTCCATTAACCGAGGAGAATTCTATGGAAAGGCAGCCCAACAAGTTAATGTACCAGTCCCAGAAGGCT\n") - f.write("GCACTGATCGAACAGCTGCAAACTTCAACCCAGCAGCAAGGAGTGACGACGGTAGCTGTCAGTACGAGTA\n") - f.write("ATTGGAGCTGAAGAAAATAAATATTCTGTTTGCTGGGTTATTGATATTTTCTTTGTAATTTGCGCTTGTA\n") - f.write("TTTCTATGGAAATTCTTGCAATTATTTTGTTTTAATTATTAAACAAGCTATTGATACTCCGGCTATTGAA\n") - f.write("CAGTCGATAAGAACATAATGTTATGTTGTTGAGAATATGTTGTCATTGTCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790965|gb|GO545715.1|GO545715 Mdas9011J14_e854.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK38342.1| seven transmembrane protein Mlo6 [Zea mays], mRNA sequence\n") - f.write("TTATCACGATGCTGCTCGGGAGGCTAAAGATTCGAGGCTGGAAGCATTGGGAGGCAGAGACTTCAAGTGA\n") - f.write("TGACTATGAGTTTTCCAACGATCCTTCGAGATTCAGACTTACTCACCAGATATCATTTGTTAGAGCACAC\n") - f.write("ACCAGTTTCTGGACTAAGATTCCTTTCTTCTTTTATTTCGGATGCTTCTTTCGACAATTTTTTAGGTCTG\n") - f.write("TTAGTAAGGCTGACTACTTAACACTGCGCAATGGATTCATCACTGTCCATTTAGGTGCAGGAAGTAAATT\n") - f.write("TAACTTCCAAAAATATATCAAGAGATCATTAGAGGATGACTTCAAGGTCGTCGTTGGGGTTAGTCCTCTA\n") - f.write("TTGTGGGCATCATTTGTGATCTTTTTGCTCCTTAATGTTAAAGGATGGCAGGCACTCTTTTGGGCATCCT\n") - f.write("TGATCCCTCTCGTTATAATTTTACTCGTTGGAACAAAACTTCAGGCCATCCTGACTAAGATGGCCATTGA\n") - f.write("AATTGCAGAAAGGCATGCTGTGGTTCAAGGGATTCCTCTAGTACAAGGATCTGACAAATNATTTTTGGTT\n") - f.write("TGGTCGGCCTCAATTGATTCTTAATCTTATCCATTTCGCGCTGTTTCAGAACGCATTCCAAATTATATAC\n") - f.write("TTTTTC\n") - f.write("\n") - f.write(">gi|226790964|gb|GO545714.1|GO545714 Mdas9003C11_e183.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O24058|MT2_MALDO Metallothionein-like protein type 2 pir|T17014 metallothionein-like protein AMT1 - apple tree gb|AAC23697.1| metallothionein-like protein [Malus x domestica], mRNA sequence\n") - f.write("AGTTTTTCATTAATTTAATCAGAAACACATAATACGATCCACCAAGTTAACACAACATAAAAACACAAAT\n") - f.write("ACGACTACTGCATGTACAAAGCAAACAGACAACAAGCAGCCATAACCTAGGACCAGATCCCAGCCTAATA\n") - f.write("GGACGTGCAGCTCAAAAAAAGCCATGGCCACTTTATTCTAAAAACACGACCTTCGTAAATTTGGATCATG\n") - f.write("ATTCATGATTACGACACACACGCATACATATATTACTGCTAAACATACAAGCCCCGCGAATCTCTTGCTT\n") - f.write("CATCAAAAGGGGACATCTGTCCCTCTCACTTGCAGTTGCAGGGGTTGCAGGGGCAGTTGTCTCCGCACTT\n") - f.write("GCATCCGTTCTCGGCAGCAACTCCCATCTCAGATGCCTCCATGTGAGACTTCTGGGGAGCAACTCCCATG\n") - f.write("ACGAGGGTCTCAGTGGTGGACCCCTCCATGTAGCTCAGATCAGGAGCCATCCCACACCCGTTGCAGCCAC\n") - f.write("TGCCGCAGCTGCAGCCGGAC\n") - f.write("\n") - f.write(">gi|226790963|gb|GO545713.1|GO545713 Mdas9011D10_e827.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92996.1| chalcone synthase [Malus x domestica], mRNA sequence\n") - f.write("TTTTTTTATTCGTCAATCCATATTTTACTCATCATTACATTGCCCAATCATGGCCCTTTTTTCATCAATA\n") - f.write("TTGCAGTAAACAACATGAAAGTAAGGGTCCTTCCTTGCACCAAGATAACCCCATGACGCCCACACACAAT\n") - f.write("ATCCAAAAAGCCAAATTCTAACCAGAAAAGGCGGAAACAATACATAAACGAAGCAAATAGATAAATCAAC\n") - f.write("ACCGATATTCATGTCATCAAGCACCCACACTGTGAAGCACAACGGTCTCAACAGTGAGGCCAGGCCCAAA\n") - f.write("TCCGAAGAGTACGCCCCACTCCAGTCCTTCTCCAGTTGTTTTGAGTCCTTTCTCACCACACTTCCTCCTC\n") - f.write("ACTTCGTCCAAAATAAACAAGACACACGCACTCGACATGTTGCCGTAATCACACAGCACTTGCCTTGTAG\n") - f.write("CTTCTAGTTTCTCCGGCTTAAGGGCCAACTTGGACTCTACTTGGTCCAGAATAGCAGGGCCACCTGGGTG\n") - f.write("TGCAATCCAGAAGAGCGAGTTCCAGTCTGAAATGCCTATAGGCTTGAAGGCCTCGTTAAGGCTCTTTTCG\n") - f.write("ATATTCTTGGAAATAAGCCCAGGAACGTCCTTGAGAATGTGAAATGTAAGCCCTACTTCACGGAGATGGC\n") - f.write("\n") - f.write(">gi|226790962|gb|GO545712.1|GO545712 Mdas9011J16_e855.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM62737.1| Quinone oxidoreductase-like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTTTTACTGGCCAATATGATACATGTCAAATATGACGCAAAACATGTTACAAAGAGATAAGG\n") - f.write("CAACATCATATGTTCATCTTTATGTACACAGCAAAAGATGGCTCAACTGTTTTCTGTTTTCCTTCTCATT\n") - f.write("CAATTGGATGTATGACTACCTTTCCGGTGGCCCGATTTGTTTCAAGGTAAGAGAAAGCCTCCACAAGCTT\n") - f.write("GGAGAAGGGGAAGGGCCCTTTGGGGTCTATCACAGGCTTCACCTTCCCAGTCTCTAAGTACGGGTTTAGT\n") - f.write("TTCTTCAGAACTGCTCCGTTGGAAGTAACCACGAATCTGAAACCCGGAGGTGTTACTGCACCTGTTAAGG\n") - f.write("CCACCACACTGCCCCCTTCTTTCACCACCTTCACTGCTTTGTCACATTGACCAATAGCATCATAGACGAC\n") - f.write("ATCAAAATTTTCCGGCAATTCTTCCAAGTTCTCCTTAGTGTAGTCGATCGCTAAATCAGCACCCAAGCTC\n") - f.write("TTCAATAACTCCAGCTTTCCAGTGCTTGAAGTGGCTGCTATTCGTGAAGCTCCAAATACATGTTTTGCTA\n") - f.write("GCTGAATCACTAGGCTTCCAACTCCACCAGCACCATTCAGAACAAGCAAAGATTTACCGGCAGACAACCC\n") - f.write("GGTCTTTTCAAGAC\n") - f.write("\n") - f.write(">gi|226790961|gb|GO545711.1|GO545711 Mdas9011J11_e852.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n") - f.write("AATTTCTCAATAAACATCATCCTGAATCCGTTAAAACACCAAATTCGAAAACAAAAGAGATTGCCTCGAA\n") - f.write("AAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGGTCTTGAAACCCTAATCAAGGACAAACTTAAACAA\n") - f.write("ACCACCGAAACCCTTAGGCTAAGAGCCACAATGGTACGTACAACAACAATATTAATTACGACGAAGAAAC\n") - f.write("ATGATGAAACATGAACAACAACAACAACAACAACAACTTAGTAGCCTGCAGGCTTGTAGGCGATGAAACT\n") - f.write("GATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATACGGATGAAGGCGTTGGGATAGGCCTTCTTG\n") - f.write("GCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCC\n") - f.write("AGTACCTTCCATCGTAGTATCCTGGGGGATTTGTGGTTCTCACGGTACACAAATCCATGCTCCAACTCAA\n") - f.write("ATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAATCAACTTCCTTGGCCAAGGACTCGGAAGAGAG\n") - f.write("AGGAGGAAGGTAAGAAGAGGGTCTCGAACTTCTTCAATCCAAGTGGAGGCCACACCTGCATACATTGCAC\n") - f.write("TCTTCCTCCAT\n") - f.write("\n") - f.write(">gi|226790960|gb|GO545710.1|GO545710 Mdas9003A10_e172.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA06245.1| elongation factor 1-alpha (EF1-a) [Cicer arietinum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTAAGAACAAAGCAACGAACATAGAAATTTAATGCAAAACGATGTTAA\n") - f.write("AGAGACAAAGCGCAGAAGTTGCAGACATTAATACGAAATTGTCCAATAACCAACTACACGACTCATCTCA\n") - f.write("ATGTATAAAGCAACCAAAAACCATAACAAATAGCATACAACACAGCTTGCCGAGCAACCCGAATCGATTC\n") - f.write("TTGCCGCTCAGCTCCTCCAACAATCCTTGCAAGCAAAGTTAGAGGGCTACGATGTAAAACTCATAAAACT\n") - f.write("GTCCAAATAAACTACGAGAGTAGCGCAAAAATGGAAAATAAGCGACATTCGACAAAACTAATCCAGTTAA\n") - f.write("GGCCGGATGATAACACAACACACTTCATTTCTTCTTGGCTGCAGCCTTGGTCACCTTGGCACCGGTTGGC\n") - f.write("TCCTTCTTCTCCACACTCTTGATCACACCGACGGCAACCGTCTGACGCATGTCTCTCACAGCAAAGCGAC\n") - f.write("CAAGCGGTGGGTACTCAGAGAAGGTCTCGACGACCATGGGCTTGGTGGGAATCATCTTAACCATACCAGC\n") - f.write("GTCTCCATTCTTCAAGAACTTCGGTTCCTTCTCAAGCTCCTTACCAGATCGCCTGTCAATCTTGGTCAAG\n") - f.write("ATCTCAGC\n") - f.write("\n") - f.write(">gi|226790959|gb|GO545709.1|GO545709 Mdas9011M13_e874.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27878.1|AF139466_1 chlorophyll a/b binding protein CP29 [Vigna radiata], mRNA sequence\n") - f.write("AACCATGTAGTCATTTAGCAAGTAGGAAAAGCTCACATGCCATTGCATACACTAATCCTTTGATCCCATC\n") - f.write("ACAATCTTTACAAGCTTAAGCAGTACATATCATGATTCAAATAATTAATCATGGTCTACTGATTAAAAAA\n") - f.write("CCAAACATGATATGCACATAAAGATACTTCTCTAAAAAGAAAAGGCGTCAATAATGGTGGTGTGGAGCGG\n") - f.write("GTCACTCAAATGGGTAGCCCAGTTGTTAAGTGGTCCCTTCCCGGTGACGGCGGCTTGCACGGCAAACCCC\n") - f.write("AAAAACGCAACCATGGCGAGGCGGGCGTGCTTGATTTCGGCCAGCTGAAGAGTGGCCTTCTTTTCCGGGT\n") - f.write("CAGCAGCAAGGCCCAACGGGTCGAAAAACTTGCCACCCGGGTACAACCTCTTTTCCGGGTCGAGCTCGGC\n") - f.write("GTTCCTCTGGAACTCGATGTAGCCAATCACTAGAACTTCGATCCAGATCAACGTGGTTAGTGAGAAAGGG\n") - f.write("GAGTGGTTGACCCAAGTAGGACGACCCTTCGATGAGCTCCACCTTTCCGGCGTCTTGCCATGTGATCCCG\n") - f.write("GTGACGGACTCGACAGTGAGAGCACCGAGCGTGGCGAGCATGGCCCACCTTCCATGAATCAGCTCGCACT\n") - f.write("CCCTAAACCTCTG\n") - f.write("\n") - f.write(">gi|226790951|gb|GO545708.1|GO545708 Mdas9011I13_e850.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P93338|GAPN_NICPL NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (Non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase) (Glyceraldehyde-3-phosphate dehydrogenase [NADP+]) (Triosephosphate dehydrogenase) gb|AAB47571.1| non-phospho, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTAATACAAGTCTCTCAGTTCTTATTGACCAAGTCTCCAACTTCATCAGGTAC\n") - f.write("AGAAGAGAAGCTTAAAGTTATTGCAGGAGCTTAAAACATCATGTAATAATCGCGTGATGCAGCCTTTCAA\n") - f.write("TAAGGGTATTGCCCATTATTCTCTTTTTCTCAACTCCATTTGTCCGACGATGACACATTTTTATAGTCTG\n") - f.write("CAGCCTAAAAATTCACTTACACATTTTACTAAATCCGCTACTACAACGACATTAAGTAGCTTCGATTACT\n") - f.write("ATATTATCACCCGATTCGTTATTAACACTGTCACTAACCCATGGTGTAAGAAGGGGTTGGCAAGTTGATT\n") - f.write("ACAGTGGTCTTGATCTTGGTCATCATGTTGATGCTGTTGGTGATTCCTTGTGAGCCAATTCCACTGTCCT\n") - f.write("TTATGCCCTGGAACGGAAAATGATCTGGTCCACGAGCAGGTGCGGAGTTTATTTGAACAGTTCCCGTCTC\n") - f.write("CATTGCATCACCAATCAAAATGGCCTTGTTGATGTCCTTTGTGAACACACAGCCCTGGAGGCCGAAATTA\n") - f.write("CTGGCATTGCAATGGGTGGATTCCTTCTTCTACCGTAGTAATCCTAATAACGGGCAAGACTGGACCGAAT\n") - f.write("GGCTCTTCCCACGCGATTCTCATAT\n") - f.write("\n") - f.write(">gi|226790950|gb|GO545707.1|GO545707 Mdas9011L09_e867.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF89961.1|AF200525_1 cellulose synthase-1 [Zea mays], mRNA sequence\n") - f.write("AGCAAACAATAAATACTTGACAACGGGGCAACATAACCGATACACAAGGCGTTCTCTCATTGTTCTTCCA\n") - f.write("CCCGACTCCCTTCTGAACGTGGAGACCATACGTAGAAGTTCAGTAGACGAATTTACCTGATTTCTTGTAT\n") - f.write("ATAGTATATACACACAGATGGCGTGGAGAGAGATGCCAGTTCCAAAAAATTAGTCCTTGAAACGAACTAA\n") - f.write("CAGTTGATGCCACATTGACCGTTTGTTGCAGCTTTTGTTTTGTCTGAAGTGAATGGGTCGATGCGCACCC\n") - f.write("ATAACAAGGAAAATATTGAAGCAAGAAGGATAGACCACACGATGACAATTGTAGGGGTACGATTTTGCCG\n") - f.write("ACCCAACAGACCCTTCAAGAATGGATACAGATGTGCTACGACCCATAAGGCGAAAAACAGTTTGCCAAAA\n") - f.write("AGTGGACCCCAAGATTGGTAACCGCTATTTATGGCATATGAAACACCGGCCACAATACCTACTATGTTCA\n") - f.write("CAAGAAGAACCGTGGTTGGAGGGATGAGCAGTGATGTCCATTTGAACACGTAGAGCTCAGCAAAATCCCC\n") - f.write("ATCCTCATCAGATGACTTTGACGTGACAGTGAAGTTGGTATCAATCCCAGCAAGAACTTTCAGGAGACCT\n") - f.write("TGGAAGACAGCGAAGAGATGAGCTGATGTTCCACAATGATCCAGAACTGTTCATTTCCCTCG\n") - f.write("\n") - f.write(">gi|226790949|gb|GO545706.1|GO545706 Mdas9011L14_e868.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAG\n") - f.write("TGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACA\n") - f.write("AACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTACATACCACAACAACATTATTTATG\n") - f.write("AAAATTGTACAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGAC\n") - f.write("ATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAAC\n") - f.write("ACCTGAGAAGAGTCGGCGCATCCGAACATGGGCAGCTTCCACATT\n") - f.write("\n") - f.write(">gi|226790948|gb|GO545705.1|GO545705 Mdas9011J21_e857.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTT\n") - f.write("GAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAA\n") - f.write("CAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAA\n") - f.write("GAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGC\n") - f.write("TTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATT\n") - f.write("GGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGG\n") - f.write("CAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAAT\n") - f.write("CCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCA\n") - f.write("AGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCACAC\n") - f.write("CTGCATGCAT\n") - f.write("\n") - f.write(">gi|226790947|gb|GO545704.1|GO545704 Mdas9011G20_e842.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_177406.1| hydrolase, alpha/beta fold family [Arabidopsis thaliana] pir|G96750 unknown protein F28P22.19 [imported] - Arabidopsis thaliana gb|AAG51842.1|AC010926_5 unknown protein; 69438-68116 [Arabidopsis thaliana], mRNA sequence\n") - f.write("CAAAAGTTGTGGAATGCTTTCTTCTTCTACCTCTCAACCGCATCAACAATTTTCCACACCCTCTTATCTT\n") - f.write("TTTTCTTCAAAACCAACTGGGATCTAGTGTTCTTCAAACTCCCAGATACTCTTGTAGCTTTATATTTCAG\n") - f.write("GCTATGTGGTCTCTCTCCTTGTACAATCGACGTTGACGACCAAACCACCGTGCACTTCTGGACTGCCAAC\n") - f.write("CACCGGCGCTTCGATAAACCCGGTCTCGTTCTGGTTCATGGCTACGGAGGCAATTCTCTGTGGCAGTTTG\n") - f.write("TGTGTCATGTGGGTGCCTTGTCCAGGAACTTCAACTTGTACGTGCCGGATTTGCTGTTCTTTGGGAAGTC\n") - f.write("TTACACGAACCGGTTGGACCGGAGCGAGGTATTCCAAGCGAAAAGTGTTGTGGACGGGTTGAAGAGATTG\n") - f.write("GGTGTGGACCGGTTCTCGGTTTACGGTCTGAGCTACGGTGGGTTTGTGGCGTATCGGATGGCTGAGATGT\n") - f.write("ATCCGGAGACGGTGGAGAAGGTTG\n") - f.write("\n") - f.write(">gi|226790946|gb|GO545703.1|GO545703 Mdas9003A20_e174.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566086.1| expressed protein [Arabidopsis thaliana] pir|T02683 hypothetical protein At2g46820 [imported] - Arabidopsis thaliana gb|AAC33500.1| expressed protein [Arabidopsis thaliana] gb|AAL38332.1| unknown protein [Arabidopsis thaliana] g, mRNA sequence\n") - f.write("TTTTTTTTTTTTAGACGGAAACAAATTATAGTAGTACTAGTTACATGTATCTCGCAGACTAAGTACGTAC\n") - f.write("ATTACATTAATTAATAACCTTGGTTAGAATATGCTTATGCAAAGTTGCAAACAACATGAAGAATGTTCAC\n") - f.write("ATCCTTATGAACAATGCTGCGAGATATTTACGTATACAGATAGATGCTTCAAAAACCGGCCACGAGTTCT\n") - f.write("TATCTTAAACAACATTACTTTTCGGGTTGTTCTAGCTGCTGCCGATTATATCTTTGTATGTAGCTTTAAT\n") - f.write("CTTCAGTGTCAAAGCCTCTCTGTCTGGTTTGTAAACAAGGTTCTTGTATGCAAACCACCCAGTGTAGCCA\n") - f.write("ATTCCTACAAGCTCAAGAACACCAGGAACTAAAGGAAGCCTATCAATTGCCGAAAGCAGTCCAGTGGAGC\n") - f.write("CCCATAGTGCAACAGCACCAGCTACTGCAAGTGAAGAAACTGCATATTTATCTTCCACTTTCTCCCAAGC\n") - f.write("TTCTTGAACGGTCTTCACAATCTCTGGCAGCTCAGTTACTGCAACTTCTGCTGGTGCTTCCCCTGTCGCC\n") - f.write("ATGGCCATGACATTGCGCGCNAACTTACGACAGTAGGCAGTGGTCTTCCCTGCGTGATTTTGAGAATGAA\n") - f.write("CTGGCGGTGGAGGAAGGGAAGGCAGGGTCACACATTGTGGTGATGAGGCA\n") - f.write("\n") - f.write(">gi|226790939|gb|GO545702.1|GO545702 Mdas9011F03_e834.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P87066|TBA_CANAL TUBULIN ALPHA CHAIN gb|AAB53194.1| alpha-tubulin, mRNA sequence\n") - f.write("CTGCAGTTCATAAAGTTTCAATTTTTATCAGAGAAAAGAGAGAGAGATGAGAGAAATCATAAGCATTCAT\n") - f.write("ATTGGGCAGGCTGGAATTCAGGTGGGCAATTCATGCTGGGAGCTCTACTGCCTCGAGCATGGAATTCAAC\n") - f.write("CTGATGGCCAGATGCCCAGTGATACCACAGTGGGCGGTGGCCACGATGCTTTCAACACCTTCTTCAGCGA\n") - f.write("GACTGGATCAGGCAAGCATGTCCCAAGAGCCATATTTGTTGATCTCGAACCAACTGTTATTGATGAAGTT\n") - f.write("AGGACTGGGTCTTACCGCCAACTCTTCCACCCTGAGCAGCTCATTTCTGGAAAGGAAGATGCTGCTAATA\n") - f.write("ATTTCGCAAGAGGACACTATACAGTTGGAAAGGAAATTGTAGATCTCTGTCTTGATCGAGTTAGGAAATT\n") - f.write("GGCCGATAATTGCACTGGTTTACAAGGATTTCTGGTGTTCAATGCTGTTGGTGGTGGTACTGGTTCTGGT\n") - f.write("TTGGGGTCCTTGCTCTTAGAACGCTTGTCGGTGGATTATGGAAAGAAGTCAAAGCTTGGGTTCACCATCT\n") - f.write("ATCCTTCTCCGCAGGTTTCAACAGCAGTTGTTGAGCCTTATAATAGTGTTCTCTCTACTCATGCCCTCCT\n") - f.write("TGAACACACAGATGTATCTGTGCTCTTGGACAATGAAGCTATCTATGATATTTGCAGGAGATCCCTAGAC\n") - f.write("ATCGAGAGA\n") - f.write("\n") - f.write(">gi|226790938|gb|GO545701.1|GO545701 Mdas9011J23_e858.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AATCGAAAACAGCAACAAAATAATTGCTGTAAAAATTTATTCATCGTATCAACTTTTCACACTTACATAT\n") - f.write("GTTTTTGCTGAAATTCTTTAAAACTAAAATATAAATCTGCGTACAATAAAACTTTGTTGTCTCTAAATCA\n") - f.write("TATTTACATCCCCACTTAAAAAGCTTGGCTTTTTATATAAAAGGAAAAAACAAAGCTTCATGGATTTTTT\n") - f.write("CGGAATTAAAAAAAAGGGAAAAAAGGAAGGGAAAAAACGATAAGCGTACGTGGGAATTTTGGAAAGACAA\n") - f.write("CAAAAGATCGACAAGATGACAAATTCAAACCCAAAACAAAAACAAAAAAAAAAAGATTTTGAGCAAAAAA\n") - f.write("TTTATGGAGGAGGAGGGGATGTGAATCCACCAAGGGGGAAAAGGTGGGTGACAAAGTTAAAAAAGTTTTT\n") - f.write("ATCTTTTACCGCCTTGACGTCCCGTACATCTGGTCAAGCAAAATGACGAGGGACATGGCCACCGACGTGT\n") - f.write("CCATATCGGGCTGCACGATGAGGCTGAAGACGTCAACTCCCAACGCTACTCCACCCACCGCCTCCTTCCT\n") - f.write("CTTGATCTCGGCCACCCTCCTCCTCTTGCTGT\n") - f.write("\n") - f.write(">gi|226790937|gb|GO545700.1|GO545700 Mdas9011N24_e880.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTATACACAAAATAATAATAATATATTATTAACATGAGATATCAATGTAG\n") - f.write("CAACATACAATAGATGCAATATAAAAATTTTCTCACTCATCATCACCACCATCTACTGTGTGTTTTATTC\n") - f.write("AGTAAGTAATAGTCCTTGTAACTAGGATGTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC\n") - f.write("TCTATATTCCCTCTAAAAAAATAAGGCGTTATATCACAAGGTTGTGGGAGGCTATATATGTTTTTTTTTT\n") - f.write("TTTACAAAAAAAAATATAACCCCCTCAAATATATATATATACAGATAATACATAGATACTTTTAAAAAAA\n") - f.write("AAGAGAAAGAGAGAGAGATCTCTATTTTTTTACACGACACAAGTGAACTACACCCACACAAACACACATG\n") - f.write("GGGGGGGGGGGGCCCAACACCTAAAGAGCGCGCCTCTCTGTTTTAACACTTGGTGTGTGTCT\n") - f.write("\n") - f.write(">gi|226790936|gb|GO545699.1|GO545699 Mdas9011O23_e883.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TTTTTTAATTCAAATTATTGTTGTCCATTACTTGGTACCAAATTTACATCACCGACAACAATACAAACAA\n") - f.write("AAGTACGAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTG\n") - f.write("GCGACTGGGTCTGCAAGGTGGTCGGCAAGATTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAA\n") - f.write("AGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGC\n") - f.write("TTCTGGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCG\n") - f.write("AGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCA\n") - f.write("AGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGC\n") - f.write("TCCGGCCTTGAACCACACAGCCTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCGGGGAAAACGCAT\n") - f.write("CCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCACGGTTCTTTGGCGAGGGTCTCT\n") - f.write("GGGTCGGCTGAGAGTCCAGCGGTGT\n") - f.write("\n") - f.write(">gi|226790935|gb|GO545698.1|GO545698 Mdas9011H09_e845.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("GAAAAAAATAGAAATTTACTCCAACATCAACAAATTTTCCACGCTCAAATCCACACTCAAACAAAAGGGA\n") - f.write("CTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTCACTTTCCGGGAACAAAGTTTGTGGCATAGTTC\n") - f.write("CAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTACCGGTGACAA\n") - f.write("TGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAG\n") - f.write("CTCAGCAAAAGCTTCTGGGTCGTCGGCAAGACCCAATGGGTCGAAGCTTCCGCCGGGGTAAAGTGGGTCG\n") - f.write("GTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAG\n") - f.write("CCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCT\n") - f.write("GAAGATCTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCT\n") - f.write("GGGAAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCAC\n") - f.write("\n") - f.write(">gi|226790934|gb|GO545697.1|GO545697 Mdas9003F14_e198.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S68465 L-ascorbate peroxidase (EC 1.11.1.11), cytosolic isoform - pepper, mRNA sequence\n") - f.write("TTTTTTTTTTTGAAATTACAGTATTATTTAATCAACGAGGATGATTACCAGCATTCCATCCAATTTAAAA\n") - f.write("ACATTCGTTCTTCAAATCGAACTAGAAGTCCCACTTCCTAAAATCTGATAAGATAAAAAAGAAAAGCACC\n") - f.write("AACTGCCTACAACCTCACAACCAAGAGGCATCCAAAAATACAAAAGAAAGGCGCACAGGCATTGGCTTCA\n") - f.write("TCCCTTGTAGTTCTCCAGCTCTGCTTAGGCCTCAGCAAACCCAAGCTCGGAGAGCTTCATGTGAGATTCA\n") - f.write("GTATAGTCAGCAAAGAAAGCATCTTCATCCGCAGCGTATTTTTCCACAAGAGGGCGGAAGACAGGGTCAT\n") - f.write("CCAGAAGAGCCTTGTCAGTTGGAAGCATTAGAAGACCTTCCTGGTCTCCACCAAGAAGCACCTTGAAGTA\n") - f.write("GGAGTTGTCAAAGATAAGGGGGTTGGGAGTCCAAGGTCCTTCAAATCCAGATCGCTCCTTGTGGCACCTT\n") - f.write("CCCAGGGTGTGACCACCGGAGAGAGTAACAATATCCTTGTCGCTGAGGCCCATGTTCTTGCAGAAGACAT\n") - f.write("CCCTCAAATGGTCATTACCCTTGGTAGCATCATGAAGACGGCCCTCTGGTGGTGGCACGGGGGCATCCGT\n") - f.write("\n") - f.write(">gi|226790933|gb|GO545696.1|GO545696 Mdas9011K18_e865.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S20941 protochlorophyllide reductase (EC 1.3.1.33) precursor - garden pea, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTGCAGTTTGCAACAGAGGTGAGTGATTTTATTCTCATTTGTT\n") - f.write("ACTAACACTAGTCATCCACACGAGAAAAATTGTCTATGACAGTAGAGCATTTGATTTCAAAATCTGCACT\n") - f.write("CTACAAATGGACCTGATCTCGGGTGACATCCTCCGCCTCCGAGGTAAAACATCAAGTTTCTATACTCAGG\n") - f.write("CCAAACCCACAAGCTTCTCACTGACCTCCCACACCTTGCGAGCCTTCTCCGCATCACTAGCTTCTTGGGA\n") - f.write("CAGTTGGTTCTCGAAGGAAGCCGAATCCTTGTTCCAGCTCCAGTAGACTCCCGACTTTGTCAAGCTTGGG\n") - f.write("TCGCTCACAACCTGAGCAAGTCTCTTTCCGGCTTCTTCTTCTGAGACGTAGCCCTTGGTGATGTACTTTT\n") - f.write("GGAATGGAGGGAACAGAAGCCTGAACAAGGGAATGTGCTCCCTGAACAAACCAGTGGTGGCAATGCAGCC\n") - f.write("GGGGTAAAGGGAAGTAAATGTTATCCCGGTTTCCTCATGGTAGCGCCTGTGGAACTCTTGCATTGTGAGC\n") - f.write("ATGTTGCAGACTTTGCTGTCCTTGTAGGCCTTGGCACCGTCAAAGTCTCCACCATCGATCATGGCCGAGC\n") - f.write("TGTTTAGACCGTTTAAGCCTCCTGCAAGTCCCCTC\n") - f.write("\n") - f.write(">gi|226790925|gb|GO545695.1|GO545695 Mdas9011G11_e840.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTGAAGAGAATTTAGTATTTGTATTCAATTTATCACATTAGCCATCAAATAAAATTTTGACATATTATA\n") - f.write("TTTAACATATCATTGGGAGATGTTTTAAGTATTCAAAAGTCTCTTTGATTTTATTGAAAAAATGAAATAA\n") - f.write("AAAATAAAAAATAAAAAATATCGTTTTTTCGCCACCCCCATAGGCTAGGCGGACGCCTATCAAGCTGCCA\n") - f.write("ACACTCCTATAACTATAACGATGATGACCATCAAAGCGGTTAAGAATCCCAAAACTATCAGATCCTTCTT\n") - f.write("CTTCCTCCTTATCTGACTTTCCAGCTGCCTGCAATGTTGTGCCATTAAAGGAATGCGTTCTCGATCTCGA\n") - f.write("TCTCGATCTCTATCTCTCTCTCGGCCTCTCTCTCTATCCCAATCTCGGTCTTGATCATAATTGGCGGTGG\n") - f.write("TTGCGGGCGGTGCGGCGTCGGAGGAATGGCGTGAGGGGGTGAGACTGGAGAGGAAATGGTGCTGGTGGCG\n") - f.write("CCTTGGATCTTCGGTTTGTCCTTGACGGAGTTGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790924|gb|GO545694.1|GO545694 Mdas9011M07_e872.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAP03871.1| oxygen evolving complex 33 kDa photosystem II protein [Nicotiana tabacum], mRNA sequence\n") - f.write("TTTTTTTTACGCATGTCAAATTTTGACGTATAATGATTTACCGTTAAAGAAGTTTGACTCCTTAAAAGAT\n") - f.write("AATGTACAAGAAAGATAATACATACAAGATAATAGGCATGATAATATACAAGAAGATAATGATCTGAGTG\n") - f.write("ATCTCAGTGCTTGTTGTTCAATTGGGTTACAAAGAGAGTTGAGCAACACCTTTTTAACTTATAGCAAAAT\n") - f.write("CTGAAACCCAGAATCACCATTAATACATAGAGGAAAACGAAACTAATCAAGCTGAGCATACCAAACTCCC\n") - f.write("TGGATTTTGACATCCTTTGGAGTCTTGGCTCCCAAGTCAGTGTCGGATGGCTGAAGGCTCTCGAACACCC\n") - f.write("CAATCAACTCACCAGTCTCAGGCTTGGTCTTTGTCACACTCAGTGTTATCTTCCCCTTCGATGCTGCTGT\n") - f.write("ATTCTTGGTGTTCTCCTTTGCCAGCTCCTCCTCGTCTCCTCTGCCTCCTGCCGGCAGTGCGACCGCATTG\n") - f.write("TCATAACCGGTGGATCCTCCTCTTCCCTTGGGGTCCAAGAAAGAGGATCCACGGTATGATGGTACTAGAA\n") - f.write("ACTCTCCCGTGAAATTTTCGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790923|gb|GO545693.1|GO545693 Mdas9003E12_e192.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n") - f.write("CAGGACTCCACTTTGATCCATGACCGCCATGCACACAGTCTCGAGCGTCGGAACTGTTAACCGGACTCCG\n") - f.write("GTGAGCCTGAACGGCTCCGGTTCCGGAAGCTCGGCCTTCTTGGGCACCACTTTGAAGAAAGCGACCTCAA\n") - f.write("GAGTCCCCTACCAAAAGATTGCATCTGCAGGCAAGTTAAAAATCAATGCGGAAGTCGACGAGAATAAGCA\n") - f.write("AACCAACAAGGACAGATGGAAAGGCCTTGCCTACGATATGTCCGATGACCAACAAGACATAACAAGAGGA\n") - f.write("AAGGGTTTGGTTGATTCTGTGTTCCAAGCTCCCCAGGGGAGTGGAACTCACTATGCTGTCATGAGCTCAT\n") - f.write("ACGAATACATCAGTACCGGACTTCGAGAGTACAACTTTGACAACAACATGGATGGGTTTTACATCGCTCC\n") - f.write("AGCTTTCATGGACAAGCTTGTGGTTCACATAACCAAAAACTTCATGAGCCTGCCTAACATTAAGATTCCT\n") - f.write("CTCATTCTTGGTATATGTGGAGGATAAGGTCAGGGAAAATCCTTCCAGTGTGAGCTTGTGTTTGCCAAGA\n") - f.write("TGGGAATTACCCCCATCATGATGAGTGCTGGAGAATTAGAAAGCGGGAATGCAGGAGAGCCCGCGAAACT\n") - f.write("GATCAGGGCAAAGTACCGTGAGGCTGCAGATATCATCAAGAAAGGAAAAATGTGT\n") - f.write("\n") - f.write(">gi|226790922|gb|GO545692.1|GO545692 Mdas9011F23_e839.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n") - f.write("TCAACACCACCAAAACTTCAAACAGAAAAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAG\n") - f.write("CATTTGCTGGCCAGACTGCTTTGAAGCAGTCCAGTGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGG\n") - f.write("CCGCTTCTCCATGCGGCGCACCGTCAAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAG\n") - f.write("TACTTGGGACCATTCTCCGAGCAAACTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGG\n") - f.write("ACACTGCTGGACTATCTGCAGACCCCGAAACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAG\n") - f.write("ATGGGCCATGCTTGGTGCACTGGGATGCGTCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGC\n") - f.write("GAGGCTGTCTGGTTCAAGGCTGGATCGCAAATCTTCTCTGAGGGCGGCCTTGACTACCTTGGCAACCCAA\n") - f.write("ACCTTATCCATGCTCAGAGCATCTTGGCAATCTGGGCTGTCCAGGTCGTGCTCATGGGATTCATTGAGGG\n") - f.write("ATACAGAGTTGGAGGAGGACCACTCGGTGAGGGACTAGACCCACTTTACCCAGGAGGGGCCTTTGACCCC\n") - f.write("CTTGGACTTGCTGATGATCCCGAAGCTTTTGCTGAACTGAAAGTGAAGGAACTTAAGAAC\n") - f.write("\n") - f.write(">gi|226790921|gb|GO545691.1|GO545691 Mdas9011F06_e836.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF71695.1|AF198168_1 phospholipid transfer protein [Aerides japonica], mRNA sequence\n") - f.write("TTTTTTTTGTATAAAAGGGGATCATTTAATTATTAATAGATGGTAATGGATTACGTACAATCCTTATACA\n") - f.write("GAACGATTCGACCCTTCCAGATTATTAAGTTCCACAAAAGCATTGTGATTTAAACAACTAAGAGGTCTGT\n") - f.write("CTAGCTATATGGCTTCGAGGAATAGTCTTCTCGGAAGCTTTATTCTCCATTCTCCAATCCTCCTATGGAT\n") - f.write("TCAGCTTACCGCAGAGCAATTTGTAGAGGGGTAAACTTTGTAAGGACAAGGAGAGCCACAGACATCACCA\n") - f.write("AGAGTGTTAATCCGGTCATAATTAATCCCGGGGATTGCTGCAGCTCCTTCCTGAATGCAACTACAAGCAA\n") - f.write("TTCTCCGGTCCATCGTGGTGTTTTGTGCAGCATTCAGCTCTTTTATGCCTTTACAGCAATCTGGAGGCAC\n") - f.write("TGTGCCTCCAAACACTCCAAAGGGTATGCATGGAGTGAGCCAAGCTACCACTTCACCACAAGTTATGGTG\n") - f.write("GCATTACTGACAAAAGGAGCTATCACAAATAAGAACACTATTGCCACGATGACCGAAAACCTGGCCATGG\n") - f.write("TTAGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790920|gb|GO545690.1|GO545690 Mdas9003D19_e189.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) (PS I subunit 5) pir|A60695 photosystem I chain II precursor - cucumber prf|1710320A photosystem I 20kD protein, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTAACCCAAATCATGTTTCTGAGGTTGCATTTTAATGAAATCAA\n") - f.write("ATTACAAGAAACACAAATTATACTCACATTGCCATCATGATTATAAATACAATGCAAATTACACAAATCA\n") - f.write("ATATTATCATCATATGTCATAGACTTGCTTGCCGGTGAACTTGACCTCAATCGGGCTGACATTCTTCCCA\n") - f.write("ATCGACCTGAAGTTCTGGCCAACCCCTTGGCGCCCAGGGTTCACCTTCTCAGGGTACACACCATCCTTGG\n") - f.write("GGTGCAAGTATTGGACCTCCCCGTTAGGGAAAACCCTGTAAAACTGGTACTTAATCTTGTACTTGGACCT\n") - f.write("AAGCCTAGTTCCAAGAGCCAAGCACTGCTCTTTCCTGGCCAGTTTCAGCAAGTTAGGACCCTCCCTCATG\n") - f.write("ATGGCAGCTCCGCCAGTCGGCATCTCAAATATCTGCTCCTTTGGTGACTCCCATGTGATCACGTAAAACT\n") - f.write("CTTCCTCCTGCGCTTTCCTCAACAGCCCGCCAGTGCTGCCACCGAAGATCGGTGAGAGGTGTTGTTGGGT\n") - f.write("CCAGCTCGGGGTGGGGTGAAGCCTACCGGGGCCTCCTTTGTGGGGGTCACGGTTTTTTCCTCAGCGGAGG\n") - f.write("CATTGATCCTCATCG\n") - f.write("\n") - f.write(">gi|226790912|gb|GO545689.1|GO545689 Mdas9011I24_e851.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTAGTACTAACAATAATAATTATTAATAATAACTTGTTTATTTAGTAAGTGAAATGCATTTCACATGACA\n") - f.write("ATTATGGCAACCTATTAAGATTAAGAGCCTGTTTAAGGAAGTTTAGCATGATAAAAGGACAGGCACTTTA\n") - f.write("TTTATTAGTACCGAGTAAGTTTGCCTGCCTGC\n") - f.write("\n") - f.write(">gi|226790911|gb|GO545688.1|GO545688 Mdas9011O19_e882.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P12302|PSBP_SPIOL Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving system of photosystem II) (OEC 23 kDa subunit) (23 kDa thylakoid membrane protein) pir|S00005 photosystem II oxygen-evolving co, mRNA sequence\n") - f.write("TTTTAGAAGAAGCTCAAAGACAATTCACAATCTTAAGGTAATTTACATTACACAAACCCTCTCAAATAAA\n") - f.write("TTTCTTATGCAACACTTGAAAGAACTTCGCAGCGCTCTCTACAAACTTTCCTTGCTCCTTTCGAACCACC\n") - f.write("TCTTCGTCTCCGGCTTGTGCCTTTAGAATCGTAGAGCTTCGCCGTCTTTTCACGGTGGCTCGTGATAAGC\n") - f.write("TCGGTGCTTCGCCTCCTTTCATTCTCCGTCGGCTCGTCCTTCGTCAACACAGATACGTAGTAGTACTGCT\n") - f.write("TTTCCGTCAATCACTCGACTAGAACTCTCCAATATGTTGGCTGTGGCCACGGCACCCGGGTCGAAACCAC\n") - f.write("CCTCGGATTCAGTCTTGCCAAAGTAGGCTTGTTTTGCCTAGCAAGTAGTCCACCTTTCGCGAGGAATTCC\n") - f.write("TCGGGGGAGCCATAGTCGGCGATGGATTTTCTTTGTCGGTTAGGGTGATTTGTGACGGACACATTTGCTG\n") - f.write("TTGCTGTCGAAGTTGTCCTCGTACCTAAGAACTTGACCAGGGAACTCAACCTCTTTGCTAGGGTTCCATT\n") - f.write("TTGCAGGAATGGATAGCTT\n") - f.write("\n") - f.write(">gi|226790910|gb|GO545687.1|GO545687 Mdas9011E23_e833.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_176352.1| 60S ribosomal protein L3 (RPL3B) [Arabidopsis thaliana] sp|P22738|RL3B_ARATH 60S ribosomal protein L3 pir|B96641 60s ribosomal protein L3 [imported] - Arabidopsis thaliana gb|AAD25547.1|AC005850_4 60s ribosomal protein L3 [Arabid, mRNA sequence\n") - f.write("AAAGCATTCAGCAAGTACTCAAAAAAGTATGAGAGCGAAGATGGGAAAAAAGACATCCAGGCTCAGTTGG\n") - f.write("AGAAAATGAAGAAATATTGCACTGTGATTCGTGTTTTAGCCCACACCCAGATTAGGAAAATGAAGGGATT\n") - f.write("GAAGCAGAAGAAAGCCCATCTGATGGAGATTCAAGTGAATGGTGGGGACATTGCAAAGAAGGTTGACTAT\n") - f.write("GCTTATAGCATGTTTGAGAAGCAGGTTCCTGTTGATGCTGTTTTCCAGAAAGATGAGATGATTGACATTA\n") - f.write("TTGGGGTTACTAAGGGGAAGGGTTATGAGGGTGTGGTGACTCGATGGGGCGTCACCCGTCTTCCACGTAA\n") - f.write("GACCCATCGTGGTCTACGTAAAGTAGCCTGTATTGGTGCCTGGCATCCAGCTAGGGTGTCGTTTACTGTT\n") - f.write("GCCAGGGCTGGGCAGAATGGTTACCACCATCGTACTGAGATGAACAAGAAGATTTACAAGCTCGGAAAGG\n") - f.write("CTGATCAAGAGTCGCACTCTGCAATGACTGAATTTGACAGGACTGAGAAGGATATTACCCCGATGGGAGG\n") - f.write("TTTCCCACACTACGGTGAAGTGAAGCAGGATTACCTTCTAATGAAAGGCTGCTGCGTGGGTCCTAAAAAG\n") - f.write("CGCGTTGTTACTTTGAGGCAGACGCTTCTGAAGCAAACATC\n") - f.write("\n") - f.write(">gi|226790909|gb|GO545686.1|GO545686 Mdas9003B05_e176.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGGGTTTGAGAGAGAAATGGGGGGAAACACAGAAATTTTGATAATTCCAGATGTGCCCTTTGCCGGT\n") - f.write("TTGCACTTAATAACAAAGAGAATGTGAATTATAACTGCCCAAGCTTGCCTTGTGGAGGCAGTTACGATTT\n") - f.write("GCATCTAGCAAATTGTGTAGGC\n") - f.write("\n") - f.write(">gi|226790908|gb|GO545685.1|GO545685 Mdas9011K17_e864.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("ATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCGA\n") - f.write("AAACAAACGAGAGTGCCTCGAAAAAGGGACAGAAAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCC\n") - f.write("CTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAAAGCCACAATGGTACATACAACAAC\n") - f.write("AACATTATTTATGAAAATTGTAAAACAACTTAAACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACT\n") - f.write("GCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTC\n") - f.write("CAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTT\n") - f.write("CCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGC\n") - f.write("AGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAA\n") - f.write("\n") - f.write(">gi|226790907|gb|GO545684.1|GO545684 Mdas9003F12_e197.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_175633.1| photosystem I subunit VI precursor [Arabidopsis thaliana] sp|Q9SUI6|PSH2_ARATH Photosystem I reaction center subunit VI-2, chloroplast precursor (PSI-H1) pir|C96562 photosystem I subunit VI precursor [imported] - Arabidopsis thali, mRNA sequence\n") - f.write("TTTTTTTTTTTTAAAAATAATATCATGATCAAACAATAATCTATTAAAATATAAATAGTAGTTCCCAAAT\n") - f.write("ATCTTTAACATATTGCCAAATTTAGGGGTTTTAATTCTGCATTAAACGTACTTTACAATTACAAAATAGA\n") - f.write("GAAGCAATTACACATACATGAGGAAAAGCATGAGAAAATGAGGATTAAATCCCATATAAGAATTAGATCT\n") - f.write("TGCCACGTGGCCCCAACTTGGGTGGAAGTTGTGGGCCCTTCTTGATTGGTAGAATGTCATCGGAGGCAGT\n") - f.write("GGCACTAAGGTAGGCAATGGTGGAAGCTCCTCCCAATATCAAGAACTTGAGGAGTAAGCCTCTCTTGGTG\n") - f.write("AATGGAGCAGCAAATGTCTCAAAGAACTTGCTCTGAAGAGGGTTGTAAGGTGAGGGCGCATCCGAACCAT\n") - f.write("ACAAGTCCCACTTCCCGGTGGTGTTGCCCAGATCCTCAAGGTCAAAGTAGATGCTCTTGTCTCCGTACTT\n") - f.write("GGCCACCACAGCACCATTCCTGATGTTTTTGGTTCTGATGCTCTGGCGAGTGGGCTTCACAACGAGCTTT\n") - f.write("GTTCCGGTGAGGGAGCTTCCGCCGAGGCCGTTAATGGCTGCAGGTTGAACAGCTGCTAGGGTTGCCAAAG\n") - f.write("ATGCCATTGCCTAACAATAATATTGGTCTACTGCTACTCTTTGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790899|gb|GO545683.1|GO545683 Mdas9011I02_e849.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188003.1| root hair defective 3 (RHD3) [Arabidopsis thaliana] gb|AAB58375.1| root hair defective 3 [Arabidopsis thaliana] gb|AAM12987.1| unknown protein [Arabidopsis thaliana] gb|AAM91201.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("CACTTTTAGACTTTAAGAGATATAACCAAGTAACCCTAGAGTAGTCATCTATGAATGTAACAAAATACTT\n") - f.write("GTACCCATCAAATGACTCAACACGGGAAGGTCCCCAAATATCTGAGTGTACAACTTCAAAGGGTTTACTA\n") - f.write("GTTCTAGATTTAGAGGGTACAAAAGGTAGCCTAGTGGCTTTTGACATTTGACAGATCTCACACTCATGTG\n") - f.write("TGTTGGTACAATAATTTGGAAATAACTTAGACATTACTGGTTCGGAGGGATGAGCTAGGCGTTGGTGCCA\n") - f.write("AAGTTGATGCTTCTGGACATGGCTTAGGTTGGCAATGGGTTCCTTAACTTGATTGAACTCCTTTGAGAGG\n") - f.write("TAGTACAGACCATTTAAGAAAAAACCCTCACCAATCTTCTTTTGAGTGACTCGATCATATTTATCATCAC\n") - f.write("AATGTCGGATATTGCCATAGCAAATAGAGCGCTTTTTTTCTCGAATGCAGTATCATCCTGGCCTCTCTCA\n") - f.write("CTTCCATCAGTACCCTCAATATCCAAGGCGAGGGTGCAAGGCTCAACGCCAACACACTTGGCAATCCAAA\n") - f.write("TGCCCTTCGTTGTTTGGCTCCTCCTATCTGGATTCATCTCCTGAAACTTAGTGTCGAACAGATGGTTCAT\n") - f.write("CAAAGTGCTCTTTCCTCCACTCTGAGGACC\n") - f.write("\n") - f.write(">gi|226790898|gb|GO545682.1|GO545682 Mdas9011H14_e846.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26909.1|AF319165_1 dehydration-responsive protein RD22 [Prunus persica], mRNA sequence\n") - f.write("ACTGCGGAATCCATCCCATTTTCGTCCAACAAGCTGCCAGAAATCTTCAACCAATTTTCAGTGAAATCGG\n") - f.write("GTTCCGTGGAAGCGGATATAATCAAGGGTACAATTCAAGAGTGTGAGAATCCAGCCATTAGAGGAGAGGA\n") - f.write("GAAATATTGTGCTACCTCTTTGGAGTCCATGATTGACTTTAGCACTTCTAAGCTTGGAGGAGGAAATGTT\n") - f.write("CGAGCAATTTCGACAGAAGCCGGAAAAGGAGCTACATTGCAGAAGTACACAATAACTTCTGGAGTGAAGA\n") - f.write("AGTTGGCGGCGGATAAGTCGGTCGTGTGTCACAAGCAGAACTATCCCTATGCTGTCTTTTACTGCCATGC\n") - f.write("AACAAAAACAACAAGAGCTTATGTGGTGCCCCTGAAAGGTGCTGATGGGGTGAATGTTAAAGCAGTAGCA\n") - f.write("GTCTGCCATACAGACACATCGGAGTGGAACCCTAATCATTTGGCCTTCCAAGTTCTCAAAGTTAAGCCGG\n") - f.write("GAACTGTTCCGGTCTGCCATTTCCTTCCCAGTGATCATGTTGTCTGGGTTCCAAACCAGAAATCTACCTG\n") - f.write("ATTTGACTGATCAACCTTTGAGTTCTACGTATGATGATGTGATCAGCTCAATTAGCATAGTTTGAGTGGC\n") - f.write("AAGAGTTTGAAATTAAATCGACCGTCGATTACTTCTTATTGTCACTATGTATTTCAGCCTATATATATAC\n") - f.write("TCATAAATGAAAGCATACTATCGTGTGGACTTGTACCAAAA\n") - f.write("\n") - f.write(">gi|226790897|gb|GO545681.1|GO545681 Mdas9011F14_e838.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTAAACAAAATAATTGCAAGAATTTCCATAGAAATACAAGCGCAAATTACAA\n") - f.write("AGAAAATATCAATAACCCAGCAAACAGAATATTTATTTTCTTCAGCTCCAATTACTCGTACTGACAGCTA\n") - f.write("CCGTCGTCACTCCTTGCTGCTGGGTTGAAGTTTGCAGCTGTTCGATCAGTGCAGCCTTCTGGGACTGGTA\n") - f.write("CATTAACTTGTTGGGCTGCCTTTCCATAGAATTCTCCTCGGTTAATGGAGTCCTGGTTTGCATCTCCAAG\n") - f.write("GGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCTCTTCACATTGTCCTGCTCCTGAACAAGCATT\n") - f.write("TGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGTTGATCGAAAGTCGGGGGACCTTCTTTTGAGT\n") - f.write("TCACAAGCTTCTTCCCAATCCCGTCAATTCCAACACCGGAAATCCACTTCCTCACTTCATCGTCATAAAC\n") - f.write("TCGAGCCCTTAGGGCACCGAAGAAATCAATGGATTGACCGGGGAATGTGTCAACAATCTTGACAACATCT\n") - f.write("TCCTGGGACACATTATCAGGCTTGAAGATTCCGGTGCAACACCGA\n") - f.write("\n") - f.write(">gi|226790896|gb|GO545680.1|GO545680 Mdas9009E19_e666.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTCTACAAAAATTAAGAGACAGCAGAGAATTAAATAATGAATAATTACAGACGAAATAATGGTGGG\n") - f.write("TGAAGCATATTCATATGCCAAAAGTATATACCATACAAAATGGACAGCACGAAGAGACATTTTTCTTTTA\n") - f.write("GCCCCTTGTTTAATGGAATCTCAGTCGGTGGGCTCTCCATGTTCCTTACAATAATGGTTCAACAACTTCA\n") - f.write("ACCCTCTCATTCAAAATTATCTTCATCGTCACCACCACCCCCCGTCGCCACCGCCACTGTATCACTCTTG\n") - f.write("TAGCAGTTGTAGGAAATTTGTAACTTGAGCTCATTTGGCCGATTCCTCGAGTCCGAGTTTCCGGAAAATA\n") - f.write("AATGTATGAGCTAGTTATATGAAGTGTTTTTCTATTCATATGTACGGAGGCCTCATTGCTACGTGACAGG\n") - f.write("CCTCGCGTACATGTTTCAAGAGGAAGGTTCTATATAACTCACACGTAAAACTTCGTCCGAACTATATCCG\n") - f.write("ATGCCCTCATAGTGTCGTACCATTGGAGAATTCGGGGCTGTAATTATGTTGGGGGAGGACTATCTGCGTG\n") - f.write("CACTTCCCAAACACATCCTCCATACTTTTACGCGAGAGAGCATATGGTGGTGTTGAACTCCTACAAGGAG\n") - f.write("TGAGGGGGCTTGAGGAGTTAATGGCGGTGTGACTAACCATGCTTTACC\n") - f.write("\n") - f.write(">gi|226790895|gb|GO545679.1|GO545679 Mdas9009B16_e647.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P02300|H3_PEA Histone H3 pir|S04520 histone H3 (clone pH3c-1) - alfalfa pir|A26014 histone H3 - wheat emb|CAA31964.1| histone H3 (AA 1-136) [Medicago sativa] emb|CAA31965.1| histone H3 (AA 1-136) [Medicago sativa] emb|CAA25451.1| H3 histone, mRNA sequence\n") - f.write("CCGTTTCAGGCCGGGAACTGTGGCGCTGAGGGAAATCAGGAAGTACCAGAAGAGCACTGAGCTCCTGATC\n") - f.write("CGCAAGCTTCCGTTCCAGAGACTTGTGAGGGAGATCGCACAGGACTTCAAGACTGATCTGAGGTTCCAGA\n") - f.write("GCAGCGCGGTGTCGGCGCTCCAGGAGGCGGCGGAGGCGTACTTGGTGGGTCTGTTTGAGGACACCAACCT\n") - f.write("CTGCGCTATTCGTGCCAAGAGGGTCACCATAATGCCCAAGGACATCCAGCTTGCTCGCAGGATTAGGGGC\n") - f.write("GAGAGGGCTTAAGAATTCCTAAATCTTAGGGTTTTGAATTTCCGCACACTGTACTGGGATATTT\n") - f.write("\n") - f.write(">gi|226790894|gb|GO545678.1|GO545678 Mdas9009N02_e703.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_682039.1| ORF_ID:tlr1249 hypothetical protein [Thermosynechococcus elongatus BP-1] dbj|BAC08801.1| ORF_ID:tlr1249 hypothetical protein [Thermosynechococcus elongatus BP-1], mRNA sequence\n") - f.write("TTTTGAAAGAAAACTGCTGCTCTTATTTATTTGGATATTGTTGCCAACAATGTATGTATATTGCTGCGCT\n") - f.write("ATATGATTACTGGATTACAGTTTCAAAACTTGTTCTTCAGCTGCAGTGAGCCTACCAGCTGAAGCTCCTA\n") - f.write("ATGAATTGGAAATACTCCTCACTTCTGCAATCATTGCAACCACATCATTGAGCTTGTTCACGGCTGAGCC\n") - f.write("GATGCCCACACCAGCAGCTCCTGCTGCTATTGCCATTGGGGCTGTAACTGCACTCAGTCCGGATGAACAC\n") - f.write("ATTACCGGAATCTTGACAGCACGGGATATCGAATATGCTGCTGCCAATGTTGGTGTTGCCTTCTCGACCA\n") - f.write("AACCAAGAACACCTGATTTCGAAGGACTAGTACATTTTCCTCCTTCGGTTTGAATGATGTCAACACCTTC\n") - f.write("CTGCTCCAGCATCTCTGCAAGCTTGACCTGATCTGGAAGGCTTAGTGTATGAGGTACAGTGACTGATAAG\n") - f.write("GTCACAGATGGAAGAATCCTCTTGGTCTCCTTTGTCAGATTCAAAATCTGCTCCGAAGTGAAAACCACTC\n") - f.write("CCATCTCGTATAAGGAGTCATAGTTTCCAATCTCAACCATCAGTGCTCCTGCTTCAACCGCAGCTGGAAA\n") - f.write("TGCCGCTGGATCCACAG\n") - f.write("\n") - f.write(">gi|226790887|gb|GO545677.1|GO545677 Mdas9009D21_e660.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_563634.1| expressed protein [Arabidopsis thaliana] pir|G86148 T1N6.14 protein - Arabidopsis thaliana gb|AAF78406.1|AC009273_12 ESTs gb|Z27282, gb|T44732, gb|Z29911, gb|AI997176 and gb|AI395420 come from this gene. [Arabidopsis thaliana] gb, mRNA sequence\n") - f.write("TTTCAATTGGTCAATTCATTACATTTACATCCATTCTAATATTACAACGTCGGCTGATCCCTTTTGAAGA\n") - f.write("ATCAAGGTGAATAACCCATTCTAATGAAAACATTACATCCATTCCAATTGATCAAATCATCAATGAAATC\n") - f.write("CCCCCTTTTTCTATATAATGGCGTCGGATTAAAAATTTCTGCTAGCAATCACATTCTATGCTAACGGTAG\n") - f.write("GACTACAGAACTGTTTCTTTTCTGCCTTTAGCTCAAAATGACTCCTGTTATTCATCAGTCTGAACTGTTT\n") - f.write("CTTTGCTGCCATTAGCTCGAAATGACTCCTTTGTTATTCCATAGTAGACTGGTTCTTCGCCTACAAAGGT\n") - f.write("AATGAAATTCCAGCCAAAAGCAGACCCACCGACAATACATGTCCCTTGAGTCTGACCATCTTCAGCCTGC\n") - f.write("TGCTTCTCGCTGGATACACCAGTTGGAAACTTATTTTCTGATGGTTTTACAAAAGCCTTTGTATCTTGGG\n") - f.write("GCTTTTCACCTGGCACATTCTTACTTCTTGCTGCCGAAACTGTTTCTGCCGTCATCTGTTTGCATAGTTC\n") - f.write("CATCAGAAGTTT\n") - f.write("\n") - f.write(">gi|226790886|gb|GO545676.1|GO545676 Mdas9009I24_e686.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9M5Q1|FUT1_PEA Galactoside 2-alpha-L-fucosyltransferase (Xyloglucan alpha-(1,2)-fucosyltransferase) (PsFT1) gb|AAF62896.1|AF223643_1 xyloglucan fucosyltransferase [Pisum sativum], mRNA sequence\n") - f.write("TTTTTTTTTCCACTCCACGAATTTTTATTTTTGCTAACATGGAATAACGTTCGTGTATATGAAAAATTCC\n") - f.write("ATGGTATTCCTGATCAAACAGTTACCACAACGGTCATATATCACAAGCTACCAACCTAAAACTCATCCTA\n") - f.write("ACGATTGACCAGCTTAAGAACCCAACTCATATCCTCACAATGCCTCCCATGAAGAACCAATGCACCTGGG\n") - f.write("TCGATTCCTGTCTTGGCCTTGCAATCGTAAAAGGGAGGTGCGTGGAAGCAAGGCTCCATTGACATTGCTC\n") - f.write("GTCGACAAGGAGGATTGGGTGCTGTACTGTTCTCCGGTTTGTAAAGTATCCACGGTGTCAGCCCCCCAAG\n") - f.write("ACTCTGCGCGACATACCCAAATGTTGACCATGAGCTTGTGACCAACACATCTGTCAAGCTTAGTAGATAC\n") - f.write("ATTTCGGCCCATGCCTTGCGGTTGTGCGTATGCTTCTCAGTTTGATGATACTCCTCGTGACTCGGCTGGA\n") - f.write("AAATGCCAACCACCTCCCCTGTCACAGTAGGATGCTCCCAGTAC\n") - f.write("\n") - f.write(">gi|226790885|gb|GO545675.1|GO545675 Mdas9009J02_e688.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CAACATGGTATTAAAAATTTAAATTTCTGGTTAAAATATTTACCAGGGCGGAAGAACTTTTT\n") - f.write("\n") - f.write(">gi|226790884|gb|GO545674.1|GO545674 Mdas9009B14_e645.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA74434.1| similar to hsr203J [Lycopersicon esculentum], mRNA sequence\n") - f.write("TTTTTTAAAGATAAGAAGTTGCAATTTTTATTTTCATTACGAAAGTATATATATATAGTGGGTATGAAAC\n") - f.write("AAACGGACCCATAAATGGCCACACATAGTAACGTTATTAGCAACTACAAAGTCGATATCTTTTAGTGCTT\n") - f.write("GTTGACAAAGTCTTTGATCCCAGAAATTAGAGCCTCAGTTTGCGCAGCCGTTTGAGGATCCATATCCACC\n") - f.write("GCAATCTTGTTAAGATAAAAGCTATGACTCATCCCTGGACTAATCAGAAGCTCCACATCCTTCTTAGCCT\n") - f.write("TCTTCATAGCGTCATAGTATTCCATCTCAGTGTCTATTATCATGTCCATCTCACCAATACATAGAAGAAA\n") - f.write("CGGCGGCAGCTTCAGAGTATCCAAAGGCGGTGCTTCGGGGCCCATCGGACAAGTTATTGGATGGTCCTTG\n") - f.write("GTCGACCCCACTGGCAGTGCCAAGCTCAAAAACTTGTCCACCATGTCTAGGGTTAGCAAAGGTGACTCTG\n") - f.write("GCTGCTCCAACTCCGACCTACTCCTCACCGCTCGAACGAAGCCTGGGTGGATAGGAATCCCACCCGCTAG\n") - f.write("CCTTAACGGACTCAAATCCACCTTCCCTGCTCGAGCGGCAATTTCATGCACGAGATTTCCCCTCGTGCCG\n") - f.write("AA\n") - f.write("\n") - f.write(">gi|226790883|gb|GO545673.1|GO545673 Mdas9009J01_e687.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P12301|PSBQ_SPIOL Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving system of photosystem II) (OEC 16 kDa subunit) pir|S00008 photosystem II oxygen-evolving complex protein 3 precursor - spinach, mRNA sequence\n") - f.write("CTAGCCACGGCTAGCCTGCCGGTGCTGCTGACCGTGTTCAAGCGTGACGAGCCACTTAGGTGGAGGCTGC\n") - f.write("CCTCCAAAACTGCCTGGGAGGAGCCGTGCATGCCAGCCACTGAAGCCATAGCTTGTGCCATTTCCTGAAC\n") - f.write("CTTCCTAACTTTCTGAGATAGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790882|gb|GO545672.1|GO545672 Mdas9009G20_e675.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTGCAGAGATGGCATCCATGACCATGACAGCTGCCTCATTCCTGACCGCAGGCTCAGCCTCAACCATCGC\n") - f.write("CAAACCTTCAACTTCCATGCCGCCGGAGCCTCTTCGTAGCCAAGGCCGCCGCCAGAGCCCCAGAGGGAG\n") - f.write("\n") - f.write(">gi|226790851|gb|GO546227.1|GO546227 Mdas9001C03_e12.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849433.1| expressed protein [Arabidopsis thaliana] pir|T09892 hypothetical protein T22A6.120 - Arabidopsis thaliana emb|CAB45064.1| putative protein [Arabidopsis thaliana] emb|CAB79339.1| putative protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("AAAAGGTAGAACCCTGCCCTGTTGTGAACTTGTGAAGGTCAAAAAATTCTACATTGCAAAAACAAATGAC\n") - f.write("ATCGGAGGTGAGAAATGAAATATACAACACTACTACAACAGCCTCGGCAACTCTCACAGTATCGAATACC\n") - f.write("CCCCCGTTCTTCCTCCCAGTACCAAACATCTGTACCATTTCATCTTTTTTCCCATTTTCTTCGACAACAC\n") - f.write("GCGGAATCCGCTACTGTCCCTCCAACTCTTCTTCGTCAGGTAATATTACAGTCAACAAAGAGTATTTCAC\n") - f.write("ACGGAGGGATATCCTGCCCTTCTCAACCACTAGCCTTGCCCCAGAAACAACCCAATAACCCGGAGTCTCC\n") - f.write("TGTGGCCCTCTTACCATCTCTGTTGTGTCAACGAATTTCCGAAGCTTCGGGGCTTGGATGGGTACCGGAG\n") - f.write("GACCTCCAGGGTAAACGGCGGAGTTTATGTTCACATCTGCAGGCCGTGGAGGTGGTTTCTGAGCTGTTGT\n") - f.write("AAAATGATGGCTGATTAGTGTTGATATGAGTCCGGAC\n") - f.write("\n") - f.write(">gi|226790850|gb|GO546226.1|GO546226 Mdas9001A12_e3.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC24588.1| late embryogenesis-like protein [Prunus armeniaca], mRNA sequence\n") - f.write("TCGAGAAAACTGGAGAAATCCCCATCCCTTACAAGCCTGATGTCGATGTTGAGAAGATCAGGTTTCAAAC\n") - f.write("CTTCTCCTTTGAGGAAACCGTTGCGGTCCTCCATTTGAAGCTGGAGAACATGAATGACTTTGACTTAGGC\n") - f.write("CTCAATGCTCTCGACTACGAGATTTGGCTGTGTGATGAGAGCATTGGGGGTGCAGAGCTCGCCAAGTCTG\n") - f.write("CCAATCTTACTAAAAAGGGCATTACTTATGTCGATGTTCCCATTACCTTCAGGCCTAAGGATTTCGGGTC\n") - f.write("TGCGCTCTGGGATATGATTCGGGGAAAGGGTACCGGCTACAGCATCAAAGGGAATATCAATGTGGACACG\n") - f.write("CCCTTTGGAGCCATGAAGTTGCCCATTGTCAAGGAGGGTGGTACTACACGCATCAAGAAGAACAAGGGAG\n") - f.write("ATGGCGGTGATGACGATGATGATGAGGATTAGAGAGGGATGTTGGGGTTGGGTTGACAAGCGAAACTAGT\n") - f.write("AGTTGTTGTCGTCTGTTTATCTGTACTGGTGTTTTGGAATAATAGATCAATATTAAGGCATGATTTCTGG\n") - f.write("TGGTAAGTTGAGCTGTTTTGGAGGAGAAATTGGTGTAATTGCTATGGTT\n") - f.write("\n") - f.write(">gi|226790849|gb|GO546225.1|GO546225 Mdas9001H15_e41.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTTGGGTAAACTCATATATTACAATTTAAAATAATGCCTCGTATCTCTTTCTTG\n") - f.write("\n") - f.write(">gi|226790834|gb|GO546224.1|GO546224 Mdas9001N19_e77.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO91861.1| TGB12K interacting protein 2 [Nicotiana tabacum], mRNA sequence\n") - f.write("TCGAGTAGAAGTGCCACGCATTCCTTCCTGCCATAACCGGCTGCATAATGAAGTGCGGTGTTTTTGTTCT\n") - f.write("TATCAAGAGCATCGACTCTTGCTCCAGCCTCAAGAAGAGCTTGAGCACACTTCACCTCACCATATCCACA\n") - f.write("TGCAAAATGTAATGCTGTCCTCCCTTCTGAATCTTCCTCATCCTTGTCAGCACCAGATGCTAAGGCAGCT\n") - f.write("TTCAAACCCTCCACGTCACCAACACTAGCAGTGTGATGAACAATTGATTCATCCTCATTTCCGGCATCTT\n") - f.write("CTGCTTCTTCTGGTGCTTCAGTAGAAGTAGCTGCATCCCCAACTGCAAGACCCATTGCTTCTCCCAACTT\n") - f.write("CTGCAAAACATCTTTATCATTCCAGTATCTCATCATGGCAGCTGGACCACCAGTTTCTATTTCTTCCAAA\n") - f.write("ATAAGTTTCAAAGAAAGATCTTCTTTGATACGTGACATGCGTTCCTCAAGCTGATCTTTGTTCGAGGGAT\n") - f.write("TGGCGAAACTC\n") - f.write("\n") - f.write(">gi|226790833|gb|GO546223.1|GO546223 Mdas9001H24_e44.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565906.1| oxygen-evolving complex 25.6 kD protein, chloroplast precursor, putative [Arabidopsis thaliana] gb|AAK64145.1| unknown protein [Arabidopsis thaliana] gb|AAC27838.2| PsbP domain protein, putative [Arabidopsis thaliana] gb|AAM62853., mRNA sequence\n") - f.write("TTTTTTTGCAATAGACAGAATTTTTTTAGCAATATATACTTCTTACACTGTCATTGGAGATTGCATTGCT\n") - f.write("CCATGACATTGGATTTCAGATGTCAAGCATTCTGAAAGAGTCTGCTACCACTTTAAGCTGGTTGCGGTAT\n") - f.write("CTTTTCCACCGTCTTTCGTTTGCTCCGACAATCAGGGTGTAGTATCTCCCGTTTCCAATGGCTATGGTTG\n") - f.write("CGAATGAAGTGGTAGCAAAGTTTGGAGATTCAAGTCCATACTCAATGGTGTAATAATTTTTCCCATCTAT\n") - f.write("GTTTTTCTCCTCGACGCCAAATATAGTTGCATACTGGTTTGGTGCAGCAAGTTTATGCCTCACCAGATCG\n") - f.write("GTAACAACCTGTTCCATTGGACCCAAATCATGGATGTCAGTTTTATTTGTGGGTATAAATCTCACTCTAA\n") - f.write("CATTATGCAGCTGCATATATCTGTCCTTGAATGCAGAGTCATGTGCTCTAAACTCAAAGTCCCTCCAATC\n") - f.write("GTTGGGGTAGTAGTATGAATACCCATCTACTTTGTCGACGAAAGCTCGAAACTTTTCCGGTATTTCTTGA\n") - f.write("GCAAAGAGGGAATTTGCATGAAGTAGACTTGTGGTTAGTGCCCCAAATCCTAAAAGTAGAGGCCTTCTCT\n") - f.write("TGCAATGGCTTTCTTCAATGGAGGCTGACTCTCCTGAGGCAGTGATTGATT\n") - f.write("\n") - f.write(">gi|226790832|gb|GO546222.1|GO546222 Mdas9001H01_e37.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_027545.1| expressed protein [Arabidopsis thaliana] gb|AAD17426.2| expressed protein [Arabidopsis thaliana] gb|AAM65678.1| unknown [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTCCACATCAACAACTCTATCCATTCTGCACCAAGTCCCAGAAGGTCATGTTGGGGTATATTGGAGAGGA\n") - f.write("GGCGCTCTTCTGAAGACAATTACAGATCCAGGTTTTCATCTCAAGCTGCCTCTGGTCACCCATTTTGAAC\n") - f.write("CAGTTCAAGTGACCCTGCAGACTGATCAGGTGAGGGATATTCCATGTGGTACAAAAGGGGGTGTCATGAT\n") - f.write("CAATTTTGAGAAGATTGAGGTTGTAAACAGGCTTCGTAAGGATTTTGTGTACGAGACGCTTCTCAATTAC\n") - f.write("GGTATCCATTATGACAATACCTGGATATATGACAAATTCATCATGAGATCAATCAGTTCTGCACCTCACA\n") - f.write("TTCTCTTCAAGAAGTTTATATTGATGTGTTTGATCAGATTGATGAAAAGATGAAAGAAGCTCTTCAGGGT\n") - f.write("GACTGTACCCGTTATGCTCCGGGTATTGAAATCATCAATGTCCGTGTTACAAAGCCTACCATCCCAGAAA\n") - f.write("GTATAAGACGTAACTTTGAGCAAATGGAAGAGGAGCGCACCAAGGTCTTAATTGCTATAGAGAGACAGAG\n") - f.write("AGTAGTGGAGAAAGAGGCAGAAACCAAGAAGAAGATGGCTATCAGTGAGGCTGAGAAGAATGCCAATGTC\n") - f.write("AGTAAGA\n") - f.write("\n") - f.write(">gi|226790831|gb|GO546221.1|GO546221 Mdas9009O02_e709.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n") - f.write("TTTTTTTTGCATTATAAAACAGGAAAGCGCTCAATATATAAATGGTTTCACCTCGCACATTGTCTCTCGT\n") - f.write("GGCAATATAATCTGATGAGTACAGAAGCCCTACTTTACCTCCCAAAAAAGGAAGCATAAATACAATTCAT\n") - f.write("CAGACACAACTGAATTAGTTAACGGTAACTTTACCGACCATGCCAGCTCCCTGGTGAGGAGAGCAGTAGA\n") - f.write("AAGAGTATGAACCTTTTTCGGTCAAGGTGATGGCGTAGGTCTCCCCGGGGGCATTCAGGAGGTCCTCCTC\n") - f.write("GCTCATCGATATCTTTCCGGCATCCACACCGCTGGGAACCTCGTCCTCGTCGAAGACAATGTTGTGTGGG\n") - f.write("AATCCAGCATTGTTCTTGAACACAATCTTCTCACCGGGGGCGACGGAGAAGCTGTTGGGGACGAAGGCCA\n") - f.write("AGCCCCCGTCATCGCTGCCGAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCGCTGGCTGC\n") - f.write("GGTGGCGGCGACGGCCACACCGACATCCTTGAGGGATGACTTGACGACGCACATCTGCCTTGGGGAGGCT\n") - f.write("GAGACCTTAACGGCAGCGCTAACCTTGGCTGCGCCGGAAGACTTGAGTC\n") - f.write("\n") - f.write(">gi|226790830|gb|GO546220.1|GO546220 Mdas9001C07_e14.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O04011|AB20_PRUPE Auxin-binding protein ABP20 precursor gb|AAB51240.1| auxin-binding protein [Prunus persica], mRNA sequence\n") - f.write("TTTACCTTCAACAACAAAGCACACACAACAAAACTTCTACTACAAACATACAAAAATCAAACGAAGCAAT\n") - f.write("CTTCTACAACGAATCAAAACCACCACTGAAAGGAAACCGAAATGGGACGTTCAACACAACAAGAAAGATA\n") - f.write("CAATATTTAGTGATAATGCTGGCTGAAATTCAAAGATGAGAGAGCTTAATTACTAATTAGTACCACCAAG\n") - f.write("AGCGGCCTTCAGTTTCTTGATCTGAGCAACGTCAAGGAAAGTAGTCTGCGCTATCAGTTCCGTTGGTAAA\n") - f.write("TCATTTTTAAACAGCGCATAGTCCAGAATCTGCAGCCCCGGGCTTGGACTACTGAAGCTAACAAATGCAA\n") - f.write("GGGCCGTAGCCTCACCTCCATTCACTTGGAAGTGCAGTAACCCCTGAGGGAAAACCATAATGTCTCCCTT\n") - f.write("CTCAAGAGTTTGTAGATAAACTGTGTTCGCTGAGGAAACAAAGCCGGCGCAGATGGTCCCTTCGATGACA\n") - f.write("ATTAGGACTTCCGAACCTCCAGGGTGTGTGTGAAATGGGATGACTCCACCAACAGCCAGGTCTAGACGCG\n") - f.write("CAAGTGAAATGCCAAGGCCGTTGACACCAGGGAACTGAGCAGCAAATGCAGGGGTGACTGCAGC\n") - f.write("\n") - f.write(">gi|226790829|gb|GO546219.1|GO546219 Mdas9001P07_e85.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_683304.1| expressed protein [Arabidopsis thaliana] gb|AAG09546.1|AC011810_5 Unknown Protein [Arabidopsis thaliana] gb|AAO22631.1| unknown protein [Arabidopsis thaliana] gb|AAO42362.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTCTGTCGAGTTTTACAACCTAATATGCACATCTGCGTGTCTAACACGTAAAAGGAAACAAAACCCCAT\n") - f.write("TTTACGCATGCAGCGGTCCCCGGCATGCCGCCAGAAACGTTTCTACAAAGCCGAAAGGGACTCGGTTCGC\n") - f.write("CACGAAACATCTGCAACGCCGCCCCCCGGGTAATCAAACAAACCGTCTAAAGCCAGGTACTCCACCCCAC\n") - f.write("CAATATAATTGTTATTAGCAAATTCAGAGTCGCCACCGATTCCGAAGTCGAACGAGTCGTAACTCGGAAT\n") - f.write("CATGTCGTTCTCGAACCCTACCATGCCATCCAATTCAACGGCCTCGGAGCCACTCGTGGTGAAATCAGCA\n") - f.write("GCCTCGATTTTTCCCTCCTCACTTGCTCCATTGGTCGGTGGAAGACCAAGCTCGTCGTCAGAAGCTTCCA\n") - f.write("GAAGATAACCAAGTTCTGGCTGCGTCGACTGGCCTGAATCTGACGTGGCTTCAGACCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790813|gb|GO546218.1|GO546218 Mdas9001I06_e46.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTGAAGATATTTTTTTTTTCCAGTAATTTATAAATGCAAAGGTCGTATTACAAGGTAGCTGCATAAC\n") - f.write("AGCAGAATCAAACAAGTACAACAACACAACCCACAATTTCAAGATAATAAAGTTACAACAACCTCATTTC\n") - f.write("TCTCTCCATGTAGGACTTTATTCTATAGCTATTTATATGCTACTCATCTCTTATTTGGAAGGAAAAGTAG\n") - f.write("CTAGTCTAGTTTAGGGAACAGTGGGAGGTAACGGCTTCCCAAGGAATGGATGCGGAGGAAATGGCTTCTT\n") - f.write("GAATTTTGGAATCGGCTTCTTGAAGAATGGATGGGGAAACGGCTTCTTGTAAACTGGAACTGGGGGAAGA\n") - f.write("AGTGGCTTCTTGTAAACTGGAATTGGCGGAAGAAGTGGCTTCTTGGAAACTGGAATTGGCGGAAGAAGTG\n") - f.write("GCTTCTTGAATTTTGGAAGTGGAAG\n") - f.write("\n") - f.write(">gi|226790812|gb|GO546217.1|GO546217 Mdas9001D13_e21.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTGGACATATGAAACTTTACGTACGTGCTATATTTCACAAAATCGTGCTACATATGGTGAATGAACAA\n") - f.write("AACAGAGCCACATATATACACAACATATGTGATCATCTGACCTAATTGCATTACAATTTGCTATCAGAAT\n") - f.write("TCACACCAGAACAACAGCATTCATCACGTTTGTTCAGGCTAGAAATTCCAATCAACATTTCCGACATAGA\n") - f.write("TTCACAGCGAAAAAAAGGTCACACCTTTTAATGCTTTATGCTCTACTTCTTAACACCATCAGCATCTTTC\n") - f.write("TCTACGACTACATTGATCTTCTCATACTTGAGATCCACAGCCCTTGCAGGAAACACAGCAAGGTACACCA\n") - f.write("GAACAACAGAATTCATCACATTTTCGGGTTAGAGATCACAAACCAGATTTGCAACATACATTCACAGAAA\n") - f.write("AAAAAAATAAAGCCACGCCCTTAAAGACCTTACAGACCTTACGCTCTACTTCTTAACACCATTGGCA\n") - f.write("\n") - f.write(">gi|226790811|gb|GO546216.1|GO546216 Mdas9001K17_e63.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567934.1| aminotransferase family [Arabidopsis thaliana] gb|AAL08279.1| AT4g33680/T16L1_170 [Arabidopsis thaliana] gb|AAL38732.1| unknown protein [Arabidopsis thaliana] gb|AAM51321.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTGCAGCAGCTGAAAAATGATTTGCATTTCCTAAAGACATAGAAATAGAATCCACAACGTTGAACATA\n") - f.write("AATGGAGCAACTGTCGATTTTATCTTCGAATCAAAATATACTAGACAGCAGATACTAGCCTCGCGAGGCA\n") - f.write("GACACTCCGGCTCACTTGTATAATTGCTTGAACCTTTTGCAAGCTTCTAATACATTTTTCCGGTGACCAA\n") - f.write("ATGCGCTAACCCTGACGAAACCTTCACCCCCAAATCCGAAACCACTCCCAGGTGTGGTGACCACATGAGT\n") - f.write("CTTCTCAAGAATCTCGCTGAATACATCCCATGAGCTTCGGCCAGGGAAGTGCACCCACACATAGGGTGCA\n") - f.write("TTCTTCCCTCCATACACCTTAAAGCCAAGAGATTCAAATGTCTCCACTATTATTTCTGTATTTTCTTTGT\n") - f.write("AGAAACCAATCACCTCACGCATAGCCTTAAGGCCTTCTGGTGAAAGGCAAGCAAGACCACCAGCTTGGGA\n") - f.write("TATATTGGATGCACCATTGAAGCAAGTACAAACAATGCGGTTGAAGTCCTTGGCAACAGGGAATCCATCT\n") - f.write("GAAAAGAGCAATTGCTTTGGAACAACAGTCCACCCCAGACGAACTCCTGTGAATCCAGCATA\n") - f.write("\n") - f.write(">gi|226790810|gb|GO546215.1|GO546215 Mdas9001F06_e27.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA11705.1| elongation factor 1 alpha subunit [Malus x domestica], mRNA sequence\n") - f.write("AGACTGGTGTCATTAAGCCTGGTATGGTGGTGACTTTTGGCCCAACTGGGCTAACTACTGAGGTCAAGTC\n") - f.write("TGTTGAGATGCACCACGAAGCTATGCTGGAGGCCCTTCCAGGTGATAATGTTGGATTCAACGTGAAGAAT\n") - f.write("GTTGCTGTCAAGGATCTCAAGCGTGGTTATGTTGCTTCCAACTCCAAGGATGATCCTGCAAAGGAGGCTG\n") - f.write("CTAACTTTACCTCTCAGGTCATCATCATGAACCACCCCGGGCAGATTGGACAGGGATATGCACCAGTTCT\n") - f.write("CGACTGTCATACCTCCCACATTGCTGTCAAGTTTGCTGAGCTTGTGACAAAGATTGACAGGCGATCTGGC\n") - f.write("AAGGAGCTCGAGAAGGAGCCTAAGTTCTTGAAGAATGGTGATGCCGGATTTGTGAAGATGATTCCAACTA\n") - f.write("AGCCCATGGTTGTCGAGACCTTCTCTGAGTACCCACCACTCGGACGTTTTGCTGTGAGGGACATGCGCCA\n") - f.write("GACTGTTGCAGTTGGTGTCATCAAGAGCGTTGAGAAGAAGGATCCAACTGGAGCTAAGATCACCAAGGCC\n") - f.write("GCCGCTAAGAAGAAGTGAACCGC\n") - f.write("\n") - f.write(">gi|226790809|gb|GO546214.1|GO546214 Mdas9001F03_e26.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF78526.1|AF195234_1 metallothionein-like protein [Pyrus pyrifolia], mRNA sequence\n") - f.write("TTTTATTCTAATATTTGCATATAAATCAAAGGGCCATGAACATTGGCCATTACATGACACAATCACAGAA\n") - f.write("ACACAAACATATGAGTGACATGTTTTCACAGACGTACAACATGTCACTCAACAGACTCAAATACTATAAG\n") - f.write("CAAACGAAAGACAAAGCCACAAAGTTATTTTTTCCCACAAACACTTTTCATTAATTAAGGGTCTATAATC\n") - f.write("CCTTAATTAATATGACACTTTTATTAATCACATCTTAATTTGGTTCTCTGGGCTTACTGACCACAGGTGC\n") - f.write("AGTTCACACATGGGCAGGTTGTGCCACACTTGCACTTTCCGTCGTTCTCGGCTGCGGGAGCGTCCACGAC\n") - f.write("GACGGTGTCCATGGAGCGGTTCTCAGTCTCCACGATCACCAAGTCGTACCCGTTTCCCTTTCTTCACGCA\n") - f.write("CTGGGAGGTGACATCACAATCGCAGTTTGCCGCAGTT\n") - f.write("\n") - f.write(">gi|226790808|gb|GO546213.1|GO546213 Mdas9001O06_e79.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK13030.1| ribonuclease-like PR-10a [Malus x domestica], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTAACTGATTTCATTATATTTATAGATAATACACTTACAGTCTGCAACTTTTTTTTCA\n") - f.write("AACAAATACATCAAGGGCAACCAGAAGATGATCGCAACCATAAACTTATTTTTCAAAGCCAAAGTGCCCA\n") - f.write("AAACCATGGCTACTTTGGGCTGACTAGAAAAAGCATACAAAGAAAAGCCACACAACCTTCGACTGAAGGG\n") - f.write("TGACACCCAAAATACCATAGAAACATATTAATTTAGTTGTATGCGTCGGGGTGGCCCTTAAGGTAGCTCT\n") - f.write("CAATAAGCTTGAACAAACCATGAGCCTTCTCTTTGCCAGCCTTGACGTGCTCTTCCTTGATCTCAACATC\n") - f.write("ACCCTTGGTGTGGTAGTGGCTGATACTCTTGATGATGGAACCACTTCCAGATGCCACCAACTTGGTCTCG\n") - f.write("TAAGAGACCTTCTCAATGGTGTCTGTCAAAGCATCTCCTTCAATCAAAGTGTAGGCGTATGAGT\n") - f.write("\n") - f.write(">gi|226790807|gb|GO546212.1|GO546212 Mdas9001K06_e61.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL86484.1|AC077693_23 putative beta-phosphoglucomutase [Oryza sativa (japonica cultivar-group)] gb|AAP55088.1| putative beta-phosphoglucomutase [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAAAAGAAATACTATCACGTTGCTTTTATTCACGAGTCGTCAAA\n") - f.write("AGAAGAGTCATTTGACAACTGTGCTTGCTAATAAGCTTTTACTCGTATACAACAACAAGATTGAGAAGTC\n") - f.write("CGAATGCCTGAATAGCGTACCAGAACAGAATCATAATATATATAAGGTTATATATTACTGGGAGTTGGAG\n") - f.write("TTGCAATTGCAACTGTTATTGCCTCTGGTGTTGCCTCTGCCGTTGCCTCGGGCTTCTTCTCCAACTTTTC\n") - f.write("CAGTGCTTCCCACAATTTCGTGTCCTCAAAATCTTTAATAACGAAGGAGACTCCAGCGTTAATCAATGAC\n") - f.write("GTCCCAGGATTCCTTGTAGCTATACCAACAACTGGCATTCCAGCTGCTACTCCAGCTGTCGTTCCTGAAA\n") - f.write("CGGAATCCTCAAAGATAAAAGTATGCTCATGTGACACTTCAAGTGTTTCAAGAGCCTTCAAATAAGGGTC\n") - f.write("TGGAAATGGTTTTGCTCGATCACATTCATTTCCAATAACGAGAATTTCAAAGAAGTCTGTGAGCCCTAAT\n") - f.write("GATGATATCATTAGCTCCCCACTTGCTCGTGGAGAATTTGTCACTGCGGCCCGTCTCAAG\n") - f.write("\n") - f.write(">gi|226790793|gb|GO546211.1|GO546211 Mdas9001N16_e76.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF78507.1|AF195204_1 carbonic anhydrase isoform 1 [Pyrus pyrifolia], mRNA sequence\n") - f.write("TTTTTTTTTTTTTACAAGCTCGAGGAAATTATAATTATTGCTGCAAAATATCGGTTACATTTGCAGACGT\n") - f.write("GCTTCCGGGGACATTGCAGATGAAATTAAGAAATAAATTAGAAGTACTTAATGATAATTAATTAGGAAGC\n") - f.write("AATTGAGTTGCATGGGAATTATGTGATTACGATCATACGGAGAAGTTGGGGTTGAGGCTAAAATCAACAT\n") - f.write("CCCAGAGCTCAAAATGTCCATTGATAAAGTCATAGTATCCTCCCTTGATTGCTAGGGTTTTCTTCAGCAA\n") - f.write("ACCATCTCTCACAAACGGATAGCTCAACAGGTTTCCGATCGATACATTCACCGCCTCCTTTTCGCAACGA\n") - f.write("CTGCATAGCTCAGGGAAAGGAGTATCAGGACCGTGATCTGCCT\n") - f.write("\n") - f.write(">gi|226790792|gb|GO546210.1|GO546210 Mdas9001C22_e18.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_178786.1| hypothetical protein [Arabidopsis thaliana] gb|AAM15495.1| hypothetical protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGAATGCCGTTACCACGTTTTTATTTGATAGGGGGGAGTATTGGCAGGGGGTTAAAACCGCCCTGGA\n") - f.write("TGAAGCGACCTCTCAGGGGGAGTATAACCGCCTACTGGATTTCGAAAATAGGGATCTCCGGATTCGGGAG\n") - f.write("CAGAGGCATTCGTGCTATTGCCTTTTCGAACAGGTGCTTTCTGAGCATCCGTCCTTGGCGGAAAGAGCCC\n") - f.write("CCTACGATCCTAAAGAAGTCTTTTTTGATTTCGTTTCCGAGGCGCGGAACGGGCTGGACGCCCATCACGA\n") - f.write("GTGGAGCCCTCGG\n") - f.write("\n") - f.write(">gi|226790791|gb|GO546209.1|GO546209 Mdas9001L09_e66.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAB64207.1| elongation factor 1-alpha [Zea mays], mRNA sequence\n") - f.write("GACAAATCGCCTTTGTTCCCATCTCTGGGTTTGAGGGTGACAACATGATTGAGAGGTCCACCAACCTTGA\n") - f.write("CTGGTACAAGGGACCAACCCTTCTTGAGGCTCTTGACCTGATCAACGAGCCCAAGAGGCCCTCAGACAAG\n") - f.write("CCCCTCCGTCTTCCACTTCAGGATGTGTACAAGATCGGTGGTATTGGAACTGTGCCAGTGGGACGTGTTG\n") - f.write("AGACTGGTATCGTCAAGCCTGGTATGGTTGTGACTTTTGGGCCAACTGGTCTGACCACTGAAGTTAAGTC\n") - f.write("TGTTGAGATGCACCATGAGGCTCTTCAGGAGGCACTCCCCGGTGACAATGTCGGGTTCAATGTTAAGAAT\n") - f.write("GTAGCCGTGAAGGATCTCAAGCGTGGTTTCGTTGCATCCAACTCCAAGGATGACCCTGCCAAGGAGGCTG\n") - f.write("CCAACTTCACATCCCAAGTT\n") - f.write("\n") - f.write(">gi|226790790|gb|GO546208.1|GO546208 Mdas9001E14_e25.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CCAAAACAAGCCGATAACATTAAGGAGGAGCAGAGTATATTAATGTGTATGAATCAACATCCAACCACTA\n") - f.write("GCCACAGATCCACATTTTCTGCCAAAATTAACACCAAATCCTCACTAAAAACACTTGACCCAACAGACAG\n") - f.write("AAAAAGAAGACGAAAAATTACTACACCAAAAGGAATCATCATCCACTTCATGTTGAATTCCAAAGATTGA\n") - f.write("AATCAAAGGAGATGACCCATAGAACCGAATACTTCCAAACACTCGAAACGAGTTTTTCATTCTTAGAAAC\n") - f.write("CACGACTCAATTAAGCAAAAACCAAACAGACCACCACCACAAGCACAGAGACGG\n") - f.write("\n") - f.write(">gi|226790789|gb|GO546207.1|GO546207 Mdas9009N19_e708.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_850942.1| leucine-rich repeat transmembrane protein kinase, putative [Arabidopsis thaliana] gb|AAL32758.1| Unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGAGTTTGAAAATTACAGTAGCCTGAAGGGAACAAGGGGACTAACTAGTAGTAGTAGATACATACAT\n") - f.write("ATCGTGCAAAAAGTCCTGCAACTATTTTACATCCACAAAACTGCAAACATACATATCTATATAATCTAAA\n") - f.write("TGCAATAATCCGAGGCTCTGGCTAATATGTTACAGGCAATCTCAGCTCTCGTAATTGGGCTGCTTCGACC\n") - f.write("AATTAATTTTCAAAGCGCGGCAGGAGTCTTGATTAGTTTCAATTCTCTATACCCTTCACTAGTTCCATTT\n") - f.write("TCTTATTACCAGCGGCATCATCTTTGCCGATAACAATTTTGAGCAATTTAAACGTCTCGTGAGCCTCTTC\n") - f.write("TAGCATTTGAACCACACTTCTCATGGAGGGTCTTAGCTCCGGCAGCCTAGCCGTGCACAGAACTGCAATT\n") - f.write("CTTAACACCTTGATAGCCTCTTCCTTGTACACCTCTGGAATATATGAGTCCACCATACTTAATATGCTCT\n") - f.write("CTCTACTCTTGAGCATGCTGCTTACCCAGCTCACTATGTCCTTGTTCTCCCCGAACTCTGCCTCTATCGG\n") - f.write("CCTTTTCCCCGTCACTAGCTCCATTAGTACCACTCCAAAGCTGTACACATCACTCTTCTCGTTCACTTTG\n") - f.write("TACGTGTATCCATATTCAGGAGCAATGTAGCCATGTGTTCCGGCAATAACGTGAGTAGAGTCCTTGCCTG\n") - f.write("CAGTGGCCTGAACAATCTTGGCAAGCCCAAAATCCGCAATTCTCGGGCTCA\n") - f.write("\n") - f.write(">gi|226790788|gb|GO546206.1|GO546206 Mdas9001D22_e22.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_188935.1| ADP-ribosylation factor, putative [Arabidopsis thaliana] dbj|BAB03042.1| contains similarity to ADP-ribosylation factor gene_id:F5N5.14 [Arabidopsis thaliana] gb|AAL36314.1| putative ADP-ribosylation factor [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCCGACACCACTTCCTGAACGATTAATCAAATATTTAACTCTAAAGGCGCTTCCTTTATCGCCTTGTCGC\n") - f.write("AAACACCGCTAAGCTTTCCCCATACGGATCGCAAAATTTCTGAAACCCCAAAGCTTTTGGGTGGATTCCT\n") - f.write("GATCCAAACCCAAAATTAATCTCGGGGGTTTCTCTTGGTTCCAATCCTCCGCTTCCCGAACCATCGGTAA\n") - f.write("CCGCCCTTCCCCGCCATCAACCGCCACCTCCTCCTCCTCCATCTTTCACCCTTCCGCCAATATCCAAATC\n") - f.write("CAGGGATTTTTGGGTTGGGGATAGAAGATGGGGGCATTCATTTCCAAGTTTTGGTTCATGTTGTTTCCTG\n") - f.write("CAAAAGAGTATAAGATAGTGGTAGTTGGGTTGGACAATGCTGGGAAGACCACTACTCTTTACAAATTACA\n") - f.write("CTTGGGAGAGGTTGTCACTACGAACCCAACTGTAGGCAGCAACGTCGAAGAGCTTGTCTACAAGAACATT\n") - f.write("CGATTCGAGGTATGGGATCTTGGTGGACAAGAAAGACTGAAGACTTCATGGGCAACATATTACCCGTGGA\n") - f.write("ACACATGCTAT\n") - f.write("\n") - f.write(">gi|226790774|gb|GO546205.1|GO546205 Mdas9001I24_e52.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTCGTTCCTATTCTTCTTTCTATTTCTGAGAAAAAGAGGGCTTTCAAAAT\n") - f.write("AAAGTAAAGGATTATTTCGTTTCGAATAGTTATTTATTAAATCGGTGGATAGGAGTATACTCTGGATCGG\n") - f.write("AATCGTGTCATGGGGAGTACTGCCTGATCATTTCTACCAACTTAAAGCCCCAATTAGTATTCTTTGTTTG\n") - f.write("TATATTATGTAAAAATGTCCTTTTGGAGAATTTACATAGTCTCCATTACTAATCCTTTCCATATGTTCGT\n") - f.write("GTTTCTAACCATCCACTCGTTTTTGCTCAATCCCCCGTTATGCTAATACATAAAAATGATAGTGAAAACT\n") - f.write("CAATACGGTTGATCTTTTGAACCCGCTTCAAGTCAGGATGACTAATCAACCAATCTTGGGGGAAACGGTC\n") - f.write("TCTTCTGTTTATGTTTATTTCCGCTTA\n") - f.write("\n") - f.write(">gi|226790773|gb|GO546204.1|GO546204 Mdas9001L07_e65.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n") - f.write("TATAATTTATTTCATGAATTTCTCAATAAACATCATCCTGAATCCGTTAAAACACCAAATTCGAAAACAA\n") - f.write("AAGAGATTGCCTCGAAAAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGGTCTTGAAACCCTAATCAA\n") - f.write("GGACAAACTTAAACAAACCACCGAAACCCTTGGCTAAGAGCCACAATGGTACGTACAACAACAATATTAA\n") - f.write("TTACGACGAAGAAACATGATGAAACATGAATAACAACAACAACAACAACTTAGTAGCCTGCAGGCTTGTA\n") - f.write("GGCGATGAAACTGATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATACGGATGAAGGCGTTGGGA\n") - f.write("TAGGCCTTCTTGGCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGCATCCGAACATGGGCAGCT\n") - f.write("TCCACATTGTCCAGTACCTTCCATCGTAGTATC\n") - f.write("\n") - f.write(">gi|226790772|gb|GO546203.1|GO546203 Mdas9001D03_e19.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n") - f.write("TCCAGCCCTCTTAGCACCGAAGAAATCAATGGATTGACCTGGGAATGTGTCAACAATCTTGACAACATCT\n") - f.write("TCATGGGACACATTGTCAGGCTTGAAGATTCCTGTGCAAACACCGATCCGGTCTTCCCTAGTGGGAGCCC\n") - f.write("AGTAGAACTTCTCCATACGACCGTCACGAATGAGAGGGGCATACAATGTGGAGAAATCGTTACCAGTGAC\n") - f.write("TATAATGGGGACTCTAGGATTCTCTTCCTTGTTGTACATACCAGGAAGCTGCACGTTTGTCGGGTTATCA\n") - f.write("GCAATGTTCATGAGGGTAGCATTCACCATCTGGTTGTTCACAGTGTACTGTGTGGTTCCACCCATCCTAC\n") - f.write("CGGCACCTGCATCGAGATCATTGATGAAGAGGGGACACATTTTTCCTTTCCTGATGATGTCCGCAGCCTC\n") - f.write("ACGGTACCCTTTGCCTTGATCAGGTTTCGCGG\n") - f.write("\n") - f.write(">gi|226790771|gb|GO546202.1|GO546202 Mdas9001F12_e28.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46280|EFT2_SOYBN ELONGATION FACTOR TU, CHLOROPLAST PRECURSOR (EF-TU) pir|S60659 translation elongation factor EF-Tu precursor, chloroplast - soybean emb|CAA61444.1| EF-Tu protein [Glycine max], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTAACCTACAAGATATATAACATTTCATGGTGGAAATTGCTTCA\n") - f.write("AAATGTCAAAAACCAGATAAAAATTGAAGCTGAAAGAGTTCAAGTTGGGCACCAAATTGCAAAAACAAGT\n") - f.write("TGAGACCACCACATAATTTGTATTTTCTATCACTCAATAATGGATTGAATAACACCAGCTCCAACAGTCT\n") - f.write("TCCCTCCTTCTCTGATGGCAAACCTCATCCCCTGCTCGCACGCCACCGGAACAATCAGCTCGACCACAAT\n") - f.write("CTTAACGCGATCGCCAGGCATCACCATCTTCGACTCCTCATCCTTATCGTTCATAATCGAAGTCACCTTC\n") - f.write("CCGGTGACATCAGTAGTCCTCATGTAAAACTGCGGCCTGTAACCCGAAAAGAACGGTGAATGCCTTCCCC\n") - f.write("CCTCTTCCTTCTTCAACACATACACAATCGCCTCGAATTTGGTATGCGGGGTAATAGTCCCGGGTTTGGC\n") - f.write("CAACACCATCCCTCTCTGGATATCAATCTTCTGGATACCCCCTAAGCAACAACCCCACA\n") - f.write("\n") - f.write(">gi|226790770|gb|GO546201.1|GO546201 Mdas9001G07_e34.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF73016.1|AF262934_1 ubiquitin conjugating protein [Avicennia marina], mRNA sequence\n") - f.write("TCGACTCCTGCAAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAGGACCCGCCTGCAGGGATTA\n") - f.write("GTGGGGCGCCACAGGATAACAATATAATGTTGTGGAATGCTGTTATATTTGGTCCCGATGATACACCTTG\n") - f.write("GGATGGAGGCACATTTAAGTTGACTCTTCAGTTTACGGAGGATTATCCAAACAAACCACCAACAGTCCGG\n") - f.write("TTTGTTTCTAGAATGTTTCATCCAAATATTTATGCGGATGGAAGTATTTGTTTGGATATTTTACAGAATC\n") - f.write("AGTGGAGTCCTATATATGATGTGGCAGCTATACTCACGTCCATCCAGTCACTACTATGTGATCCCAACCC\n") - f.write("AAACTCTCCTGCAAATTCAGAAGCTGCTCGCATGTTTAGCGAGAACAAGCGTGAGTACAACCGAAGAGTG\n") - f.write("AGGGAAATCGTGGAACAGAGTTGGACAGCAGACTAACCCCGTCAGGGGG\n") - f.write("\n") - f.write(">gi|226790757|gb|GO546200.1|GO546200 Mdas9001I16_e48.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q43517|FER1_LYCES Ferredoxin I, chloroplast precursor pir|T07175 ferredoxin [2Fe-2S] I precursor, chloroplast - tomato emb|CAA99756.1| ferredoxin-I [Lycopersicon esculentum], mRNA sequence\n") - f.write("TTTTTTTTTTTCACTTCAAACAGAGAGAGATTCATACAAGGGTGAGTTTACAAGATACAATGATCTCCAT\n") - f.write("ACCACAAATGAGAGTACAAAAACATTAAGCAACTCATATAATTAGAAACAAGACAACCTTAACCCGAAAC\n") - f.write("AAACTAAAGCCAGATCCAACCAGCCAGCAGCCATCAAAACATGACATCATCATGAGAAAGCTCAAAAGCA\n") - f.write("CTTAACCAGTAAGCTCCTCTTCCTTGTGGGTCTCAAGTGTGACGTCAGACGACGGATAAGCCACACAAGT\n") - f.write("GAGCACAAATCCACCGTCCATCTGCTCATCATCCAAAAAGCTCTGGTCCGACTGATCCACACCCCCACTC\n") - f.write("ACAACTTTGCCGGCGCACGAGGAGCAAGACCCTGCCCTGCATGAGTAGGGAAGGTCAATCCCGGCCTCCT\n") - f.write("CCGCCGCGTCGAGAATGTACACGTCGTCGGGGCACTCAAACTCTTGTGGCCCTTCTGGTGTGAGCAGCTT\n") - f.write("CACCTTGTAGGCAGCCATCGCCACACGCCCTCCGCGGTTGGCCTTGAGCCCGAAAAGGGCCTGACCGACG\n") - f.write("TTGGGGGATAACCGCAGGCTGGTCATCGGCTGGCCGCG\n") - f.write("\n") - f.write(">gi|226790756|gb|GO546199.1|GO546199 Mdas9009P07_e713.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565494.1| expressed protein [Arabidopsis thaliana] pir|B84595 hypothetical protein At2g20940 [imported] - Arabidopsis thaliana gb|AAD29822.1| expressed protein [Arabidopsis thaliana] gb|AAM15213.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTCTGTAACATAAGTAATTGAGATCCGAATGAACCTAACAATCCTGTTCAAGCTAATCAGCATAACTTAC\n") - f.write("ATGATGAGATTTGCACAACACTTACATTATTAATGACAAAAAAGAACGGTATACGATCAAAGATCCAAAT\n") - f.write("CTGAATAGACGAAACAAAAATAACAATAACAATAATAAAAATCTCCTCACTGATTTGCTACGGGTGCGAT\n") - f.write("CACCACTCTTCTGCAATGCTTAAACTCAATCCACTTTCACTACTTTGTGCAAACTTTAGGATTCCATGTG\n") - f.write("ATGATTTTGTCGGTAATTACTATAACTTCCTTGGTTAATATAGTTCCGTTGCTCCCCAGGCAAAGATGTT\n") - f.write("CATAGACCGCCGGTCTTGATGAGCCTTCTCCTGGCCAAAAACCTAAACACGGGAGGAGTAAGCGCCAGAA\n") - f.write("TAATAGGAACCCGAATCGGAAACAGGGCCTTGTTGCAGAACAAAGCCAATGCCAGAGCACCACCAGTCGA\n") - f.write("AGCCGCGAGCTCAGCCGTCCGACTCCTCTCCTTCTCCACAACCACAGCCGTCGATTGCCCATTTTCCGAT\n") - f.write("ATGGGTCCGTCCCGAAACTCCGACCCATCGGAGATCACAGGTGGGTTCTCTGGGTTTTCGT\n") - f.write("\n") - f.write(">gi|226790755|gb|GO546198.1|GO546198 Mdas9001N22_e78.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|C71443 ribosomal protein L15.DL4730C, cytosolic - Arabidopsis thaliana emb|CAB10520.1| ribosomal protein [Arabidopsis thaliana] emb|CAB78742.1| ribosomal protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("AACCCTAGCCCCGACTGCCCAACCCTGCGCGTCGCAGCTCATTTCTGAACCGGCCATGGGGGCTTACAAG\n") - f.write("TACGTATCCGAGATATGGAGGAAGAAGCAGTCTGATGTGATGAGGTTCCTCCAGAGGGTCCGCTGCTGGG\n") - f.write("AGTATCGCCAGCATCCTTCGATTGTCCGAGTTACAAGACCCACACGCCCTGATAAGGCGCGTCGTTTGGG\n") - f.write("TTACAAGGCCAAGCAGGGTTATGTTGTTTACCGTGTCCGTGTGAGGCGTGGTGGCGCAAGAGGCCTGTTT\n") - f.write("CCAAGGGTATTGTATATGGAAAGCCCACAAACCAGGGTGTGACACAACTCAAGTTCCAGCGAAGCAAGAG\n") - f.write("GTCTGTTGCTGAGGAGCGTGCTGGGCGCAAGTTGGGAGGCCTCAGGGTTCTCAACTCATACTGGCTCAAT\n") - f.write("GAGGATTCGACCTACAAGTACTTTGAGGTCATCATGGTTGATGTTGCTCACAATGCCATCAGGAACGACC\n") - f.write("CAAGAATCAACTGGCTCTGCAACCCTGTTCACAAGCACAGAGAGCTTCGTGGTC\n") - f.write("\n") - f.write(">gi|226790754|gb|GO546197.1|GO546197 Mdas9001H11_e39.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_201433.1| GATA zinc finger protein [Arabidopsis thaliana] dbj|BAB10711.1| GATA-binding transcription factor-like protein [Arabidopsis thaliana] gb|AAM97115.1| GATA-binding transcription factor-like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTACGAGACTTTTAATGTTGGATTTAATTCCTAACAAATTTTATCACAAGGTTTAAATACTAATTTTT\n") - f.write("TTTAGTATGGGGCCATCTTTCCACTACCGTAACAACACGGAGACCATTAATTGATAATACAAGAAAAAGT\n") - f.write("ATAGAGCTAAAACCTAAAATCATGGCTAAATTCTAAAAGCTTCCTAAAAGCCTAGTACTACCACCCACCA\n") - f.write("ACAAAAATGTACAACACAATTGGGTCCATCCCAATCAAGCCGGTTCAACTGCACTATTCTCTAACTTTAA\n") - f.write("AAACTCCGAATCATTCGGTTCAACCGCGGTTCGGGCTCGCCAACCTCTTTCCTCTTCCTCATCTCCAACA\n") - f.write("CTTTACGGTGACTATTCGAGTGGACATCACCAGAGAAAGTCGGGCTACAAGCCGGCCTATACTCCCCTCG\n") - f.write("TGCCGAA\n") - f.write("\n") - f.write(">gi|226790753|gb|GO546196.1|GO546196 Mdas9001E02_e24.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T51616 chlorophyll a/b-binding protein [imported] - garden pea gb|AAF13731.1| PSI light-harvesting antenna chlorophyll a/b-binding protein [Pisum sativum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTAGTAGATGTAATGAGAATGATAATACTAATTGCCACCATGGTTCCT\n") - f.write("GTACACCGGTAAAACATTTTGTCTACATTGATGCTCACCATTTCACACTCACTCAAAGAACATTAATTCA\n") - f.write("TTGTTACAACATAAAAAAGAACAGAATTTCCATATTTTCTTCTTCCACTTTTCTTGCGTTGCAATGGATC\n") - f.write("TAGAAGCCTCTTAGGGTTTGGATAATGGTGTTATGCCATGGGTCTGAGAGGTGCTGCAACAGGTTGTCGA\n") - f.write("ACGGTCCTTTTCCGGTCACATTGTGTTGAACCACAAACCCTAGGAATGCCAACATTGCCAGTCTCCCATT\n") - f.write("GGCAAGTTCCTTCTCCTTGGCCTCGAGAGTCGGTGCGAAGTTGAGGGGGTTGAAGATGCCGCCTGGGTAA\n") - f.write("CCCACATCACCTGGGGGCAAGCTGTATTGCTTGAAGATGGGGTCTTGGTTCACACTTCCTGGGTTCTTGA\n") - f.write("\n") - f.write(">gi|226790739|gb|GO546195.1|GO546195 Mdas9001C19_e16.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S51658 light harvesting chlorophyll a protein precursor - Norway spruce emb|CAA57409.1| light harvesting chlorophyll a /b-binding protein Lhcb1*2-2 [Picea abies], mRNA sequence\n") - f.write("TCGTGCCGGATGCAGTTTTTAAAGCTTGAGCTTACATACAAGCAGGTAGCTTAAAGATCATCTATTGTAC\n") - f.write("ACACTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAGGCCCAGGCATTGTTGGTAACAG\n") - f.write("GATCAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAAGAAGCC\n") - f.write("GAACATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCCCTCT\n") - f.write("\n") - f.write(">gi|226790738|gb|GO546194.1|GO546194 Mdas9001F23_e30.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTAGGGGTTTCGCTACAAAAAAAAAGAAAAATCCTTTCTTGTCGAAGGACCCTTGTCGCCAATATTTACA\n") - f.write("GTCTGGCGTAGACTCCAAAAGTTTCTAACTTCATGTTCACAGAATTACTTGACAATTTG\n") - f.write("\n") - f.write(">gi|226790737|gb|GO546193.1|GO546193 Mdas9001C12_e15.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM13846.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGGTGTTGGATGATTTTGAGTCCTCGATTCGGGAACTCTCTCTTTCCTTGATTGTTGAAATGCTTAA\n") - f.write("GAACCAGAAAGATGCAATGGAAGATTCTGTTGAGGTCGTAATTGAGAAGCTGCTTCATGTTACGAAGGAT\n") - f.write("GTCGTTCCCAAGGTTTCAAATGAATCCGAGCACTGCTTGAGTATCGTTTTGGCCCAGTATGATCCATTCA\n") - f.write("GATGTCTAAGCGTTATTGTCCCTCTGTTGGTAACTGAAGATGAGAAAACTCTTGTTACTTGCATCAACTG\n") - f.write("TTTGACAAAGCTTGTGGGCCGGCTTTCACAAGAGGAATTGATGGCTCAGTTGCCATCATTTTTGCCTGCA\n") - f.write("CTTTTCGA\n") - f.write("\n") - f.write(">gi|226790736|gb|GO546192.1|GO546192 Mdas9001K04_e60.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n") - f.write("AAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCATTTGCTGGCCAGACTGCTTTGAAGCAG\n") - f.write("TCCAATGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCCGCTTCTCCATGCGGCGCACCGTCAAAA\n") - f.write("GTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTACTTGGGACCATTCTCCGAGCAAACTCC\n") - f.write("GTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGACACTGCTGGACTATCTGCAGACCCCGAG\n") - f.write("ACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGATGGGCCATGCTTGGTGCACTGGGATGCG\n") - f.write("TCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGA\n") - f.write("\n") - f.write(">gi|226790735|gb|GO546191.1|GO546191 Mdas9001G22_e36.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAA\n") - f.write("CGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCA\n") - f.write("AATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTACATACAACAACAACATTA\n") - f.write("TTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTG\n") - f.write("ACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCT\n") - f.write("TTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCAT\n") - f.write("AGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAAC\n") - f.write("CCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAAA\n") - f.write("\n") - f.write(">gi|226790734|gb|GO546190.1|GO546190 Mdas9001A20_e4.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n") - f.write("TTTCCTTCTACTTGTATCAAAATTAGTTTTGCAATGGCTGCTTCCATGGCTCTCTCTTCCCCAACCTTCG\n") - f.write("CCGGCAAAGCCGTGCAACTTTCCCCGGGAGCCACCGAGCTTTTCGGAAACGGAAGAGTGTCCATGAGGAA\n") - f.write("AACTGCTACCAAACAAGTTTCCTCTGGCAGCCCTTGGTATGGCCCTGACAGAGTCAAGTACTTAGGCCCA\n") - f.write("TTCTCCGGTGAGCCCCCAAGCTACCTCAAGGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCTGGAC\n") - f.write("TCTCAGCCGACCCAGAGACCTTCGCCAAGAACCGTGAGCTCGAAGTGATCCACTCCAGATGGGCCATGCT\n") - f.write("CGGAGCTCTTGGATGCGTTTTCCCCGAGCTCTTGTCCCGCAACGGC\n") - f.write("\n") - f.write(">gi|226790733|gb|GO546189.1|GO546189 Mdas9001B21_e10.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77603.1| plastidic aldolase [Nicotiana paniculata], mRNA sequence\n") - f.write("CTTTGCCAGAGGAGATAAGATTATATTAAACTTTGCTCTCTCACTAGGCTGCCACTCTTTGTAGCTAACA\n") - f.write("ATGGCTTCTGCATCTCTCCTCAAGTCTTCTCCGGTTCTCGACAAATCTGAGTGGGTGAAGGGTCAGACCC\n") - f.write("TCCGCCAGCCTTCCGCCTCTTCGGTCGTCAGATGCCTCCCCACTGCCCCGTCTGGTCTACCATTCGTGCC\n") - f.write("GGTTCCTATGCTGATGAGCTTGTTAAGACTGCTAAAACTGTTGCATCCCCAGGCCGTGGAATCTTGGCCA\n") - f.write("TGGACGAGTCCAATGCAACTTGTGGNCAGCGTCTTGCCTCAATCGGGTTAGAGAACACTGAGGCCAACCG\n") - f.write("CCAAGCCTACCGTACCCTCCTTGTGACTGCCCCTGGCCTTGGCCAGTACGTCTCAGGTGCCATTCTCTTC\n") - f.write("GAGGAGACTCTCTACCAATCCACCGTTGATGGAAAAAAGATCGTTGATGTGCTCGTTGAGNCAGGCATCG\n") - f.write("TCCCTGGGATTAAAGTCGACAAGGGTTTGGTGCCCCTAACGGGTTCCAACGATGAGTCATGGTGCCAAGG\n") - f.write("TCTTGACGGTCTTGCCTCTCGCACAGCTGCCTACTACCAGCAGGGAGCTCGTTTCGCCAAATGGCGTACC\n") - f.write("GTTGTGAGCATCCCCAATGGCCCATCAGCTCTTGCAGTAAAGGAAGCAGCATTGGGGTCTTGCCCGCTAC\n") - f.write("GCTT\n") - f.write("\n") - f.write(">gi|226790512|gb|GO545671.1|GO545671 Mdas9009F15_e669.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n") - f.write("CTACACTGTTTTTTCCTTCTACTTGTATCAAAATTAGTTTTGCAATGGCTGCTTCCATGGCTCTCTCTTC\n") - f.write("CCCAACCTTCGCCGGCCAAGCCGTGCAACTTTCCCCGGGAGCCACCGAGCTTTTCGGAAACGGAAGAGTG\n") - f.write("TCCATGAGGAAAACTGCTACCAAACAAGTTTCCTCTGGCAGCCCTTGGTATGGCCCTGACAGAGTCAAGT\n") - f.write("ACTTACGCCCATTCTCCAGTGAGCCCCCAAGCTACCTCAAGGGCGAGTTCCCCGGTGACTACGGCTGGGA\n") - f.write("CACCGCTGGACTCTCAGCCGACACAGACACCTTCGCCAAGAACCGTGAGCTCAAAGTGATCCACTCCAGA\n") - f.write("TGGGCCATGCACCGAGCTCTTGGATGCTTTTTCCACCGCAGCTCTTGTCCCGCAACGGCGTCATGTTCGG\n") - f.write("CGAGGCTGTGTGGTTCAAGGCCGGAGCCCAGATCTTCTCCGAGGGCGGTCTCAACTACT\n") - f.write("\n") - f.write(">gi|226790511|gb|GO545670.1|GO545670 Mdas9009C04_e650.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_084793.1| photosystem II protein D2 [Lotus japonicus] sp|Q9BBT0|PSBD_LOTJA Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein) dbj|BAB33191.1| PSII D2 protein [Lotus japonicus], mRNA sequence\n") - f.write("CTCGAACGTTCAGAAAATGCTATGAGGTGTTCGAAAATGGTTGAAGTAGTTGAATAGGAGGATCACTATG\n") - f.write("ACTATAGCCCTTGGTAAATTTACCAAAGACGAAAATGATTTATTTGATATTATGGATGACTGGTTACGGA\n") - f.write("GGGACCGCTTCGTTTTTGTAGGTTGGTCTGGCCTATTACTCTTTCCTTGTGCCTATTTCGCTTTACGGGG\n") - f.write("TTGGTTCTAAGGTACAACCTTTGTATCTTCATGGTATACC\n") - f.write("\n") - f.write(">gi|226790510|gb|GO545669.1|GO545669 Mdas9009K12_e691.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGCAAAATAAAACAAACAAAACATAACCTAACCTTCCAACATTTGCTACAGGGATTTCCAACGATAC\n") - f.write("ATAACATGCCAAAGATCATTATTCCCACAGATTTTAGTCATCCCTACTCTTGAGCATATACTTAATCATA\n") - f.write("GTTACCATTCACTAGCTCACATTTAATCGTTTAAAACAACATTATGGACGTAGTAACATGCCTTAGAGAA\n") - f.write("TCCACTCAATTCCTTACTGGATACACTCTTATTTTCACACAGATTTTCTAACTACTCTCCCTATACTAAG\n") - f.write("TATATGTGAGAAGATTGATGTAAACATGGAAACGAACACTCACACATGTTATAAAAGAAGCAATTTTCTG\n") - f.write("GAATGATTAAGCATTTATAGATATGATCTCATGAATGGAACGCTACTACTTAGATGCGAGAACCAGGGAC\n") - f.write("ACCATATGCTCAAACCAATCCCAAACTCCACATATTGAAATACATAACACTCAAGATAGAAGTTAAGGGT\n") - f.write("TGTAACGGGGCTTGGGGAATGGTTAACAAAGAAAGGATAGGGAAAACAAACGTTCTTCAAGCATTAGTAA\n") - f.write("GCAAAGTAGTAAATTTGAGACTTAGAATTCACTTAGATTGTAGAAATTAACTTTAAAACACAAAGGGAAG\n") - f.write("ATTTAAACAACTTCTTAGGGCCGAATTCATTGTTTTGGACCCTT\n") - f.write("\n") - f.write(">gi|226790509|gb|GO545668.1|GO545668 Mdas9009N14_e706.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T08089 chlorophyll a/b-binding protein type III Lhcb3.1 precursor - rape (fragment) emb|CAA43802.1| LHC II Type III chlorophyll a /b binding protein [Brassica napus], mRNA sequence\n") - f.write("CTTCTACACACTTCCAAGCTTCAACACAATTCCACGGATTACTTCATCACAAAACAAATCAAGTCAACTG\n") - f.write("AATTAAGTTGCGAAAGCTTGGAAAGTCATGGCAGCAGCTGCTAGCTCGAGCACTCTTCTAAGAACAACCC\n") - f.write("CATTTCTTGGCCAAAGCCGAGGACCAAGCTTCAACACTCTTAAGGATGTTGTGCCAATGGGAACTGGCAA\n") - f.write("ATACACCATGGGCAATGATTTGTGGTATGGACCGGACAGAGTGAAGTATTTGGGACCCTTTTCTGCTCAG\n") - f.write("ACTCCTTCGTACCTGAACGGAGAATTCCCCGGTGATTACGGATGGGACACCGCAGGGTTGTCAGCTGACC\n") - f.write("CCGAGGCCTTTGCTAAGAACAGGGCTCTTGAGGTGATCCATGGCCGGTGGGCTATGCTTGGAGCACTAGG\n") - f.write("CTGCATCACCCCAGAAGTTCTCGAGAAATGGGTGAGAGTGGACTTCAAAGAGCCAGTGTGGTTCAAAGCA\n") - f.write("GGAGCTCAAATCTTCTCCGAAGGCGGCCTCGACTATTTGGGTAACCCCAACTTAGTCCATGCTCAGAGCA\n") - f.write("TCCTAGCGGTGCTTGGGTTCCAAGTCATCCTCATGGGTCTCGTTGAAGGATTCCGCATCAATGGTCTTGA\n") - f.write("TGGTGTCGGAGAGGGCACAACCTCTACCCGGGTGGGCAATACTTC\n") - f.write("\n") - f.write(">gi|226790508|gb|GO545667.1|GO545667 Mdas9009K14_e692.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P23322|PSBO_LYCES Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving system of photosystem II) (OEC 33 kDa subunit) (33 kDa thylakoid membrane protein) pir|T06368 photosystem II oxygen-evolving co, mRNA sequence\n") - f.write("TTTTTTTTTACAAGAAAGATAATACATACAAGATAATAGGCATGATAATATACAAGAAGATAATGATCTG\n") - f.write("AGTGATCTCAGTGCTTGTTGTTCAATTGGGTTACAAAGAGAGTTGAGCAACACCTTTTTAACTTATAGCA\n") - f.write("AAATCTGAAACCCAGAATCACCATTAATACATAGAGGAAAACGAAACTAATCAAGCTGAGCATACCAAAC\n") - f.write("TCCCTGGATTTTGACATCCTTTGGAGTCTTGGCTCCCAAGTCAGTGTCGGAAGGCTGAAGGCTCTCGAAC\n") - f.write("ACCCCAATCAACTCACCAGTCTCAGGCTTGGTCTTTGTCACACTCAGTGTTATCTTCCCCTTCGATGCTG\n") - f.write("CTGTATTCTTGGTGTTCTCCTTTGCCAGCTCCTCCTCGTCTCCTCTGCCTCCTGCCGGCAGTGCGACCGC\n") - f.write("ATTGTCATAACCGGTGGATCCTCCTCTTCCCTTGGGGTCCAAGAAAGAGGATCCACGGTATGATGGTACT\n") - f.write("AGAAACTCTCCCGTGAAATTTTCGGGCTTGCCAGAGGCTACCAGCTGCTTGATGGTAAAGAGGAAGGGCA\n") - f.write("CGCGCTCGCCTCCCGGGAGCTGGACTGTCACTGCAGCGTAGTCAATTCCGTCTTTCTCTTCGAACTTGAT\n") - f.write("GGAGCCATCTGGAGCAACTTCGAAAGGTCCTTCGAT\n") - f.write("\n") - f.write(">gi|226790507|gb|GO545666.1|GO545666 Mdas9009E04_e664.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_051097.1| ribosomal protein L22 [Arabidopsis thaliana] sp|P56795|RK22_ARATH Chloroplast 50S ribosomal protein L22 dbj|BAA84424.1| ribosomal protein L22 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGCCCGGGGCTTTAATTTTTTCACAGTTGTGCCCTCGTTGACTTCGGCTTTACTAATGATTAAACTT\n") - f.write("GTTTCGTTCAAACCCTTATTGTGATTAGCATTTGCTGCTGCAGAATAAACCAATTTTAAAATGGCATAAC\n") - f.write("ATGCTCGATAAGGCATAAGTTCTAGTATCATAAGTGTTTCTTCATAGGACCGCCCACGAATTTGATCAAT\n") - f.write("TACTCTTCTCGCTTTGTGAGCAGACATACATATATGTTGACCTAAAGTGTATACTTCTGTATATTTCTTC\n") - f.write("ACCTTTCTCTTCTGTATCATAAGATTCACCTCTCATTAATGAACGATAAGCATCTATATTTTATTATTTT\n") - f.write("TTTATTAATTATTAACGACGGGATCTATTATCATTTTTCGCATGCCCCCGGAAATTTAGAGTAGGTGCAA\n") - f.write("ATTCTCCCAATTTATGTCCTACCATACGATCCGTTATATAAATAGGCAAATGCTCCTTTCCATTATGGAT\n") - f.write("AGCGATAGTATGCCCGATCATTGTCGGTATAATGGTAGACGCTCGGGACCAGGTTACTATTATTTCTTTT\n") - f.write("TCTGCTTTTGTGTTAAGTGTATTTATTTTTCTTAATAAATGATTTGC\n") - f.write("\n") - f.write(">gi|226790499|gb|GO545665.1|GO545665 Mdas9009L06_e696.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849293.1| expressed protein [Arabidopsis thaliana] gb|AAL91159.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("ACAGCTTATCTAGTCATAGAGGCGATACAGGGGATGGGAGAGAGTTTGTGCACGAAAACTGCGATTGCTA\n") - f.write("CTAAACTACTACTACCGGTTGACCGGTCATTAGCCAGAGCTCAGGGGAGCTCCAGGTTCCCGTCAACCGT\n") - f.write("GGAGTGGCTTCGGAATCAGAATTCAATTCGTCTTTAGAAGACCGATCATCCTTCACCTCATGCTCACAAA\n") - f.write("GCTTCGACTGATGATCACTCAGCTCGGCCTGCATATGTACATTTATACTCGCCATCCGGTCAAATGTTCT\n") - f.write("TCAAACCATCCTACCGTTTTCTTCTTCCTTTTCTCGTTTCATGCTCAAGCAAGCCTCAACACCGCCACCG\n") - f.write("CCATCAATGTTCCGGCTCTCAAGTAAATCTCGTTCATGCTTCTATCTACCCTTTTCATTATTTCCTCTTC\n") - f.write("TTGTAAACCTGGCTTCTTTGAATTCTTCCTGATTTGAACAACTGTGTCCCTCAGTTTATTCACCCCCCAA\n") - f.write("GAGAGCCAGACTAATGCAAATGCAACTCCGGTGTTCAAGAGTTTGGATGCACAAAGGGGTACCCTCCCAG\n") - f.write("AAGCTACTTTACAGAGGACAGAGAAAAGGACAGCCAAGCCAGTTCCAGCGATACCAGCAGAAAACTGGGT\n") - f.write("TAGGAGTTCCGGAA\n") - f.write("\n") - f.write(">gi|226790498|gb|GO545664.1|GO545664 Mdas9009C03_e649.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P08282|GLN1_PEA Glutamine synthetase nodule isozyme (Glutamate--ammonia ligase) (Cytosolic GS1) pir|AJPMQ1 glutamate-ammonia ligase (EC 6.3.1.2) beta, cytosolic - garden pea gb|AAA33669.1| glutamine synthetase (cytosolic GS1) (EC 6.3.1.2), mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTTGTCAAGAATTACAAGTAAAATGACATTAAAACCAACCAGCC\n") - f.write("CTTTGAAAAATACGGTTCATAGATGACACTTATTCAACACAATGGGCAGAATGATGAGGAATTGGAGCAA\n") - f.write("TTAACCACATCTTGGCACTTTTAATAGGGAAAATAGCAACGCAATACAATTTAAAGGACAAAGCTAATTC\n") - f.write("TAGTTTGTAGCTAAGGACACACAAGGATCTTTTAAACGGACCTGGCAAAACACATTTCCAGCCTCAATGA\n") - f.write("AAGACGGGACTTGGAACTGCACGGGTGTAAGTGCAGCGGTGTGTGCTCATGGCTTCAACAGAATGGTGGT\n") - f.write("TTCTGCCATCATAGAAGTGACAACATATGGATCCATGTTCCACGCAGGCCTCCTGTCCTCAAAATA\n") - f.write("\n") - f.write(">gi|226790497|gb|GO545663.1|GO545663 Mdas9009E03_e663.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O04011|AB20_PRUPE Auxin-binding protein ABP20 precursor gb|AAB51240.1| auxin-binding protein [Prunus persica], mRNA sequence\n") - f.write("TTTTTTTTCAATAAATAGGGCATTTACCTTCAACAACAAAGCACACACAACAAAACTTCTACTACAAACA\n") - f.write("TACAAAAATCAAACGAAGCAATCTTCTACAACGAATCAAAACCACCACTGAAAGGAAACCGAAATGGGAC\n") - f.write("GTTCAACACAACAAGAAAGATACAATATTTAGTGATAATGCTGGCTGAAATTCAAAGATGAGAGAGCTTA\n") - f.write("ATTACTAATTAGTACCACCAAGAGCGGCCTTCAGTTTCTTGATCTGAGCAACGTCAAGGAAAGTAGTCTG\n") - f.write("CGCTATCAGTTCCGTTGGTAAATCATTTTTAAACAGCGCATAGTCCAGAATCTGCAGCCCCGGGCTTGGA\n") - f.write("CTACTGAAGCTAACAAATGCAAGGGCCGTAGCCTCACCTCCATTCACTTGGAAGTGCAGTAACCCCTGAG\n") - f.write("GGAAAACCATAATGTCTCCCTTCTCAAGAGTTTGTAGATAAACTGTGTTCGCTGAGGAAACAAAGCCGGC\n") - f.write("GCAGATGGTCCCTTCGATGACAATTAGGACTTCCGAACCTCCAGGGTGTGTGTGAAATGGGATGACTCCA\n") - f.write("CCAACAGCCAGGTCTAGACGCGCAAGTGAAATGCCAAGGCCGTTGACACCAGGGAACTGAGCAGCAAATG\n") - f.write("CAGGGGTGACTGCAGCTATGATGATGTTTGTAGTGTTGCCAGCAACACCTAGGCCCGAGAAAACAAAGTC\n") - f.write("ATCTACTTTAACATTTGCAG\n") - f.write("\n") - f.write(">gi|226790496|gb|GO545662.1|GO545662 Mdas9009I12_e684.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n") - f.write("TTTTTTAAGAGCACCTACTGCATAGTGTACATTACAATACAAGATTACATGACACCAATCCGACATAGGA\n") - f.write("AAACAACATTATTTTTTTTTTACCCTTAACATCCTTAAAAAGTGCTTCTCTCCTTCCTCCCTCCCCTCAA\n") - f.write("TTATAACCTAAAAGAAAATGACTTAAAATGTGTAAAAGCAACTTCCATCATCACTTCTAGCCGTTGGATC\n") - f.write("AAAGTTTTCTCAGTTGGATCAGTGCAACCTTCAGGAACTGGAACATTCACTAGCTGCGCTGCTAGGCCTC\n") - f.write("CCACAGGAGCTCTCTAAATATCAAGGATCTAACCATAGAAAGTTCCTGTATTCATAGCATCTGAGTTAGC\n") - f.write("ATCACCAAGAGCAGCCTCGCTCAAGTACTTATCAGCCAATTGAACTCTCTTCACATTCTCTTGCTCTTGG\n") - f.write("ACAAGCATGTTTCCGTACTCGAGGAGCTTTTCGATAGTCATCTTCGGCTGCTCGAAAGTTGGGGGTCCTT\n") - f.write("CCTTTGAGTTCACAAGCTTCTTCCCAATGCTATCCACGCCAACACCCGTAATCCACTTCCTCACTTCATC\n") - f.write("GTCGTAAACCCTAGCCCTCAAGGCACCAAAGAAATCAATAGATTGGCCTGGGGAAGGTGTCAACAAGCTT\n") - f.write("GACAATGTCTTCCTTAGCAAC\n") - f.write("\n") - f.write(">gi|226790495|gb|GO545661.1|GO545661 Mdas9009D24_e661.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("CTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAG\n") - f.write("AAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGC\n") - f.write("TAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGA\n") - f.write("GGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGG\n") - f.write("ATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACAT\n") - f.write("GGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGAATCCTGGGGATCTGTGGTTCTCACGGTACACG\n") - f.write("AATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGATGTAGTCAACTTCCTTGG\n") - f.write("CCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCA\n") - f.write("CACCTGCATGCATTGCACTCTTCCTCCATTGCTTGCAAT\n") - f.write("\n") - f.write(">gi|226790487|gb|GO545660.1|GO545660 Mdas9009D02_e655.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P17067|CAHC_PEA Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) pir|S10200 carbonate dehydratase (EC 4.2.1.1) precursor, chloroplast - garden pea emb|CAA36792.1| precursor peptide (AA -104 to 224) [Pisum sativum], mRNA sequence\n") - f.write("TCGAGTTTGCCCATCACATGTTCTGGATATGCAGCCGGGAGAGGCTTTTGTTGTCCGCACAGTTGCTAAC\n") - f.write("TTGGTCCCACCCTATGATAAGGTTAAATACGCTGGGACAGGGGCGGCCATTGAGTATGCTGTCTTGCATC\n") - f.write("TCACGGTTTCATACATACTGGTGATTGGGCACAGTGCCTGTGGAGGAATCAAGGCACTCTTGTCTATTCC\n") - f.write("AAAAGATGGGTCTACCCTCGGCACTGACGTCATATAAGACTGGATTCGTATTGGATCGCCGGCAACGAAC\n") - f.write("AAGGTGAAGGCAGATCACGGCCCTGATACTCCTTTCCCTGAACTATGCACTCGTTGCGAAAAGGAGGCGG\n") - f.write("TGAATGTATCGATCGGAAACCTGCTGAGCTATCCGTTTGCGATAGAGGGTTTGCTGAAGAAAACCCTATC\n") - f.write("AATCAAGGG\n") - f.write("\n") - f.write(">gi|226790486|gb|GO545659.1|GO545659 Mdas9009E02_e662.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q04960|DNJH_CUCSA DnaJ protein homolog (DNAJ-1) emb|CAA47925.1| cs DnaJ-1 [Cucumis sativus], mRNA sequence\n") - f.write("TTCAAATTGATGCTATGTTACGGTGTGCAAATTCGCCATTTTAACAGCAGAACAAAAGCAGCAGAACAAA\n") - f.write("TTCTTAGCATTCAACAACAGACCAACAGACCAAACCACGTTTAAGTAGAATAAGCATCTCCTTAACAGCT\n") - f.write("ATTGTTCCGAAGAAGTTTCGGATTCACACACCAAACCAGAAATAAACACTGGGAAGCTAGACCAACAGAC\n") - f.write("CACGGTGCCGATAACTTTTATTTTTCTCAAATAACTTCATAAAGCTTGCTTAATCTAATCATTGCTGAGC\n") - f.write("ACATTGGACCCTTTGGGCACCACCATGCATGTCCTCATCCTCGTCATATGCCTCTTGCGCATGTGCTTGC\n") - f.write("TTTCGACGCATTTCCTCCTCTATGTTTACATCATGCAGCGTGGTCTCCTCACATTCATCCAACTCCATGT\n") - f.write("CGGTAAGTTGTGCCGAAGTCCTGGGGGGAAGGACAGCCTCCAGGGCCTTGCACTGTTCTGGGTTCAGTGA\n") - f.write("GTCGGGGAACTCCACTGTGAAATGAATATATAACTTACCCTTCATGAATGGCCTCTGGTACATTGGCATG\n") - f.write("CCCTCATCGTTTATAGCCTTGAATTGATCAGGCTTTACAACTTCTCCAGGATGAGATTTAAT\n") - f.write("\n") - f.write(">gi|226790485|gb|GO545658.1|GO545658 Mdas9009C24_e654.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC16504.1| contains ESTs C26074(C11585),AU092275(C11585) unknown protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGGAATCGATGAAGCGAAGCTTTCCTTGCAATCGGAAGATCACAAACAACGGGTCGAGGGGATGGCT\n") - f.write("TGACGCCCTCCTGAATCGCTTGATTGCCAAAGTTAGGAAACATGTTGGAGCTCGGAGGAACTGAACTGCT\n") - f.write("GGAATTAACGGGACTCTTGCCCAAATGAGAGGCAAAGGCGTTGTTAGTCTTGGCCGGAGGTGAAGCCGGA\n") - f.write("GCGGTGTGGCTCTGAGAACTCTCCTTGCTTGCTAAGAGCATGACTTCCTTGGCCTTGTCCGCACGAAAAT\n") - f.write("CGTTGAACACGATTACTTGTCCACCATAAAAGATGGTCATTTGTGCCTTCTGAGGCTCTCCAGGGGCAGA\n") - f.write("TTTCTTCACACTAGAATCAGCCGTCATGGGGACCTCTTCTCTGGGAGTGGGGGCAGAGGGACCAAAACCA\n") - f.write("GCTTGTTGAGGAAACAAATCCATGGATTTGAAGTCTCTCACCGCCCGTTGGCATGTTCCGAGAATTTTCC\n") - f.write("ACAAATGGAAAGAAGTTCATGGGTGGGGCTTTCTGGACAAAACATCTCAGGTGTACCTCCCTTACATTGA\n") - f.write("TGCATGTTGTTGCAT\n") - f.write("\n") - f.write(">gi|226790484|gb|GO545657.1|GO545657 Mdas9009C22_e653.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27880.2|AF139468_1 photosystem I reaction center subunit III [Vigna radiata], mRNA sequence\n") - f.write("CACAAATAGAGGAAAAAAACCATGTCTCTCACAATTCCCACAAACCTTTCAAAACCCATGTTTCAGCCAA\n") - f.write("AACTTAGCTCCCCATTGGCCGCAAAGCTGCCAAGAACCGTGGTCTTCTGCTCTGCCTCCCCAAACCCTAA\n") - f.write("CCCTACCCCAGAGAAAATATCGACTGCATCGCCCATGCAGGCTTTCTCCACTGCACTCGCACTCTCCTCC\n") - f.write("ATCCTCATTGGCTCGGCCCCCATGCCTGCAGTTGCTGACATCTCGGGACTCACCCCATGCAAAGACTCCA\n") - f.write("AGCAGTTCGCCAAGCGTGAGAAGCAGCAGATCAAAAAACTCGAGTCCTCACTGAAGCTCTATGCACCCGA\n") - f.write("CAGTGCACCCGCCCTAGCCATCAAGGCCACCATAGAGAAGACTCAGAGGAGGTTTTCCAACTATGGCAAG\n") - f.write("CAGGGTTTGCTTTGTGGGTCGGATGGGCTCCCCCATTTGATTGTCAGCGGTGACCAGAGGCACTGGGGTG\n") - f.write("AGTTTATCACGCCTGGTATTTTGTTCCTGTACAT\n") - f.write("\n") - f.write(">gi|226790483|gb|GO545656.1|GO545656 Mdas9009H14_e681.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTCGGTGGGAATTACGATTCAAGGCGGCCACCGCGGCTCGTCCGCCGCGAGGGCCAGGCCATCGACATGA\n") - f.write("GCCTTTGGGGGCCGGGGCCCCTACTGCAGGTCGGCAATCGGGCGGCGGGCGCAGGCGTCGCTTCTAGCCC\n") - f.write("GGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCACGGTAGCTTCGCGCCACTGGCTTTTCAACCA\n") - f.write("AGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGAATTACTATTGCGACACTGTC\n") - f.write("ATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTATTGGTGGGTGAA\n") - f.write("CAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAAC\n") - f.write("GTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCA\n") - f.write("AATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCA\n") - f.write("AACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAAGACACCTGCGT\n") - f.write("TATCTTTTAA\n") - f.write("\n") - f.write(">gi|226790482|gb|GO545655.1|GO545655 Mdas9009J24_e690.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|A84674 60S ribosomal protein L10A [imported] - Arabidopsis thaliana, mRNA sequence\n") - f.write("TAGACTTTCCTTCAAAATTTTCCAAAAGCATTCAACTAAAACAACAGAGTACACATTGTACTTTAACGAC\n") - f.write("GAAATCCAAGTTAATGAAAACAAAATATAACACTGAAACATATGCAATAAATGTCTTAGACAAAAAGTTT\n") - f.write("GCCGATGCTTCCTTCGCTTGGAAAGTCTCTGATAAAGATTATGAACTTACTAGATACGGATAGCTTTCCC\n") - f.write("CATCGTACTCTTCAAGTTCAAAGACCTCACATTCTGCCAATTCTTCTTCAACAGTGCAACTAAGAAATTG\n") - f.write("ACACTGACTTGCACATTCAGGAAAATCTGCTTCTCCTCCATAGCAAGATTGCCGACAGCAACACCCATGC\n") - f.write("AAAGAACCTTCTTAAGTTGGAACTTCATCATAACTTTGGTCTCGTTAAGTTTTGCCTCCACAGATTCCTG\n") - f.write("ATGACTCACCAAGGTTGGGAACTTACCTGCCTTATTAAGACCACGGCCAAAAAAAACGAGGAATCT\n") - f.write("\n") - f.write(">gi|226790481|gb|GO545654.1|GO545654 Mdas9009M11_e702.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ACTATGGCTACGCTCCAACTCACTCCCTCCCCTTCTCTCAACCTCCCAAATCAAATACGCACAAACACCA\n") - f.write("ATCTCTCCGCTTCATTCCAGCTCAATCTCCGGCCGCGCCACCGATCATGGCGGTCCT\n") - f.write("\n") - f.write(">gi|226790473|gb|GO545653.1|GO545653 Mdas9009K19_e693.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA88898.1| cysteine protease component of protease-inhibitor complex [Zea mays], mRNA sequence\n") - f.write("TTCCAGTTGTATAACTCCGATGTATTTACAGGACGTTGTGGGACGGCATTGGACCATGGTGTGACAGTTG\n") - f.write("TGGGATACGGCACAGACAAGGGGCTTGATTACTGGATAGTGAGAAACTCATGGGGTGCAAGCTGGGGAGA\n") - f.write("GAAGGGATACATCAGGATGCAGCGTAATCTGGGCAACACCGCTAATGGGATATGTGGAATTGCCATGGAG\n") - f.write("CCTTCTTACCCGATAAAGAAAGGCCAGAATCCCCCTAACCCCGGTCCTTCTCCTCCATCTCCGATAAAGC\n") - f.write("CCCCGTCAGTTTGTGACAACTACTACTCCTGCCCTGAGAGCAACACGTGCTGCTGCATCTACCAGTTTGG\n") - f.write("AAACTATTGCTTTGATTGGGGATGTTGTCCACTTGAAGGTGCCACCTGCTGTGATGACCATTACAGTTGC\n") - f.write("TGCCCAAGCGAATATCCTGTCTGCGATGTCAATGCCGGAGCTTGTTTGATGAGCAAGGGCAATCCCTTGG\n") - f.write("GAGTGAAGGCATTGAAGCGCACCCCCGCGAAACCCCACTGGGCTGTTGGTGGCGGAAAGAGCAGCAGTGC\n") - f.write("TTAAGCAAAACACTCAAGCCTCGATGCAGTGGTTTAACAAAAGCTAAGAAGGAAGAGACATCCAAGCATT\n") - f.write("ATTGATAATCTTCTC\n") - f.write("\n") - f.write(">gi|226790472|gb|GO545652.1|GO545652 Mdas9009L08_e698.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF02817.1|AC009400_13 unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGTTGGAGGAAACAAAGATATATTAAATGTTAGAAAACAAAAAAGTTA\n") - f.write("TACAAGTGATTAACTTACATTTGGAATTTTATAACTATTCACTGCCAAAATCTTCATAACTTACACCTTC\n") - f.write("TGAGACGGTGTCCAATCTGTTATTGTCCCCTTGATGTTCTCTGTCACGAGAATCCAGGAAGTTGTTATTA\n") - f.write("TCTGTAGCCAAGAAGGGTGATCTAGGATAGCTCTCCAGTATGTCTGAACTCTGAGAAAAGTCAGTTGCAA\n") - f.write("GATCCGAAAAGCTCAAGATTCGAGGAATCTGACCTAAAAGACCAAATGATGAACTGTCTGCATCAAGCAG\n") - f.write("AGATTCATTTAGGGACTGTGAATTGGACTCTACGCTATTGAATGCTGCAACAGAAGCATCTCCAATAGCG\n") - f.write("GGCCGGGTTTCCAGGATGTTTCCATCAGCACTAAACATGTACGAACTGCCTGAATATCCAACTTCTGATT\n") - f.write("TGACAATTCCCCCATTCATTCCATGCATCAGACCTATGTTGGAGATCTGGTTCGAAAGCATGTTTGGTTG\n") - f.write("GACATCAATCCTACCGGTATGAGCAGACATTTTACCAGCATTGTGCATACTGATGTGCAATGAAGATCCA\n") - f.write("CCATTAGTAAAAGCATTATGTAGGCAAGAACCAACTTGGTGGTGTATAATTTCTGTCTTCAGCGCTGTTC\n") - f.write("CTACATGC\n") - f.write("\n") - f.write(">gi|226790471|gb|GO545651.1|GO545651 Mdas9009K21_e694.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40281|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA) pir|S39551 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) - apple tree emb|CAA79857.1| ribulose-1,5-bisphosphate carbo, mRNA sequence\n") - f.write("TTTTTTTTTTATTCTCACAACATAACATTATGTTCTTATCGACTGTTCAATAGCCGGAGTATCAATAGCT\n") - f.write("TGTTTAATAATTAAAACGAAATAATCGCAAGAATTTCCATAGAAATACAAGCGCAAATTACAAAGAAAAT\n") - f.write("ATCAATAACCCAGCAAACAGAATATCTATTTTTCTTTCAGCTCCAATTCACTCGTACCGACAGCTACCGT\n") - f.write("CGTCACTCCTTCGCAGCTAGGGGTTCGAAAGTTTAGCAGCAGTTTCGATCAGTGCAGCCTTTCAGGGACA\n") - f.write("GGTACATTTAACTTAGTTGGGCTGCCTTTTCCATAGAATTTCTCCTCGGTTAATGGAGTCCTGGTTTGCA\n") - f.write("TCTCCAAGGGGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCTCTTCACATTGTCCTGCTCCTGA\n") - f.write("ACAAGCATTTGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGTTGATCGAAAGTCGGGGGACCTT\n") - f.write("CTTTTGAGTTCACAAGCTTCTTCCCAATCCCGTCAATTCCAACACCGGAAATCCACTTCCTCACTTCATC\n") - f.write("GTCATAAACTCGAGCCCTTAGGGCACCGAAGAAATCAATGGATT\n") - f.write("\n") - f.write(">gi|226790470|gb|GO545650.1|GO545650 Mdas9009L07_e697.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTGAACAAAATTATATATGTCATTAAACCGAAATTATTGAACACAAATGCAGAGCAAGCCG\n") - f.write("TATTACATTGGTCTTAATGGATACAAATTCAGGTACATGCCAACAAATATTACCCTTGCTCCCTGCATGT\n") - f.write("CAAAAATGAAACAAAATTGAACATGCATTTTCACCACTCCCTTCCACACTCTTACAAACATGCATATGCT\n") - f.write("GATGACAACC\n") - f.write("\n") - f.write(">gi|226790469|gb|GO545649.1|GO545649 Mdas9009M03_e701.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_171617.1| pyruvate dehydrogenase E1 alpha subunit [Arabidopsis thaliana] gb|AAB86803.1| pyruvate dehydrogenase E1 alpha subunit [Arabidopsis thaliana] gb|AAK96625.1| At1g01090/T25K16_8 [Arabidopsis thaliana] gb|AAL36074.1| At1g01090/T25K16_, mRNA sequence\n") - f.write("TTTTTTTTCTAAAAGAACATGAACAAAATTGAAAAGATAAACAAACATATGTCCTGCTTTTACAGTAGAT\n") - f.write("AAAAGCTGATACAATCTTCTGACAAGTGACAAGTAGCTGCTAGCAGTAACTAAAAATTTAACGCCACGCA\n") - f.write("GGCATACCTAGGAACAGAGAGCTAGCACTAGTTGATTGCTAGAGGCTCCAACCAGCGGAGATTTAGACGT\n") - f.write("GAGCTGTGCCCTGAGTGAACTTAGGATCCTCACATCTGTAGCTGCCATCAGGCCCGATTCCAAAACCCTT\n") - f.write("GGGATCGGCAAACACATTCTCGAGCAGCTGGCTGCGAGGTGGAAGAGGACTCTCATCTGCAAACTCAACG\n") - f.write("GCATCCTCAACCACCTCGTCGATCTTCTTATGGATGGCCTTCAAGTCTTGTTCGGTCGCCAAATTGTTAT\n") - f.write("CAAGTATGTATTTCTTGAGGGCTGTGATGGGGTCTCTGGCAGCGTAGTGTGCCTTCTCAGCAGGGTCACG\n") - f.write("AAGCTCATCGGGATCAGCCAATGAGTGTCCTCTGAATCTGTATGTTTCACATTCCACCAAAGTTGGCCCT\n") - f.write("TCTCCTCTCCTGGCCCTTCCAATCGCCTCCTTTGCCACCTCCCTCACCTTCAGCACATCCATCCCATCCA\n") - f.write("CATGAACACCTGGCATACCGAATGCACGCC\n") - f.write("\n") - f.write(">gi|226790468|gb|GO545648.1|GO545648 Mdas9009F21_e671.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P36491|PSBA_POPDE Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) pir|S42492 photosystem II protein D1 precursor - cottonwood emb|CAA55040.1| D1 protein [Populus deltoides], mRNA sequence\n") - f.write("TGGAACTTCAACAGCAGCTAGGTCTAGAGGGAAATTATGAGCATTACGTTCATGCATAACTTCCATACCA\n") - f.write("AGGTTAGCGCGGTTAATAATATCAGCCCAAGTATTAATTACACGACCTTGACTATCAACTACAGATTGAT\n") - f.write("TGAAATTAAAACCATTTAAGTTGAAAGCCATAGTGCTGATACCTAAAGCGGTGAACCAGATACCTACTAC\n") - f.write("AGGCCAAGCAGCTAGGAAGAAGTGTAAAGAACGAGAATTGTTGAAACTAGCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790461|gb|GO545647.1|GO545647 Mdas9009G05_e672.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77604.1| plastidic aldolase NPALDP1 [Nicotiana paniculata], mRNA sequence\n") - f.write("CTTGCCCGCTACGCTTCCATTGCTCAAGACAGCGGGTTGGTCCCAATTGTCGAGCCAGAGATCTTGCTTG\n") - f.write("ATGGTGAACACACCATTGAAAGGACTTTCGAAGTGGCCTTGAAGGTCTGGGCCGAGGTTTTCTTCTACCT\n") - f.write("AGCTGAGAACAACGTCTTGTTCGAGGGTATCCTCCTCAAGCCAAGCATGGTTACTCCTGGTGCTGAGGCC\n") - f.write("AAGGAAAGAGCCACCCCTCAACAGGTTGCTGACTACACCCTCAAGCTCCTCCACAGGAGAATCCCCCCAG\n") - f.write("CTGTCCCCGGAATCATGTTTTTGTCTGGTGGACAATCTGAAGTTGAGGCAACCCTGAACTTGAATGCGAT\n") - f.write("GAACCAATCACCAAACCCATGGCACGTGTCCTTCTCCTACGCCAGAGCTCTCCAAAATACCTGCCTGAAG\n") - f.write("ACATGGGGAGGCAGACCGGAGAACGTGAAGGCAGCTCAGGATGCTCTGCTCATCCGTGCCAAGGCCAACT\n") - f.write("CACTTGCACAGCTGGGCAAGTACACCGGAGAGGGAGAGTCAGAGGAGGCAAAGAAGGAATTGTTTGTCAA\n") - f.write("GGGCTATGTGTACTAAGTAATTTGTACCGACGCTGTAGATGATGAAGAACAAAGGGAAGATGATGATGTT\n") - f.write("GA\n") - f.write("\n") - f.write(">gi|226790460|gb|GO545646.1|GO545646 Mdas9009G10_e674.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB64530.1| polyphenol oxidase [Pyrus pyrifolia], mRNA sequence\n") - f.write("TCGAACAACCCATAATTTGCAAGGCGAGACCTTCTCATCGGAGGGCTAGGAATATACGGCGGATCAAAGA\n") - f.write("TGAGCGAAATCACAGGGAATTCCGGCGAATCGGCGGCCGCCGAGACTACTCCAAACAGGGTCGTCGAACT\n") - f.write("CAGTGAGTTACCGATCACTCTGGACTCGGTTATCAGCGTGATCGTGCCGCGGCCAAAGAAGTCTAGGACC\n") - f.write("AAGGCGGAAAAGGAAGCGGAAGAGGAGGTGCTGGCGATTCAGGGGATCGAGTTCGTAGCGGACGACACCG\n") - f.write("TGAAGTTCGACGTTCACGTGAACGATGACGAGGACGCGCTGAGTCGACCCGACAAGGCCGAGTTCGCCGG\n") - f.write("GAGCTTCGTGTATTTGCCGCACAAGCGGAAGGAGGTGAGGACGAGCCTCCGCCTTGGGATAACGGACTTG\n") - f.write("CTGGAGGACTTGGGCGCTGACGGCGACGACAGCATTAAGGTTACCTTGGTGCCTAAGTATATCATACGGC\n") - f.write("CCGTTACCGTCCGTCAGATAAAGATCGA\n") - f.write("\n") - f.write(">gi|226790459|gb|GO545645.1|GO545645 Mdas9009N05_e705.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_190595.1| AP2 domain transcription factor, putative [Arabidopsis thaliana] pir|T45572 hypothetical protein F11C1.100 - Arabidopsis thaliana emb|CAB62305.1| putative protein [Arabidopsis thaliana] gb|AAK73937.1| AT3g50260/F11C1_100 [Arabido, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTCCGTCACAAAGGCCATAAAATTCAAAGACTATAATTTCAAGAAAAGAAACATT\n") - f.write("ACTGATTGCCCTTCAGTTGGTTTGTTGTTACAATTGAGAAACTATATCAAATTACCAATCGAAACGGAAT\n") - f.write("TCTTGTGATTCCATTTCCTGATCGGACCCAATAAACCCTTCTCTGTATTTTTACTTTATTGCACACCTAA\n") - f.write("ATACCTACTCATAACAATAAACAGCTGGTGATCGGTCGGCCTTCTCAATTAACTTTCATCGGAGTTTTCT\n") - f.write("GGGTCGGGGTACTCATTTAAGTCGGGCTTCAAAGAGCCACCCCGGCTCAACGTTGTTTTGGACTGCGACG\n") - f.write("TCGGCGATGAGCGGAGAGCGGTTTGAACAGCGTCGACCTTAGCCCCGACCTCCGTAGCTTTCTTCCGTAT\n") - f.write("CGAAGCCGCCGACATGTCGTGGAGCTGCTGGCCGTCCAAATTCATAACTTATACCCAAACGCTGCCACAA\n") - f.write("ATGTACTTTCACACAACATATAATTGTTGTCTTGGGTCACTCAGAAATGGGTACAGGAATACGTACTAAT\n") - f.write("ATCACAGGCACCATAGGTCCACAAGATCCTAGGCTTAATTCCATTTTTCTGCAAACAACATATTCTTCTA\n") - f.write("CCAA\n") - f.write("\n") - f.write(">gi|226790458|gb|GO545644.1|GO545644 Mdas9009B15_e646.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCGTCTAGTAGCTGGTTC\n") - f.write("CCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGTGAACGAGTTCTATCGGGTAAAGCCAATGATTAGAG\n") - f.write("GCATCGGGGGCGCAACGCCCTCGACCTATTCTCAAACTTTAAATAGGTAG\n") - f.write("\n") - f.write(">gi|226790457|gb|GO545643.1|GO545643 Mdas9009I03_e683.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77604.1| plastidic aldolase NPALDP1 [Nicotiana paniculata], mRNA sequence\n") - f.write("TTTTTTTTTTCTCTCATCACCAAGAAGTTTATTAACTTGCTAAAAGGTGCATAAAATGTTCAACAAAAAT\n") - f.write("AGTCTTTCATGGCTATAAAGCATTACACACATTAGAGATGCATGTCTGGTTCCTCCATTAACATCAACAT\n") - f.write("CATCATCTTCCCTTTGTTCTTCATCATCTACAGCGTCGGTACAAATTACTTAGTACACATAGCCCTTGAC\n") - f.write("AAACAATTCCTTCTTTGCCTCCTCTGACTCTCCCTCTCCGGTGTACTTGCCCAGCTGTGCAAGTGAGTTG\n") - f.write("GCCTTGGCACGGATGAGCAGAGCATCCTGAGCTGCCTTCACGTTCTCCGGTCTGCCTCCCCATGTCTTCA\n") - f.write("GGCAGGTATTTTGGAGAGCTCTGGCGTAGGAGAAGGACACGTGCCATGGGTTTGGTGATTGGTTCATCGC\n") - f.write("ATTCAAGTTCAGGGTTGCCTCAACTTCAGATTGTCCACCGGACAAAAACATGATTCCGGGGACAGCTGGG\n") - f.write("GGGATTCTCCTGTGGAGGAGCTTGAGGGTGTAGTCAGCAACCTGTTGAGGGGTGGCTCTTTCCTTGGCCT\n") - f.write("CAGCACCAGGAGTAACCATGCTTGGCTTGAGGAGGATACCCTCGAACAAGACGTTGTTCTCAGCTAGGTA\n") - f.write("GAAGAGAACCTCGGCCCAGACCTTCAAGGCCACTTCGA\n") - f.write("\n") - f.write(">gi|226790456|gb|GO545642.1|GO545642 Mdas9009A06_e639.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566245.1| expressed protein [Arabidopsis thaliana] gb|AAF27013.1|AC009177_3 unknown protein [Arabidopsis thaliana] gb|AAM62522.1| unknown [Arabidopsis thaliana] gb|AAO44023.1| At3g05070 [Arabidopsis thaliana], mRNA sequence\n") - f.write("CGGGGAAAATACAAGAATACATTCAGTTTCCACAAAAGCACAGCAGAAAGTTTATCATCAATAATAAAAC\n") - f.write("TAAAAGAAGCTCACTTCCAAGTCGCTACTTGCATACAGGTGGAAGTCAACTCTATTCAACATGTTTAAAA\n") - f.write("GTGAGCGAGAACAATCTTCTCAAGTTTAATTCGAAAAACTTGGGTGATTTTCTTTCCTTTTTCCCCTTTT\n") - f.write("GTTTTTCCGTTGCCAAGGTTAAGAAAAATCAATTCTAGTCTTCACCATTTCTGCCATCTCCATCCAATTG\n") - f.write("CTTTTGCTTCTCCTGTTCCTCCATAAGTTTAAGCATTGCCTTTTGGGTTCGCTTTTCAAGCTTATCAAGC\n") - f.write("CTCTTCTGCACATCCCTGCGAAGTTCCCAGTTTGGTTTTTTAGGAACAATATTCACAAACGGGTCCTCTT\n") - f.write("TCTTCTCTGATGGAGGTGGTACTCCTGCAACAGGGTCTTCAAACTTTGGCAGCACTGGTGGAACAAGCTT\n") - f.write("TCCCTCCTGAAGCTGCTTATCATGAGGAACATAATTTCGGAATTTCATGTTGGTATTAGTTTCGTCACTA\n") - f.write("ATTGGATTGCTTTCATTAGTGTTATCGTGAACTTGTGCGGAATCCTCATCTG\n") - f.write("\n") - f.write(">gi|226790449|gb|GO545641.1|GO545641 Mdas9009G07_e673.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("TTTTTTTTTGTCCGAAAAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTTT\n") - f.write("CCACGCTCAAATCCACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTC\n") - f.write("ACTTTCCGGGAACAAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGC\n") - f.write("AAGGTTCTCCAATGGTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCC\n") - f.write("AACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAAGCTTCTGGGTCGTCGGCAAGACCCAATG\n") - f.write("GGTCGAAGCTTCCGCCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCC\n") - f.write("CTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTA\n") - f.write("GGGTTTCCCAAGTAGTCGAGACCGCCCTCACTGAAGATCTGGGCTCCGGCCTTGAACCACACGGCTTCGC\n") - f.write("CGAACTTGACACC\n") - f.write("\n") - f.write(">gi|226790448|gb|GO545640.1|GO545640 Mdas9009L03_e695.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_175633.1| photosystem I subunit VI precursor [Arabidopsis thaliana] sp|Q9SUI6|PSH2_ARATH Photosystem I reaction center subunit VI-2, chloroplast precursor (PSI-H1) pir|C96562 photosystem I subunit VI precursor [imported] - Arabidopsis thali, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTGCCAAACTTAGGGGCTTTAATTCTGCATTACAGGTGCTTTACAAG\n") - f.write("TACAAAATAGAGAAACAATTACACACACATGATGAAAAGCTTGAGAAAATGAGGATTAAATCCCAAATAA\n") - f.write("AATTTAGATCTTGCCACGTGGGCCCAACTTGGGTGGAAGTTGTGGGCCCTTCTTGATTGGTAGAATGTCG\n") - f.write("TCGGAGGCAGTGGCACTAAGGTAGGCAATGGTGGAAGCTCCTCCCAATATCAAGAACTTGAGGAGTAAGC\n") - f.write("CTCTCTTGGTGAATGGAGCAGCAAATGTCTCAAAGAACTTGCTCTGAAGAGGGTTGTAAGGTGAGGGCGC\n") - f.write("ATCTGAACCGTACAAGTCCCACTTCCCGGTGGTGTTGCCCAGATCCTCAAGGTCAAAGTAGACGCTCTTG\n") - f.write("TCTCCGTACTTGGCCACCACAGCACCACTCCTGATGTTTTTCGTTCTGATGCTCTGGCGAGTGGGCTTCA\n") - f.write("CAACGAGCTTTGTTCCGGTGAGGGAGCTTCCGCCGAGGCCGTTAATGGTGGCCGGTTGAACGGCTGCTAG\n") - f.write("GGTTGCCAGAGATGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790447|gb|GO545639.1|GO545639 Mdas9009A18_e641.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564615.3| expressed protein [Arabidopsis thaliana] pir|H96569 unknown protein, 54928-56750 [imported] - Arabidopsis thaliana gb|AAG52277.1|AC019018_14 unknown protein; 54928-56750 [Arabidopsis thaliana] gb|AAK60317.1|AF385726_1 At1g52870/F, mRNA sequence\n") - f.write("TTTTTTTTAGTTACAAAATCTCATTCTTCTTACTCTTCTTTATGGCATTATTATTACAAGTATACAGTTT\n") - f.write("CTCCAAGCTACAACATGAGTTGCAGTACCTGTTGAAATTTACAGCTACTCCAATGAATATACATAGCACG\n") - f.write("AGATCGCCAGGGGGAGCTGACTGAATTTGAGAACGAATATAGAACACATTTGGCAGAAAAATTATTATTT\n") - f.write("GTATCGTATATGTTTGGTTAGGATAACCAATAATTGCTTGTCTCCCAAGCTGCATAGCTCATGCTGCTTC\n") - f.write("CTAGTATATTGTGGTCTGCACAGCCATTGAATGATGATCTCCCCTAACAACTACTTTCCTCGCAGTTCTC\n") - f.write("GTATAGAAATTTTGCGCTTCCAAACACTAATAGGGTGGAAACAGTGGTTATTGCGTTGGCTGTAGAAAAC\n") - f.write("CGTCTCAGTACCATGCTTTTCAGAATTTAGTCCTTTGAAGAACTGCTTGACGAAGAAGCAGAATCTGCAC\n") - f.write("CAGAAGATGCCTCGGATAAACTGGAATCTGCATTCTCATTTGAATAAGTTGAGAGAATAGTAACCCAAAT\n") - f.write("AAGCTCCACACAGTCCACCCAAAGAAGCCTTTGTTCAACAGGGATCAGGCCATACGTAACCACATGAGCA\n") - f.write("AATGGCCAAAGTTTCCATCCCGCTGTCAGCATTGGCACAAATGTAGCCCTCAATTCATCAAAAATCTTGG\n") - f.write("TTGGGGACTCAAAACGCAAGAACCCCAAAACCACAAAATAGATGCTGTTCCAAATCGCTG\n") - f.write("\n") - f.write(">gi|226790446|gb|GO545638.1|GO545638 Mdas9009H06_e678.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9MTP0|YCF3_OENHO Photosystem I assembly protein ycf3, mRNA sequence\n") - f.write("TCGAGAAAAAAAAATGGGATATATCTCTGAGAAATCTCATTCAATTAGATAGGGTAATTAAAAAATAGGA\n") - f.write("CACCAAAAGAATTTGACCGCTGAGCCGTATGAGGTCGGAAACTCTCAAGTACGGTTCTAAGGGAAGGAAT\n") - f.write("TTACCCCCCTATTCCGACCGGGGAGAACAGGCCGTTCAACAAGGAGATTCCGAAATTGCGGAGGCTTGGT\n") - f.write("TCGATCAAGCCGCCGAGTATTGGAAACAAGCAATAGCGCTTACTCCTGGTAATTATATTGAAGCACAGAA\n") - f.write("TTGGTTGAAGATTACAAGGCGTTTCGAATAAGAACAGTTTATTATTTAATTTAGATATTTAGTTTTATAG\n") - f.write("ATTTTTTATATTTGTTATAATTCATTTTCTAATTAATTGTTTGTTGTCCCTATCGAGGATCATTTCTCTG\n") - f.write("GGAAGAACCAATCAAAGAATTTCATTATATCCCTTCTAAGATCCTTCTATTTCGTCTGGTATTTCGTAGG\n") - f.write("AATAAACGATATATACAGATAAAGTGGAGAATCCATTTTTTTTTCTTCTATTAAAACTAATAAAAGAGAC\n") - f.write("CTTCGAATGACTAAATTTAAATACTGAGATGTCTCTTAGTAATGACTTCTCGCGAAATTTTGATTTGGAA\n") - f.write("TAGAGTACGGAATAGAGTAATATGTTCTATGTAAGACATAAAGTATAAAGTAGT\n") - f.write("\n") - f.write(">gi|226790445|gb|GO545637.1|GO545637 Mdas9009C06_e651.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTAGCAAAATGGAACTTAATTACTGCCAAGAAAGAGGAAGAGTTACATACTTCTAGCAGAACA\n") - f.write("ACCTGGATAACATAATTACTTCAAAGTTCAAACCCTCAAAATTCAAAGTAAAAAAAAAGAAAAACACCAG\n") - f.write("AAACAAATAACTTCCCTTAAGTAATTTCTTTCATCATACGGTCACAATCTGCCATCTCTCTCTCTCTCTC\n") - f.write("TCTCTTCCCCTTTCCCAAAAGCTGGTAGCTTTAATCGTACCCATTAAAAGAGTAGCTTGCAGAAGGTGAG\n") - f.write("CTTTCCTCTGGAGAATTGGTGTCACAGTTTGCTGCTGATCCTCCTGATGAACATGCTTGATTAGATCTGC\n") - f.write("CCCCAATCCCAAAGATACCGGCTTTGATACGACCTCTTTTTGGTGGCAAATTGGTCAAGTCCCTCCCTTT\n") - f.write("TCCTTTCCTCTTCACTGGGTTGCTGCTGCCGCCTTTGGTTTCCATTTTTTTTTTCCTCAGCTGAATTATG\n") - f.write("GTGGAAAAGAAAGAAATTGAGACAGAAGAGAGGAGTCGCAGAGGGCCAGATGGTAAAGTGAAGTAGAGAG\n") - f.write("GTCTCCACTGTACTATATATAGAGATATTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790444|gb|GO545636.1|GO545636 Mdas9009A09_e640.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI-D) (PS I subunit 5) pir|A60695 photosystem I chain II precursor - cucumber prf|1710320A photosystem I 20kD protein, mRNA sequence\n") - f.write("TTCAATATAACACGTTTTACTTCAACTACTCTCCCTACTAATCTATGGTAAAAATATCTCATATAAACGA\n") - f.write("AAAAACATATTAACCCAAATCATGTTTCTGAGGTTGCATTTTAATGAAATCAAATTACAAGAAACACAAA\n") - f.write("TTATACTCACATTGCCATCATGATTATAAATACAATGCAAATTACACAAATCAATATTATCATCATATGT\n") - f.write("CATAGACTTGCTTGCCGGTGAACTTGACCTCAATCGGGCTGACATTCTTCCCAATCGACCTGAAGTTCTG\n") - f.write("GCCAACCCCTTGGCGCCCAGGGTTCACCTTCTCAGGGTACACACCATCCTTGGGGTGCAAGTATTGGACC\n") - f.write("TCCCCGTTAGGGAAAACCCTGTAAAACTGGTACTTAATCTTGTACTTGGACCTAAGCCTAGTTCCAAGAG\n") - f.write("CCAAGCACTGCTCTTTCCTGGCCAGTTTCAGCAAGTTAGGACCCTCCCTCATGATGGCAGCTCCGCCAGT\n") - f.write("CGGCATCTCAAATATCTGCTCCTTTGGTGACTCCCATGTGATCACGTAAAACTCTTCCTCCTGCGCTTTC\n") - f.write("CTCAACAGCCCGCCACTGCTGCCACAGAACATCGGTG\n") - f.write("\n") - f.write(">gi|226790437|gb|GO545635.1|GO545635 Mdas9009F17_e670.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565671.1| expressed protein [Arabidopsis thaliana] pir|A84684 hypothetical protein At2g28370 [imported] - Arabidopsis thaliana gb|AAD20689.1| expressed protein [Arabidopsis thaliana] gb|AAK53025.1|AF375441_1 At2g28370/T1B3.11 [Arabidopsis, mRNA sequence\n") - f.write("TCGAGTGTTTTTTCCCATACACGCATTCATCGAGATGCCAGTGACCAGAAATTCAAGAGAAAAGATGGTA\n") - f.write("ACACAGCGAACCAGGATATGAAAGCCATCGCTGTAGCTGTTTCAAATTGGGCACAATGGTTGTGGGCACA\n") - f.write("GCTGCTAAGATCATTGTCAATAAGAACTGTGATGCCTGCAGAAGCACAAGCTGCAGCAAATGTAAGAGTG\n") - f.write("GATGTCACCCCATCACCAAGGGTGAACAAACACACAACTCGATGGTTCTGCAAGGAACGCCCAACTAGAA\n") - f.write("GGGCATAAACGTCAACAACGCCCAACGAGAAGCTCCACAAACACTGCAAACCAGTAGCTGCAACAAGGTA\n") - f.write("GCAAAACGCAGTGACGGAGGGGAAGTCAGAGGTGGTGGCCATGACGACGAGCGAGGCGGCGGAGAAGAAG\n") - f.write("AACTGGGCGAGGCGCAAGACGAGGCCGCCCGGGGTGCCGGGCATGCCAGGAAGATCCTTCATTCGGACCC\n") - f.write("GGGGTGGGTTCGGGCCGGCGCCGTCTGTGGTGGGTACATCTTCAACTGGGTGAACCGACCCATGGCTCAC\n") - f.write("GTTCATCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790436|gb|GO545634.1|GO545634 Mdas9009D16_e659.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192813.1| aldolase -related [Arabidopsis thaliana] pir|T01902 hypothetical protein T12H20.10 - Arabidopsis thaliana gb|AAC35519.1| similar to 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolases [Arabidopsis thaliana] emb|CAB81176.1| putative, mRNA sequence\n") - f.write("CCGATTCTCCTTTATAAGATAATAATATGAGTACGAAAATCACTCTGTGTATCTTTGCCTCCAATCCAAT\n") - f.write("CCTTCTAATTATTTAATTTGGCCGGCAATTTGACCTTCATTATGAAAACACCAATGGACTCAAAATTTAC\n") - f.write("AAATAAGCGAGTCCAAAATTCTAATTATTTTCGTCAATATTTCTCCCAGCCAAAAAAGACAGCTTTCAAC\n") - f.write("AATCTGCCTCTTCATTCGCTCCAGTACTTCTCATCAGCATCCTTCTCGTCCTCCCGCTCATCATCTGCAC\n") - f.write("CGTCCATCAAGCTCATCTTGAACCGCTTCACGTCCTCCACCGCCGCGCTCCTAAACAGCCCTACATCGAC\n") - f.write("GGCTCCCGACACCATGTGGTATCCACGTGTCCCCAAA\n") - f.write("\n") - f.write(">gi|226790435|gb|GO545633.1|GO545633 Mdas9009F08_e667.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9FVI1|ADF2_PETHY Actin-depolymerizing factor 2 (ADF 2) gb|AAG16974.1|AF183904_1 actin-depolymerizing factor 2 [Petunia x hybrida] gb|AAK72616.1| actin-depolymerizing factor 2 [Petunia x hybrida], mRNA sequence\n") - f.write("GCCATCGGAGGAGAGACCCCCTTTCCCTATATCTTCTCCTCCTTCTCCGTCGCCATCAGAGAACTAAACA\n") - f.write("GGCAGCAAAAATGGCCAACGCAGCATCTGGTATGGCTGTGCACGATGATTGCAAACTGAAGTTTTTGGAG\n") - f.write("CTTAAGGCAAAGAGGACCTACCGCTCCATAGTTTTCAAGATTGAGGAGAAGCAAAAGCAGGTTGTGGTGG\n") - f.write("AACATGTTGGTGAACCAGCAGAAACCTATGAGCAGTTCACTGAGAAGCTTCCTGCTGATGAATGCCGATA\n") - f.write("TGCTATTTTTGATTTTGACTTCCTTACACCAGAAGGTGTCCAGAAAAGTCGGATATTCTTCATTGCCTGG\n") - f.write("TCTCCTGATACATCAAGGGTGAGAAGCAAGATGATCTACGCAAGCTCCAAAGACAGATTCAAGAGAGAGC\n") - f.write("TCGATGGCATTCAGGTTGAGTTGCAAGCGACTGATCCTACTGAGATTGGTCTTGATGTCATTAAGAGCCG\n") - f.write("\n") - f.write(">gi|226790434|gb|GO545632.1|GO545632 Mdas9009A02_e638.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566596.1| expressed protein [Arabidopsis thaliana] dbj|BAB02017.1| emb|CAB36779.1 gene_id:MRC8.3 similar to unknown protein [Arabidopsis thaliana] gb|AAK96874.1| Unknown protein [Arabidopsis thaliana] gb|AAN15376.1| Unknown protein [Arabido, mRNA sequence\n") - f.write("TTTTTTTTTATCATGTCAATTGGTGAAATAGGCTGTGTTTTCGGCACACTAAAAAATTAACACTTTCCAA\n") - f.write("ATGAGAAAGAAGAACCAGAAGAAACCCTATTCAATTCTTCTTCTTCATTTTTGTGGAAATAGGAACAAAA\n") - f.write("GATGCAGCCTACAAGCTACAATAAATAAACAGAGACAGAAACTTCACAATTACATAGAAAAAGAACTTAC\n") - f.write("ATTGTAGAGACTGTGCAAGCATTTGGAGCAGCCACCAAGACCAGGAAACCAATTGCCATTGGCGCCGCTG\n") - f.write("CTCAAGCAATCTCTCTCCAACTTCTTCACCTTTTCATCCCCAACAAGCTTCCCTCTTTCGTTCTCCGAAA\n") - f.write("ACGCCTCGGGACAGCTCAAGGGGTGCAATCTTATCCCGCAATAGCAGTACACAACATCACAGGTCTCATT\n") - f.write("CGGCTTGATTAGCTCGATACCTCTGTTTTTCAGCGCCTTTCCCAAGTCCTGAACACAAGTTTCCGTGTCG\n") - f.write("TCCGGCAGCAGTGGCAAATCATAAGACTGACCGGCCACTGCTGAGCCCACCCTGCCTACTCTGCCGAGAG\n") - f.write("CGGTGTCAGAGTAGGCAGAGTAGAGCCACGAGGCCAGCGCAGGACAGCACCTGCTGCGCTGCAAGTGACC\n") - f.write("TGAGGCATCGCCTTTGGTGGCGGAGCATGCGGACTTTATGCCATG\n") - f.write("\n") - f.write(">gi|226790433|gb|GO545631.1|GO545631 Mdas9009M02_e700.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T07014 phosphoglycerate kinase (EC 2.7.2.3) precursor, chloroplast - potato gb|AAC26785.1| phosphoglycerate kinase precursor [Solanum tuberosum], mRNA sequence\n") - f.write("TGAAAGGGTCGCAAAGAACAAAATTATTAGATTGCTCGGACGGCTGCGTTTGTCCCTCCCCGCCATCTCT\n") - f.write("TATGGAAACTTTATATAGACATAATGGGACCTTATACTGAAGGTAACATCAGACATTCACAACTCGAACT\n") - f.write("CACATCTTCCTACATGCCATTTCTCGTTTACAGACTCGAATGAAACACCAACACGGTGGGCAGGGAAAAA\n") - f.write("AACAAACAGGAAAAAAGATTGTTCTTACACAGGAACTGGTGTGGCTTCGTCAAGAGCAAGTACACCAGGA\n") - f.write("AGTTCTTTGCCTTCCAACAACTCCAAACTCGCACCACCACCAGTTGATATGTGGCTCATCACACTAGCGA\n") - f.write("CTCCTACTTTCTCCACGGCTGCAACAGAATCTCCACCTCCGATGATTGTTGTCACTCCCTTCCCACTAAG\n") - f.write("TTCCGCAAGCTTCTTTGCAACAGACTCTGTTCCTTCTGCGAACTTGTCAAACTCAAACACTCCCATCGGT\n") - f.write("CCATTCAACATTATGGTTTTAGTGGTATCCAGTGCAT\n") - f.write("\n") - f.write(">gi|226790426|gb|GO545630.1|GO545630 Mdas9009E13_e665.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATCAACA\n") - f.write("CCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATT\n") - f.write("AAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCT\n") - f.write("TGGCTAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCC\n") - f.write("TGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATG\n") - f.write("AAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGA\n") - f.write("ACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTA\n") - f.write("CACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCC\n") - f.write("TTGGCCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGA\n") - f.write("GGCCACACCTGCATGCATTGC\n") - f.write("\n") - f.write(">gi|226790425|gb|GO545629.1|GO545629 Mdas9009C12_e652.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565301.1| expressed protein [Arabidopsis thaliana] gb|AAD17434.2| hypothetical protein [Arabidopsis thaliana] dbj|BAC42227.1| unknown protein [Arabidopsis thaliana] gb|AAO50598.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTGGTCGTGATCGTCTACTCATATTACATACGTATCCATGTCTTCAAATGAGAAGCTCCTACAAGT\n") - f.write("TTGATTTCTACTATTACTTGGAAATTAGGGTTTACACAAAGCATAAGCCAGTGGATATCAATCCTTGACG\n") - f.write("CCAGCCTCCTCCTTCAACATTGCGATGAACTTTGTCTTTCTCATCAGGTGTCATTCCCTCTGCCGAGCAA\n") - f.write("TCTCCAACTCCCCACTCTGCCCCCCGTATGCAGTACTTGTCTTGAATTTCTTTACTATTCTTTTCTTTGT\n") - f.write("TGAGCTTGGATTTTTCTAGTAGCTCCTTGAGTATTGGAGTTGATCTGAATCTTGCATCATTTTCTGCGTA\n") - f.write("CTTTTTCTGGTTTTCTTCGTTGAAGCGTTTGAGGAAGTCGATTTGAGGCATCTCAGGACCTGGAACTGAT\n") - f.write("TCAATTCCAGTCGATCCTGATAGTAATCCAGCACTAGCTGGATTTGAGCCGAGAAGAATGGCAGCTGAAG\n") - f.write("CAGCCAAAGAAAGAGAGGTTTGGAGAAGAACATGGCGGGGAGACGTCGGCGCCGGAGAAGAACTAGAACA\n") - f.write("AACTACTACTGGGGTAGGTCTTTTATGGACATCTAACTT\n") - f.write("\n") - f.write(">gi|226790424|gb|GO545628.1|GO545628 Mdas9009H07_e679.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK73147.1|AC079022_20 putative RING-H2 finger protein [Oryza sativa], mRNA sequence\n") - f.write("TTTTACACACTTAATTAAGAATTAAATTTCAAATTCTATAATCTTCATAACACGCAGAACCAAAGATGTT\n") - f.write("TTGCTACAAATTGAGCCAATTTTGTGCTGCTTTTTTTTATGAACACAGAACCCCAAACCGGCAAACTCGA\n") - f.write("AAGTTCTTCGAAACTCAATGCTATAATAATCAAAGTATTTACACTGATGAATATTTCAATAAATTAATAA\n") - f.write("ACAAAACAAAAAAAGAAGAAGAAGCCAAAACTGTGGTCTTTCTAATCATCCAACACCCACGCCCTCCTAC\n") - f.write("GCCGGTGTACGAACCGCCCAATCACCGAACTTGACTGACTTCTAGTCAAACCCGGCCCGGATTCAGATTC\n") - f.write("CGACCCGGACCTCGAAGACGATGAATTGGGACGTAATCGCCCCCAGAACGAAGCTATATTACGAAAAGCA\n") - f.write("CTCCGAATCCCGCGACTTTCGCTCCCTCTACTCCTCGATGCCCATAATACCCTTCTTGGAGCCCCGTTAC\n") - f.write("CATTGAACCCGCCGTCCATTTCTGTGTACACAACCGGTAATTCCCTCTCGCCGGGTCTTCTGCCGCCGGA\n") - f.write("GAATCTCCCCACGGCAAATCCGCCGCCGGGTAATCTCCAGATGGTCAAACCCATCGTCT\n") - f.write("\n") - f.write(">gi|226790423|gb|GO545627.1|GO545627 Mdas9009F13_e668.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191173.2| chloroplast lumen common protein family [Arabidopsis thaliana] gb|AAM13110.1| putative protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGCAATTTCAGCGCGATCAAAACAATTCCTGCTGCAGGTTCTGGCAGCAGAATACCACAGGAAATCA\n") - f.write("GCAACAGGAACTTCTCCCTCTCGTCGTATGTGCTGTCTTTCAGGATCAAGTAATATAACTACTTGGTTTT\n") - f.write("TCTTTTGCAACTTCTTTGAAATTCTGGCCGGCAGCCCAGTCCCTCTAATCCCATATTTAACATGGCTTGC\n") - f.write("ACCTGTCACCACCACTAGCATACCACTTGCTCCTCCATCCGCCATGGCCTTTAAAATAATCTGGGACATA\n") - f.write("GTATAATCCTCAACCACTCTTGCTTGTGCAGAAAGATACGAGCTTGGCCCAAAAGGAACAGATTGACTCC\n") - f.write("GGGAATTTGAATCAACTGGTGGTCTGCGTGTGATAGAAGTGAAGCCTGATATGAAGCCTGAACCCGCTGG\n") - f.write("AGGAGCATATGTTTTTCGATCAGCCTCTGAAAGCCCACTAATTCCCTCTGCTTGGACAGTCCTTAAAACC\n") - f.write("TTGAGTGGAGTTCCACAAGCCACTAGCCGAATTCCGTTATCCCGACAGTAACTCAGGAGAGGCTCATACT\n") - f.write("CCTGCCAGCGTTGAGGTGGCCAATGTGATGTGTAGGACTTCAAAGCTTCTCCATCTATGCTTTTGTCCAT\n") - f.write("GTACTGATT\n") - f.write("\n") - f.write(">gi|226790422|gb|GO545626.1|GO545626 Mdas9009L20_e699.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q05145|MDHP_MESCR Malate dehydrogenase [NADP], chloroplast precursor (NADP-MDH) pir|S33066 malate dehydrogenase (NADP) (EC 1.1.1.82) - common ice plant emb|CAA45270.1| malate dehydrogenase (NADP+) [Mesembryanthemum crystallinum], mRNA sequence\n") - f.write("TCGAATTTTTTTTTTTTTTTTTTACGGTTATTTGCAACTCAAACACATAAATTTAGACATAAATGTTCAG\n") - f.write("GATCTAGGCTGCACAGCAGAAACCTCAAAATTTAACGACTTTTACATTACTCCCTCTGGTTTATTTTCAT\n") - f.write("GCTCTTACTACATAAATGATGCTCCATTATTTGCCTCATGTGCTCTATGTGGTATCGTATCCTTCGTAAA\n") - f.write("AGTTCTCGAGACGTGGAACTTGTCTGCTGAGGATTACATCTCTCCAGGAAGCATAGTATCCTCGGGTAAA\n") - f.write("TCACACACAGCGATACCCTGCCCAGTAAGGTGAGCGACGCATCTTTTCTCAGCTAGTAATTCAGCTTCGC\n") - f.write("TCTTTTTTATTCGCTTGCGAAGATAGTCATCAAATTGTATGTCCTTTACAAGTTCATAGTCGCCGTCTCC\n") - f.write("TTTAGATCTGCATGGCATACTGAATACTAAATCCTCTGCTATACCATAGGGATTTCCATTTGTGTAAACT\n") - f.write("GCAGATGAAAACCAATCGCCCTCTGGGGTAGGAGTAATCAAAGACTTTATGGCATCTGCAATTGACATGG\n") - f.write("CAGTTGATGCAGCTGACGATCTTCCCCATTTCTTGATGAGCACACCTCCTCTCTTCTGGGATAGTTCGGT\n") - f.write("AAATTCTTC\n") - f.write("\n") - f.write(">gi|226790403|gb|GO545932.1|GO545932 Mdas9008L08_e615.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTGATGCTCGAAAAGTAGTAGAGCCAGACTTTTATCGCATTGAGAACCTACGAAAGAAGCTCCCAA\n") - f.write("ATGTTGTTGGTTCAGCATTTCCAACAATAATTAGAAGTTTGTCTTTACCGGTCTCAGTTGCTCCACCTCC\n") - f.write("CCTTATTTTGGGGTAATTTAATACAATTTTTTCTTGGATGGTGCTAACTGAGCAGCCTCTCCATAAATGG\n") - f.write("GGGTAAGGCTAGCCGACATTCACCTCTCCCAGACCCTGCGTAAAGCAGGAGCCTTGTGCACTGGGTACGA\n") - f.write("CCGACACACCTCTCTCAATTGTCGGCCGTTAGAACGAATAAATTGAAGAATATCAAGTATCAGAAATTAA\n") - f.write("TAAGAAATGTGTGGGAGATAAAAATGAGTGTGTAAATAGCATCATTTTTTTTAACCGAAACAGTAGCAAT\n") - f.write("TTCAATAAAATATATTATGCATGGTTTAGAAAAGGGAACAAAAAAAATTGGGAACTCAGATTTAAGCATG\n") - f.write("GTTTAGAAAAGGACTAAGTCACCACACCAGAGAATATTATTCACCACAATAGACTGAAAAAGCATAAAAA\n") - f.write("GGAAGTGAAGGGGGAGGAGGAAAGAGCAAATGTCTCTCCTTTCTCTTCCCTTTAGATGATTTTTGCCCC\n") - f.write("\n") - f.write(">gi|226790402|gb|GO545931.1|GO545931 Mdas9008L02_e612.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB41987.1| FtsZ-like protein [Nicotiana tabacum], mRNA sequence\n") - f.write("ATGAAAACGACGATGGCTGCATGGAAGAACCCGAACGAGCTAATCTGGACGACGTCGTCCTCAATTCCCG\n") - f.write("CAGCATTTCACCACCACAAGCCACTGCCTTCCCTCAGAACGTGCATTCCTCTGAGCAGCAAAAGAAGAAG\n") - f.write("CGCATGGAAGCGTCACCGTTTCGGGGTTGTCAGCTGTTCCTTTGCTCCCATGGAATCGGCCAAGATTAAG\n") - f.write("GTCGTTGGGGTCGGCGGAGGCGGCAACAATGCTGTTAATCGCATGATTGGCAGCGGTTTACATGGTGTTG\n") - f.write("ATTTCTATGCCATAAACACGGATTCTCAAGCGCTCTTGCAGTCTGCTGCCGAGTACCCGCTGCAGATTGG\n") - f.write("GGAGCTTTTGACTCGTGGGCTAGGTACTGGTGGGAATCCACTTTTGGGGGAGCAAGCGGCAGAAGAGTCA\n") - f.write("AAAGAGGCTATTTCTAATGCTCTA\n") - f.write("\n") - f.write(">gi|226790401|gb|GO545930.1|GO545930 Mdas9008E08_e581.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL11502.1|AF367442_1 NAD-dependent malate dehydrogenase [Prunus persica], mRNA sequence\n") - f.write("TTTTTTTTTTTTGAATCAAGGCAGATATGGATTATTTTACGTCAATGGGACAATCCCATTCAAATATGCA\n") - f.write("ACTAAAAGAAGAAAAAAGTCGAAGTGTCCGAATAGAATATTGGGCTCAACAACTGTAAAACCCACAAAAG\n") - f.write("CAGCTTCTGCATCATTAACATATCTCTCTATCTTAACAATGGCATTATTCAAAACTTCAGCTGCTTTTCT\n") - f.write("CACACATTGCAGGGAGGCCAACTTACAACCACACCAAGGAAAGGCCAAGAGCATCTAAGAGAGGCAAGAG\n") - f.write("TATGCCAAAGCTTTCTCCTCACTGAGCTCCTCTGCAGTTGCATCCAACTTCTTCCTCGAGAACTCGTCAA\n") - f.write("TAGAGAGTCCTTGAACAATCTTCCACTCCCCATGTTGGCAAGTGACTGGGAATGAGAAAATGAGACCAGA\n") - f.write("AGGTACATCGTATGAGCCGTCAGAGTAAACACCCATGGAAACCCAAGTGCCCTCCGGGGTTCCAAGTACC\n") - f.write("CAATCACGAATGTGATCACAAGCAGAACTTGCAGCAGATAATGCACTTGACAGCTTACGGGCCTTGATGA\n") - f.write("TTGC\n") - f.write("\n") - f.write(">gi|226790400|gb|GO545929.1|GO545929 Mdas9008L22_e619.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ATTCACATTAAAATTACCATACAACCCCAAAGCTACACGAGCAAAAGAAACAAGAAAAAATAAATTGAAC\n") - f.write("AAAACATGGAGCACATGTCTATATATAGCTTTTCATTTTCATTTGTAGA\n") - f.write("\n") - f.write(">gi|226790399|gb|GO545928.1|GO545928 Mdas9008P19_e637.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTGCATCCAAGTATCAATTCCAAACTGAACCCGCAGAATGAAATTCATCACTCTTTTGATCAGTCTATC\n") - f.write("TTTCGGTTTGACTCTGGCGGCGGGCGCGGTTGTCACTTGCGGCGATAGGGAATATAGTGAAAAGACATGT\n") - f.write("CTCACAACGTCTCGAATATGTAGGATATGACTTCAATCCACCAGATGGAGTTTTCGATGGTACCCGGCCT\n") - f.write("TATCAGAAGGTACCATTAACCGGTTATGATGGAGGTCGAGGTTCGTTGGATTATCTTATTGTCGACTCCT\n") - f.write("CCGATAATCTAGTTGGCGCCGTCACCTTCGCTTCAGGTGGAGGGTCATACACTATGTGCAGCGTCAGCTA\n") - f.write("ATTACAACCCATGACGGATAATTTATTTGGCCGTCGAGAGGAAACGGGATCAGACACATCTGATGGGATG\n") - f.write("ATGTGAGCATGATGCAGCAAAATTTGTGACGGCCTTAGACTACATGTACCAACACGACAGTCATTATCTA\n") - f.write("ATTATCTTTCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790398|gb|GO545927.1|GO545927 Mdas9008J20_e606.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK13030.1| ribonuclease-like PR-10a [Malus x domestica], mRNA sequence\n") - f.write("ATTAACTGATTTCATTATATTTAAAAATAAAACACTTACAGTCCGCAACTTTTTTTTCCAACAAATACAT\n") - f.write("AAAGGGCAACCAAAAAAAGATCACAACCATAAACTTATTTTTCAAAACCAAAATGCTCAAAACCATGGCT\n") - f.write("ACTTTGGGCTGACTAAAAAAAGCATACAAAAAAAAACCCCACAACCCTCCACTGAAGGGTGACACCCCAA\n") - f.write("ATACCATAAAAACATATTAATTTAATTGTATGCCTCCGGGTGGCCCTTGAAGTAACTCTCAATAAACTTG\n") - f.write("AACAAACCATGAACCCTCTCTTTGCCAGCCTTGACGTGCTCTTCCTTGATCTCAACATCACCCTTGGTGT\n") - f.write("GGTAATGGCTGAAACTCCTGAAGAAGGAACCACTTCCAAAAGCCACCAACTTGGTCTCGTAAGAAACCTT\n") - f.write("CTCAATGGTGTCTGTCAAAACATCTCCTTCAATCAAAGTGTAAGCGTAAGAATAGTTTGCTTCCTCAACC\n") - f.write("GAATCGATCTTGTGCTTCACGTAACTTTT\n") - f.write("\n") - f.write(">gi|226790397|gb|GO545926.1|GO545926 Mdas9008P05_e634.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTGAAATTAATGTACTCAAATTAATAAAGCTTCAAGGATCCATCATTTCATCCACCA\n") - f.write("ACAAAAAGGGCAGATTTTCCATCCATCCAGATGCGCACAGAAGCAATTTTGTGCATGAATATCATCATCG\n") - f.write("CTGCAGAGACAGTTTTGAGTTCCTTGACTCTTTTCAGTATATCATAAAACAGTCACAACCTAAAGCTTTT\n") - f.write("GAAGAATCGAAAACCGAAAAAAAAAAAGGGCAAACATTTCCAATCAGAGAATTCCATGAAGTGAGCTGCA\n") - f.write("AATATTGATGGTGATTCGATCTTTGATGAATATATATTCTCCCACATGTCCTGTTGCCGTTCCAAAATAA\n") - f.write("GTTTCCGTCCATGCACCGGTCCACCATTCCGGTCAGGTCATAAGGTGGTGCCTATTTCCTGCTCTCTCTA\n") - f.write("TCTTCTGGAAGTAAATGTAGCATTGGTCATCCTGCCATGTTGTTTCCCAACAGCATTTGAGCTCAGCCGG\n") - f.write("CCATTAGGCAAGCCTGAGCTTTGGGTACTGCTCATGCTTGATCTATCCAGAACTGCTCCATTTCCACCAT\n") - f.write("TCAAAAGTACAGATGACTGGCTTGGCCTAGTGTCAGGGCTGTTCAGTTCCCAAGAATCTTT\n") - f.write("\n") - f.write(">gi|226790396|gb|GO545925.1|GO545925 Mdas9004P19_e323.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_191788.1| ADP-ribosylation factor [Arabidopsis thaliana] pir|T48021 ADP-ribosylation factor-like protein - Arabidopsis thaliana emb|CAB71889.1| ADP-ribosylation factor-like protein [Arabidopsis thaliana] gb|AAK49618.1|AF372902_1 AT3g62290/, mRNA sequence\n") - f.write("CAATAATCGAATTACAACTCAGAACAGAATTGTATCCAAAATCCAACCAAAAGAAATACAACCCGATTTA\n") - f.write("AAAAGGTCCTAGATGAAAACAGCATTCCCACAACAAATACAAGAAGCAGATTTAACAACAATTCAATCGT\n") - f.write("CTCAATAGCATAAAAAAAAAAAAAAAACAACTAGATAATATTCACCCCTGCATCCAGAATTTCCGGTCCA\n") - f.write("CAAAAAGACTCCTCGATACAATCACGCCTTGTTAGCAATGTTGTTGGAGAGCCAATCCAGCCCCTCGTAT\n") - f.write("AGACCCTCCCCGGATGTTGCACAAGTGCTCTGGATGTACCAGTGACGCTGTCTCAGAGAGTGGAGGCCAA\n") - f.write("GCTTATCAGTAATTTCAGCAGCATTCATTGCATTGGGAAGATCTTGTTTGTTAGCAAATACGAGCAACAC\n") - f.write("AGCATCACGCAGTTCATCCTCATTCAACATCCTATGTAATTCGTCCCTTGCCTCAACAACACGGTCTCTG\n") - f.write("TCATTGCTGTCCACAACAAAGATAAGACCCTGCGTGTTCTGGAAGTAGTGCCTCCACAATGGTCGGATCT\n") - f.write("TGTCCTGACCCCCGACATCCCAGACGGTGAAGCTGATGTTCTTGTACTCCACGGTCTCCACATTAAACCC\n") - f.write("\n") - f.write(">gi|226790371|gb|GO545924.1|GO545924 Mdas9005J02_e371.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB12722.1| gamma tonoplast intrinsic protein [Pyrus communis], mRNA sequence\n") - f.write("TTTTTTTTACAAAAGATAAATGGAATTTAGTGACACAACAGCGGAGAGCATGCAAAACAAATTACAAATC\n") - f.write("AACGATGGAGATCAACTCATGACGACAACGATCATGATCATGATTTTCTTGATGAAACGAAACACAAGAA\n") - f.write("CTCAAAGGTCCAAAACCCAGCATGCATGCAAATGTAATTAAATCTTATGACTCCTTAATTAAGCTTACTT\n") - f.write("AAGGCTTAATCAATTAGTAGTCAGTGGAGGGCAGTTGCTCGTGGCCGCTGTTGCCGATGAACACGAACTC\n") - f.write("GTAGATGACCCCGGCGATCCCGGCGCCGATCAAAGGCCCGGCCCAGTAGACCCAGTGGTTCTCCCAGCTC\n") - f.write("CAGCTCACCAACGCCGGCCCGAAAGAAACGGCCGGGTTCATGGACGCCCCGTCAAAAGCCCCACCCGCCA\n") - f.write("AAATGTTGGCGCCAACGATGAAACCAATCGCGATGGGCGCGATTGTCCCCACGCTCCCTTTCTTCGGGTC\n") - f.write("AATCGCGGTCGCGTAGACCGTGTAGACCAGTCCGAACGTCATCACGATCTCGAAAACGAACGCGTTCCAC\n") - f.write("ACTCCCACTCCCGGGGACAGGGAGAAAGCAACGGTAGTCTGGCCGTTGGTGACCAACT\n") - f.write("\n") - f.write(">gi|226790370|gb|GO545923.1|GO545923 Mdas9005M12_e381.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGGAAAAATCAGAAAAAGAAGAACATAATTTCGCGTGATGCAGATTTTTTGTTTTTTTTTTTTTTGG\n") - f.write("GTATGATGATATATTTTACACTAAGAGGAGGGGGAGTTCGATTAAGTCACACAATGGGCAACCTAATTTG\n") - f.write("GTATTGAATTATCCATCTACGAGATTCAAACCTAAAGCCTCTCATTTACAAGTGAAGAAGAATACTACCA\n") - f.write("GATCGTGAGTGACCGAGCGTTGTAGAGTATGCCATAAGAAAAATGAGCTATGCAAGAAATTGCGATCCTT\n") - f.write("GTTTCGTGCTCTATTTTTCAACGGTTACAAATATAATCTTGAGAGAGTAAAAGAAAAACTCGTATAATCA\n") - f.write("CTAAATTGTTACAACAATTTGTCACAAAAGAGAACATTTGTCACCAATTTGTGGCAGAAATTCTATCCTT\n") - f.write("TTCGTGAAGGAACTTAACACCAGCTGCTACTGCTAACAGAAAACAACGAGTAGAGCAACCACGACGACGA\n") - f.write("TCGAGCAAATTAAAGCCTGCACCTGTACGATTTTTCAGCACAAAGGGAAATAAAATGTCGATACTAACAT\n") - f.write("CAAAGGACAAAAATGGTAGGCAAAATCTGCATAATTTCTTACTGCAAAGGGATGTGGCATAATATC\n") - f.write("\n") - f.write(">gi|226790369|gb|GO545922.1|GO545922 Mdas9005I12_e368.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO33770.1| unknown [Oryza sativa (indica cultivar-group)], mRNA sequence\n") - f.write("CCAAAATCTCTCTCAAAGCTTGAAACTTTAAGCCTTTTGGTCCCAACCCATTTCCCAAGGGCGCGGTTTC\n") - f.write("CACCGGTTCTAGCCGGGAAAAGCTGACTTGGGTCGCCGGAGAGTTGAACCACCACCATGGACGTTGACTT\n") - f.write("GTGGGCTTCCAGGGTTCACGCAGCTAAGAGCCTCTCTGCTGCTCATGCTGCAAGGCTTCACTATGATAAT\n") - f.write("CATATGGGTTTGGAAGATTCTGAAGGAGATGACGACACAAAATCGTGTTTTCCATGCCCTTTCTGTTATG\n") - f.write("TGGATATTGAAGTCCCAGTGCTTTGCAGCCACTTGGAGGAAGAACACTGCTTTGACTTTAAAAATGCAGT\n") - f.write("TTGTCCTTTGTGCGCTGCGAATCTGGGGAAAGATGTAATTGGACATTTTATGGTGCACCATGGAAGCTCC\n") - f.write("TTCAAGCACAGGAGAAAATCTCAAAAATCCGGTTTGTGGACTGGTAGTTCAGCAATGCTGGGGAAGGCAC\n") - f.write("TGCTTAAACATGGAAGGACATATGCACAGGAAACTGCACCTGATCCTCTCCTCTCACCATTTATCTGCAA\n") - f.write("TATATCATTTTCAGACCCTACAGGTATCCCCGAAGATGTTTG\n") - f.write("\n") - f.write(">gi|226790368|gb|GO545921.1|GO545921 Mdas9005N15_e388.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_445525.1| hypothetical protein [Chlamydophila pneumoniae AR39] pir|G81516 hypothetical protein CP0988 [imported] - Chlamydophila pneumoniae (strain AR39), mRNA sequence\n") - f.write("CAACTTGTTCCGACCTAGGATAATAAGCTCATGAGCTTAGTCTTACTTCACCGTCGAGAAACGAAAGAAG\n") - f.write("ACTTCCATCTCCAAGTTTAACTCAGACGTAGCTCGCTTCTTTTTGGGTGTGAAGCAGTGTCAAACCAAAA\n") - f.write("TACCCAACAAGCATTAGCTCTCCCTGAAAAGGAGGTGATCCAGCCGCACCTTCCAGTACGGCTACCTTGT\n") - f.write("TACGACTTCACTCCAGTCACTAGCCCTGCCTTCGGCATCCCCCCCCTTGCGGTTAAGGTAACGACTTCGG\n") - f.write("GCATGGCCAGCTCCCATAGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGAATTCACCGCCGTATGGC\n") - f.write("TGACCGGCGATTACTAGCGATTCCGGCTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGGACGG\n") - f.write("GTTTTTGGAGTTAGCTCACCCTCGCGGGATCGCGACCCTTTGTCCCGGCCATTGTAGCACGTGTGTCGCC\n") - f.write("CAGGGCATAAGGGGCATGATGACTTGACGTCATCCTCACCTTCCTCCGGCTTATCACCGGCAGTCTGCTC\n") - f.write("AGGGTTCCAAACTCAACGGTGGCAACTAAACACGAGGGTTGCGCTCGTTGCGGGACTTAACCCAACACCT\n") - f.write("TACGGCACGAGCTGACGACAGCCATGCACCACCTGTG\n") - f.write("\n") - f.write(">gi|226790367|gb|GO545920.1|GO545920 Mdas9004L06_e303.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD27882.2|AF139470_1 chlorophyll a/b-binding protein CP24 precursor [Vigna radiata], mRNA sequence\n") - f.write("CACTTAAGTATCTATTAAATTGAAAAGGATAAAAAAAAATTGTAATTAGTTATATCTACATATTGAAAAG\n") - f.write("TAAATGCCAAATGGTTTACAAGCCAAGAGCACCAAGGGGCGTCTTTCCTTGCCCAGCTTCAAAGTAGAAA\n") - f.write("ATGAGCATAGCCACCATAGCAAGCCTTGCATGCTTAATCTCAGCCAGTTTCAGTCTCTCCAACTTTTCAC\n") - f.write("TGTCTGGAACGTAAACCCCGTCCTGGATGGAGCCGGCGAAGCCCAAGGGGTCGAAGAACTTGCCACCCGG\n") - f.write("GTAGCCTTGCTCTCCGGTGGAGTTGGCGAAGTTCTCCGAGGTCTTGGACCAAGGTGTGGCCCACTCGACG\n") - f.write("GACTGGGACTCAGGGTTGTAGAAGTCCACCCATCTCTTGCTTTCCACCCATCCCATGAGCAAGAGCTGAG\n") - f.write("TGCCGAGCAGTGAGCCGAAGGAGAAGGGTGCGATGGCACTGGGGTCAGCTCCGGCTTCGAACCATGGGAT\n") - f.write("ACCACTCCAGGCCTGGCCAACAAAGATGCCAACGACTGCCGCCATTGCCCACCGGCCGTGGATGAGCTCC\n") - f.write("GCCTCTCTGTACCACTTGAGGAACGCCGGGTCCTTGCCTAGTCCTAGTGGGTCAAAACCGTAGTCACCTG\n") - f.write("GAAGCGAGCCATCGAGCCA\n") - f.write("\n") - f.write(">gi|226790366|gb|GO545919.1|GO545919 Mdas9005K11_e376.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAC48323.1| 2-Cys peroxiredoxin [Pisum sativum], mRNA sequence\n") - f.write("CCCCATCTTACAAGTTTCTGATCAAATAAAATTACATAGGCTCACCCTGTTTCCATGATAAAATAAAAAG\n") - f.write("TGACAACAATGAAATTGTATGCTACTTGAATATGCTGAAAATCGGGCAAGTCCCATTGATTGGGGTTTAT\n") - f.write("TGTGACATGCAAATGCTCAAAATTACCAAGGATTGGAAAAAAAGGTTACACAAATACAAAACTCGTTTAC\n") - f.write("ACGTCCTATTTGAGTCCAACATGGACATGCAGTGTACTACCTCTATATTGCGGAAAAGTACTCTTTGCTG\n") - f.write("CCCTTGGGGTCTGGCTTCATGGACTTCTCCCCGGGCTTCCACCCTGCAGGGCAAACTTCATCGGGATTGT\n") - f.write("CCTGCACGTACTGCAAGGCCTGGAGCGTTCTCTTAGTCTCATCCACACTACGGCCAATGGCAAAATTGTT\n") - f.write("AATGGTGGAGTGTTGAATGACCCCTTCCTTGTCAATAATGAAAAGTCCTCTCAAAGCGATTCCCTGA\n") - f.write("\n") - f.write(">gi|226790365|gb|GO545918.1|GO545918 Mdas9005B21_e332.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O04867|GLN1_ALNGL GLUTAMINE SYNTHETASE (GLUTAMATE--AMMONIA LIGASE) (GS(1)) emb|CAA69937.1| glutamate synthetase [Alnus glutinosa], mRNA sequence\n") - f.write("ATGCACTCAATTAACAAAAACAGCTAAAAAAAAAAAAAAAAGATGAGGCTTGCAATTTTCAAAAATTACA\n") - f.write("AGTGAAATGGCATTTAAACCAACCACCCCTTTGAAAAATATTATTCATATAAAAAACTTATTCAACACAA\n") - f.write("CGGGCAAAATGATGAGGCAATGAAGCAACAGCATAATAAAGTTTAAAGGACAAAGCCAACTCTAGTTTGA\n") - f.write("AGCTAAGGACCCACAAGGATCCATCCAAAAGGATCTGGTAAATCACATTTCCAACCTCAATGAAAAACAA\n") - f.write("TTACGTTGTCACAAAACTTATAAATGCACGCGTGTAGGTGTGGCTGCGTGTGCTTATGCCTTCAACAAAA\n") - f.write("GGGTGGTTTCTGCAATCATAAATGTGACAATGTATGGATCCATGTTCGATGCAGGCCTCCTGTCCTCGAA\n") - f.write("ATAGCCCTTGCCAGCTTGTTCTGTGTCTCTACCAACACGGATAGAAGCACCGCGGTTGGCTACACCCCAT\n") - f.write("TTGAATGTATTGATATCAACAGTTTCATGCCTTCCTGTCAAACGG\n") - f.write("\n") - f.write(">gi|226790336|gb|GO545917.1|GO545917 Mdas9005I04_e367.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCAATATCCACTGTTCTTAAACATTTCTTAACATGCTTAAGAGCAGAACAAACAATTGGCAACTGCCAAT\n") - f.write("ACACAAACATCTTATATAATCTTAGAACATATACATATAAACATTACAAGAACAACGATTCCATGGATAA\n") - f.write("ATTTTTCCATCCATGTTCCGATAATTAGCTATATATTACATTAGCAAGTCACTGAATCGTCGATCAGCCA\n") - f.write("CTAGAGATGTTACACCAACAACCCCCGGTCCTCCTCTTCGTTGTGGTCAGAAGCCGGAATCCTTGGATCT\n") - f.write("TAACATTCATAGGACTGCTAAACTTTAGTTAATAGATTCTGCTGTCTGCAAAAGCTTTATCGAACCAACT\n") - f.write("AACAAAATACGATGATCCAGCTAGATGCAGAATCACACACTCCTTTGCATCCAACAACCAAAGCCTAGCC\n") - f.write("CTCGTCGTACAAGAACCAGGCCAAAGCAGGATCTTAGTGCCACAATTATCAATACAACAGTAAATTACTA\n") - f.write("TAGCTACACAATCTTACAAACTGCAAACAATCCCTTCATTATTCTGGGAGTGTCAAGCTTAGGTTATATA\n") - f.write("TCATCGAGTGGTATAAGTCAATTTTATCAATTATCGGAGAGCACGAATTTA\n") - f.write("\n") - f.write(">gi|226790335|gb|GO545916.1|GO545916 Mdas9005N19_e390.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T15056 photosystem I chain IV - wood tobacco dbj|BAA07667.1| PSI-E subunit of photosystem I [Nicotiana sylvestris], mRNA sequence\n") - f.write("AGCACAGAAACAAATATGGCTAGCTGTGGCATCGCATCAGCTGCCTCAGGCTTTGTGGTAGCACCAAATG\n") - f.write("TTGCAACCACCAACGCAGGCTCAACTTCTAGCCGAAATAGCATGCTGTTTTTCCCATCAAAACCCAACAC\n") - f.write("CAACACCAGAAGCAATGCTAGGTTTGTGACGAGGTCAGCAGAGGAAGCCGCTGCTCCAACGGCAGCCACC\n") - f.write("AAGACTGCACCAGAGGGGGAAGCTACCCCTAAGCCTAAGCCACCACCAATTGGACCCAAGAGAGGCACTA\n") - f.write("AGGTGAAGATTCTGAGGAAGGAATCCTACTGGTTCAAAGGCATTGGATCTGTTGTAGCTGTGGATCAGGA\n") - f.write("TCCGAATACCCGTTACCCGGTCGTGGTCCGGTTCAACAAAGTTAACTATGCCAATGTGTCAACAAATAAC\n") - f.write("TATGCTTTGGACGAGATTGAAGAAGTTAAATGAGTTTGTAGTAGCACTGTAAATTGTAATCTTAATTACA\n") - f.write("TTCTCCTTCTATCAAAAAAAAAAAAAAAAAACCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790334|gb|GO545915.1|GO545915 Mdas9005B01_e327.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P10748|AROA_LYCES 3-phosphoshikimate 1-carboxyvinyltransferase, chloroplast precursor (5-enolpyruvylshikimate-3-phosphate synthase) (EPSP synthase) gb|AAA34136.1| 5-enolpyruvylshikimate-3-phosphate synthase precursor (EC 2.5.1.19), mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAACAGCAGAATTGCATTGCAAATTCTTTGAACCAAATACTTAA\n") - f.write("CAAACCGAGCAACGTATGCCTTTCTTGACATCAAGTTTGTCCCAAAGAAAGGTACAAAAAAAGACCCACG\n") - f.write("AACCAAATCATGAATCACCAATATTGAGTAGAATCAGATCACAAATATTAGAAACAATAACGAGCTCAAC\n") - f.write("TTGCAAAGACAAATCATCCAAAATTACAGGGGAATAAAGAGAAACTGAAACAAGTGTGGCTTCCATCTGC\n") - f.write("ACTTCTTTGGCTGTAGAGGCACAAGGACAATCCCTCTCTCTCCCTATCTACAGATAAATATATCTTATAA\n") - f.write("CCACTGTTCAATGCTTGGTAAACTTCCTGAGGACTTCAAAGTAATCGGGGAATGTTTTTCTGGTACAACC\n") - f.write("GGGATCCTTGATAGTAACTGGAACGTCTCCACAGGCAGCAAGAGAGAAAGCCATGGCCATTCGGTGGTCA\n") - f.write("TCATACGTGTCTATTGCAGTCAAGTTTAATTTTTCTGGCGGTGTGA\n") - f.write("\n") - f.write(">gi|226790333|gb|GO545914.1|GO545914 Mdas9005F15_e357.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TTTTTTTTCAGTTAAAATTCCCCATTGATGCATTTTTTGAAGCTTAATTTTACATACAAGTAGGTAGCTT\n") - f.write("AAAAATCATCTATTGTACACACTGATTAGGTGTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAAGCCC\n") - f.write("AAGCGTTGTTGGTAACAGGATCAGCCAGATGATCAGCAAGGTTCTCAATGGGGCCCTTTCCGGTGACAAT\n") - f.write("AGCCTGCACAAAGAAGCCGAACATTGAGAACATGGCAAGCCTTCCATTCTTGAGTTCTTTGACCTTAAGC\n") - f.write("TCTGCAAATGCCTCTGGGTCATCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCTGGGTACAGTGGGTCGG\n") - f.write("TGATCTCACCAAGGGGTCCTCCGGCAATGCGGTAACCCTCAACAGCACCCATGAGAACCACCTGGGTTGC\n") - f.write("CCAGATTGCTAGAATGCTCTGTGCATGAACTAGGCTTGGGTTTCCAAGGTAATCGAGGCCACCTTCACTG\n") - f.write("AAGATTTGAGCTCCGGCTTTAAACCACACTGCTTCTCCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCG\n") - f.write("GGAAAACACAGCCCAAAGCACCAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTCTTGGC\n") - f.write("AAAGGGTTCGGGGTCTGCTGATAGCCCAGCAGTGTCCCATCCGTAGTCACC\n") - f.write("\n") - f.write(">gi|226790332|gb|GO545913.1|GO545913 Mdas9005G12_e361.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTAAAATAAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACA\n") - f.write("CCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGT\n") - f.write("CTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTAC\n") - f.write("ATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAAA\n") - f.write("CTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCT\n") - f.write("TGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGT\n") - f.write("CCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCA\n") - f.write("AATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTA\n") - f.write("\n") - f.write(">gi|226790331|gb|GO545912.1|GO545912 Mdas9004N12_e313.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTAGTTTCATCTTTTTTCATCATAAAAAGGATTTAAAATAGTTAGATGCCAAAGTGAAATAATTGT\n") - f.write("TAAAAGGAGTCGACCATATAAAGTTGACAATGAAATGAAGCAAAAGGGACCCGTTGTGAGTCATCGACAC\n") - f.write("GTACTCGCATGCGTGCCTCTCCATTTGTTAGGTAACATTAAAAAGTTAAAACAAAACAATCACTTGGTCC\n") - f.write("CCATTCCCCAGTCTCTCTCTCTCTTCCTTTTCAAAATTTGTGTTTATACACTGTACACATAGTTTTATTC\n") - f.write("CTCATCCTCTCATTTCACTGCTAGATATTTTTTAATTTTAAAATTTACATTTATACATTGTATAAATTTT\n") - f.write("AAAATTTAAACTTATTTAACGATAATAGATAATGATGAGGAAAAAACAATTCTTCCCCATAAAGGATGCA\n") - f.write("TAAGATTCAAAAGTCGCGCTGCAATATTATAGAGAAAAGAGTGTTAGTTATTATCCATGTGTACCCTCAA\n") - f.write("TTCTAAATTATTATAATTTTTTCTTTTAAAATAATTACTAGTTTGTTTCGATTTATCATTGGATTTT\n") - f.write("\n") - f.write(">gi|226790330|gb|GO545911.1|GO545911 Mdas9004P11_e321.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172076.1| glycosyl hydrolase family 19 (chitinase) [Arabidopsis thaliana] pir|C86193 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF29391.1|AC009999_11 Contains similarity to a basic endochitinase from Arabidopis thaliana gb|A, mRNA sequence\n") - f.write("CTGCATTGGTGGCCGTGGTGGCGCTGAGTGTTTTCCTGTGTGCCAGCAGCGACGGCGATTACTCGTCCAC\n") - f.write("CGTGGCGAAAGTGAAGATTGTGAGGGGGAAGAAGCTGTGCGACAAAGGGTGGGAGTGTAAAGGGTGGTCA\n") - f.write("AAATACTGTTGCAATCTCACCATCTCCGATTACTTCCAGACTTACCAGTTTGAGAATCTGTTCTCCAAGA\n") - f.write("GAAACACGCCGGTGGCGCATGCCGTTGGGTTTTGGGATTACCAGGCGTTTATCACCGCCGCGGCGCTTTT\n") - f.write("CGAGCCTCTTGGGTTTGGGACCACCGGTGGGAAGCTTATGCAGATGAAGGAGATCGCCGCCTTTCTTGGA\n") - f.write("CATGTCGGCAGCAAAACCTCCTGCGGTTACGGTGTGGCCACCGGAGGACCATACGCTTGGGGGCTTTGCT\n") - f.write("ACAACAGGGAAATGAGTCCCATGCAGTCATACTGTGATGACTATTACAAGTACATATATCCCTGCAGCCC\n") - f.write("TGGAGCTGAATACTATGGCCGTGGTGCTTTGCCTATCTACTGGAACTACAATTACGGTGCAGCTGGAGAC\n") - f.write("GCTTTGAAGGTGGATCTGTTGAACCATCCAGAATACATTGAGCAGAACGCTA\n") - f.write("\n") - f.write(">gi|226790306|gb|GO545910.1|GO545910 Mdas9005B05_e329.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGTTGCAAAACGAATAAATTTATTATCTATTTTTCAGTGGCATAACA\n") - f.write("AACGATAAGATTTTCTGTACTGTAATCAGTTACACAGCCAGACAATCGATAGAAGAAAAAAAATCAATAT\n") - f.write("TATCATGAGGATACACATTCTAAAATAACCCTAAATCATTATTGCCAACATAACAGAACGCTCTTGAGAA\n") - f.write("AGTGAACAAATATTACAAAGGTAACATCCCACTGCAACTATATATAACAAGCAACAACTTTTGAGTTACC\n") - f.write("TAAGATCCAATTGCTAGCACCATAACAGATGACTGTTATCTCGCATGTACAAGTCAAGACTCCTGGGGCG\n") - f.write("TCTCAAATCTCGTTGGAGTGTCAATCCCCATCATACAGCAAATGCCCGATATTAAGATTATAAGCAAAAC\n") - f.write("AATTCCAACTAGAAGTCCCTCTAGAAGAGATGATTTTAATAGACAAACTTCATCACAGGCCGTAGAATTG\n") - f.write("GCTGATGCATTTCCTGAACCACTTTCGGCCAGAAATCTTTCTAATTCTCGATGAGAAGGATATTGGATCG\n") - f.write("ACTTACTGGGATCTGAAACATATAGAACTCCAT\n") - f.write("\n") - f.write(">gi|226790305|gb|GO545909.1|GO545909 Mdas9005D21_e343.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAP43511.1| oxygen-evolving enhancer protein 3 precursor [Pisum sativum], mRNA sequence\n") - f.write("TTTTTATTTAATATCACTAGATTTCCTCCAAATAGCATCCGAACAATTTGATCTCACAAACAGTCAAACA\n") - f.write("AAGCTCTTAAAAAGCCTTATACATCAAATACATTAATCCCTTTTAGGGTTTAACCAAGCTTTGCAAGAAC\n") - f.write("ATCATTGAGGGAAGATACGGTCGCGGCGTAGTACTTCTCTGCTTCCGGGGTGCTCTTGATCTTTGCTGCG\n") - f.write("TGGTCCAAGCCGTCAATGTCTTTGAAGAGCTTTCCAGCGAGTTCCTTGAGGGGCTCCTTCTCGGGTTTAG\n") - f.write("GTTTGGCAGAAATGACGGTCTTGAGGTCATAACGGAGATACGAGGATCTGAGACGAAGATCGTTCTGACG\n") - f.write("TAGGGCCATGCCTTTTTGTCAATGAACTCCTTGACAGCTACAATTTCCTTGGCTGACTCCTTCGCCCGCG\n") - f.write("CGGCAGCCTGAGCCGGAGTGAGTGGTTGGAGGAAGAACCTCTCCTTCAACGGCAGGTCAAGGTCTCTTGC\n") - f.write("CTCATCCGAGTTTAGGGTTCCAGGCAATCCTCCGGAGGGAGGTGGAGGAGGACCGATTTTGATGGGCTTA\n") - f.write("GCCTCGGCAAGCACAGCTTGAACAAATGACCCGGACGCCAAACCAACTGCGACGAGA\n") - f.write("\n") - f.write(">gi|226790304|gb|GO545908.1|GO545908 Mdas9004L22_e306.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_192880.1| short-chain dehydrogenase/reductase family protein [Arabidopsis thaliana] pir|T10561 hypothetical protein F25E4.30 - Arabidopsis thaliana emb|CAB81242.1| putative protein [Arabidopsis thaliana] emb|CAB82146.1| putative protein [A, mRNA sequence\n") - f.write("TTTTGAGCAGTATAAGAAGACTATTCAGCTTGAAAGGATATTGTTCAACTTTTGAATTATAAGTTACAGC\n") - f.write("ATTCTTGGAGTCTATTATTCAAAAACAAACAACCACCACTACGCATTATCCCTGTAAATAGGGTTGGTTG\n") - f.write("TATGAATCTTATAACGACACAATGCAAAGGGCACTTTCTTAAGTCTTTATATAGAGTTTTAAGTTTTACA\n") - f.write("GAAGATCATTTAGTCAAATCCATGCTAAAATCCCATAGTTTCTTTGCCATCTCCACGTCTTGACCTTGTG\n") - f.write("GCCTTGGCTTGGATAGGTTACAGTCCGAGAAATATTCACCGGTCACCCCCTTGACTTGTGGATGCAGTGC\n") - f.write("CACGTAACACGTCGTTGCTGCTCCCTGCTGAACATTTTTAAGCACAGCTCTACCAAGCACGTTAACAAGC\n") - f.write("CCGTTAATAATGCTGTAATAACGAAACAGATTGGTAACAATTGCACCAGGGTGAAGCGAGTTTGCAGTAA\n") - f.write("TATCAGCTCCTTCTTCCTTTAAGCGTCTTGCAAGCTCATTAACAT\n") - f.write("\n") - f.write(">gi|226790303|gb|GO545907.1|GO545907 Mdas9005C13_e335.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CCTAAACGGAACACGGGAATTTTATTGATAATAAAAAAAAATTTACTTCTAAACAAAGGGACATAAACCT\n") - f.write("AACCCCTCCTAAAACAAAAAAAAAGAAATACAAAAAAAAAAGGGGGACTTGCCCCTTACCCCTTTTGAGT\n") - f.write("GGCTTCCTAATCGAATCAAGTGCTCAAACAATAACATTGCGAACAATAATAAAAATTACATATTCACGGC\n") - f.write("CACACCCTTGTACTAGTGTGAAGGGACCCCCCAAGTAGGCACTACTTGTACTGGGGTTGCCATGTAATTG\n") - f.write("ACTGTCCCAGAATTTTCCAACCATCCAATCTCCTCGGGGTTCACCCC\n") - f.write("\n") - f.write(">gi|226790302|gb|GO545906.1|GO545906 Mdas9004P14_e322.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172076.1| glycosyl hydrolase family 19 (chitinase) [Arabidopsis thaliana] pir|C86193 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF29391.1|AC009999_11 Contains similarity to a basic endochitinase from Arabidopis thaliana gb|A, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTACGAGAACAAAACGGTTCATATATTGCATATAACAACTTACACAGACGATG\n") - f.write("CATTTCGACGATGGAAAAGAATAGATTTCAAAACCCAGAAAGTAAATAACTTAAGTATGGCAACAAATCA\n") - f.write("ATCAACAGTTTACACATTCTCACAGATATGCATCTTCACGAGCGAGGTTCCAAGTAATCCATTAACATCT\n") - f.write("ACCTTCGACGCCTTTTTATTAATACTTCACCTTGTAGAGAAGACGGGTTTCGATTTTCCTTCTGAATTTC\n") - f.write("TAAGCTGATGGAAGAAGAAGATGGCTTTGATAGGGCAGGCAACCTAACACGATATAGATCTCAAGAAGAT\n") - f.write("GCAGTAACAGCAGGCTGGATTGGGTTAAATGCAACCTGCTCGGCACAAGTTAACACTTCATGAGGCCCTG\n") - f.write("CCTCGTCTCGGTTGACACCCATAAGGTCCAGGTAGTACTGGTAATGTGAAACGATGTTGTTCATGGCATC\n") - f.write("AATGTCACCCTTGCCACAAACTGATTCCCCATAAAGAATATTCATTGTAGTGCCCAATCCAGGAAACCGC\n") - f.write("TTACTCAAGGTATCGGTCTTGGTAGGCTTCCAGTCTCCAACAAATG\n") - f.write("\n") - f.write(">gi|226790301|gb|GO545905.1|GO545905 Mdas9005D09_e340.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF76226.1|AF272572_1 14-3-3 protein [Populus x canescens], mRNA sequence\n") - f.write("TCGAGTTCTCTTTTTTTTTTATTTTGAATACATGCTCCCCAATGTTATATCTGGTAAAAAAACAACACAA\n") - f.write("GCCATTGGAAATCTGAAGAAACAGTGAAGAAAAACACTAATTTTTAACACTAAATCATATAGCACAGCAC\n") - f.write("TCACAGCACTGAACCAAATTCTTCTCACCAATTATAAAACGCAATTTTGCGATCTGTTGGAACATTCCAA\n") - f.write("CCCTAGGCTGGAACATTTCAACCCTAAGCGCTGACGCGCTCAAGACCGTCAAGTTCATAGGCAAATCCTT\n") - f.write("CTACAACCCACATGGCATCTATTACAAAGGTCCCAAGATAAATGGGTACATAGTACAAATTCTACGAACC\n") - f.write("ACAAGCCTCGTTACTGCTGTGTTTCACTGGATTCGCGCTTTGATGCTTCCTTGATTTCGTCCCCAGCATC\n") - f.write("ATCCGTGATATCAGAAGTCCAGAGTGTCACATTGTCACGGAGGAGCTGCATGATCAAAGTGCTATCCTTG\n") - f.write("TAGGATTCCTCACCCAATGTGTCAAGCT\n") - f.write("\n") - f.write(">gi|226790275|gb|GO545904.1|GO545904 Mdas9005J14_e374.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTACTTGCAAGGAAACGATAGTATATTCCAAAATTAGCAGTTTACAGAGAAATATAAATATTGT\n") - f.write("TTTCAAGAAATTAATATGATTGCAAATGTAATAGGTCCATACATAGTGAGGTAGGATAAATGATGGAAGA\n") - f.write("CGCACTGAAATTTGAGGTCCATAGGTTGAGAAGAGTCCATAGCATTGATCCATATATGGATAGCTTGCAC\n") - f.write("AGATCACATGCTAGCTGAATCCGAACTCAAAATGACCACGATATTTTCCCAGCAATGATCACAAAGATAT\n") - f.write("TGATGCCTGGGACTTCTGTCCATCCCTGAAAACAATGGAATAATATACCCATTAAAAAACGTCACAAAAA\n") - f.write("GATTTACAGTAACTGTCCCAACTATTATAATTATATGGTTTTATTGGCATATTCAGACTTCAAAATAAAA\n") - f.write("GCTGGCAGTTTGCACTCGTAAACAATTTCTCTTTACAAAACTAAATAAATTGTAATGACCCAAGAAATCA\n") - f.write("AAATTTGATTAGGCATTAGAAACAATGTTACCTTTTGGAGAAAAGGATGCTCAACCAAATGGAAGCCCAA\n") - f.write("ATTTAAAACAGCAACTGAATGAAAATCTGACGTTATAAAATCCATAAGAAGCGTGTAATGCGTCTAATTT\n") - f.write("AAAAAGTCTCTCACACCTGTAATTGCACGTAACGGTT\n") - f.write("\n") - f.write(">gi|226790274|gb|GO545903.1|GO545903 Mdas9004L20_e305.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD21625.1| putative chlorophyll a/b-binding protein [Phalaenopsis sp. 'KCbutterfly'], mRNA sequence\n") - f.write("TTTTTTTAAGGAGCTTGGGAGTTTTTTACTGCATACAGCGGTTTCAATACAAGCAGTTTCTAGTAAAATT\n") - f.write("GCATCAGAACTAATGGAGTCCACAACAAGAGAACCTCAACACAAGCAGTAAGTTCGGGTAATGTTACAGA\n") - f.write("TGAACGGCCATGGCTTGAGGTTTCTTCACTTTCCAGGGACGAAGTTGGTGGCGTAAGCCCATGCGTTGTT\n") - f.write("GGCCACTGGGTCAGCGATGTGGTCGAAGAGGTTCTCCACCGGTCCCTTTCCAGTTACAATAGCCTGAACA\n") - f.write("AAGAATCCGAACATTGAGGTCATAGCCAGACGCCCGTTCTTAAGTTCCTTCACCTTCAGTTCAGCAAAAG\n") - f.write("CTTCGGGATCATCAGCAAGTCCAAGGGGGTCAAAGGCCCCTCCTGGGTAAAGTGGGTCTAGTCCCTCACC\n") - f.write("GAGTGGTCCTCCTCCAACTCTGTATCCCTCAATGAATCCCATGAGCACGACCTGGACAGCCCAGATTGCC\n") - f.write("AAGATGCTCTGAGCATGGATAAGGTTTGGGTTGCCAAGGTAGTCAAGGCCGCCCTCAGAGAAGATTTGCG\n") - f.write("ATCCAGCCTTGAACCAGACAGCCTCGCCGAACTTGACGCCATTCCTTGACAAGAATTTCTGGGAAGACGC\n") - f.write("ATCCCAGTG\n") - f.write("\n") - f.write(">gi|226790273|gb|GO545902.1|GO545902 Mdas9004N15_e315.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25754.1|AF334834_1 putative chaperon P13.9 [Castanea sativa], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAGTTGAAATTCGTAATCAAATTCGACCCGAAACAGCAAATTAACCG\n") - f.write("CCGTATAATATGAATCCCATAAATTTCCATCCATATACAATGTCACAAGACTATATCACTATGCATAGCC\n") - f.write("AATGTACACAAGTCCAAAGCTAGGAAGGTTGTGCAGCTAATGGTTTTTTTCATCATTCGGCCGTACTATC\n") - f.write("GGAAGTACTCATGAAACCTCCGAGAAACCCAGCTCCGTTGCAATTTCCGCACAACATCTCTTTTCTTCCA\n") - f.write("CCGCAGAGCCAGCACGAGTCACCGGCTTTAAACCGTCCACCGAAGAGATCAACAGAGTTCACTCCACTAC\n") - f.write("CTTTGCACTGTGAGCACAGAACATTTGCATCACAATCAGGGCAAATCATGCTGTTAGGTTTTACGCTTTC\n") - f.write("ATTGCTTTTCTCAGCCTTAGCTTTGAGCTGGTTAAATCTAGCGGCAGGAGAAATTTGCAGCAGCTTATCT\n") - f.write("ATTCGAACCAGCTTTTGAGTAGCGCTATGGTTGCCTGGTTCTGGGGTGATTTTCAAGGAACTTGAAGGTG\n") - f.write("CCAAGTACAAAGCATAAGCCATTGGAGAATGAGGAGGGAGCTAGCAAGTTATGATGAAAACTAGTTTGAA\n") - f.write("TG\n") - f.write("\n") - f.write(">gi|226790272|gb|GO545901.1|GO545901 Mdas9005B03_e328.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("AATTGTTGTCCTTTACTTGGTACCAAATTTACATCACCGACAACACTACAAACAAAAGTACAAAACAATT\n") - f.write("CCGAGCTCTCACTTTCCGGGAACGAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACCGGGTCGGCAA\n") - f.write("GGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAAAGAATCCAAACATGGA\n") - f.write("GAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCATCGGCA\n") - f.write("AGGCCCAACGGGTCGAAGCTTCCTCCGGGGTAAAGAGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAA\n") - f.write("TTCTGTATCCCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATG\n") - f.write("GACCAAGCTAGGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCAC\n") - f.write("ACGGGTTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCT\n") - f.write("\n") - f.write(">gi|226790271|gb|GO545900.1|GO545900 Mdas9004K04_e298.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TGACCCAATCCATCAAGCATACAGTCCGAGTCTCCGAGTCTCGGGGAGATATGAATAGGG\n") - f.write("\n") - f.write(">gi|226790270|gb|GO545899.1|GO545899 Mdas9005G21_e363.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197001.1| seed maturation -related protein [Arabidopsis thaliana] pir|T51442 seed maturation-like protein - Arabidopsis thaliana emb|CAC01816.1| seed maturation-like protein [Arabidopsis thaliana] gb|AAM98229.1| seed maturation-like protei, mRNA sequence\n") - f.write("TTCGTCCATGGCGGCGACAGCTCGCGCCGTCATTCTCTCCCGCTTCACCGACCTGTCTCTCAAGCCTTCC\n") - f.write("CAGCCGCCGCCCCCGATTACCCGCCACCTCCTCGTCCGCCCCTTACTCCCCTCCTCCTTCCGGCGGCGTC\n") - f.write("GTTTGTCCGCCAGCTCGACTTCCGCCGTCCGATGCCTCATGTCCGGCGTCGACGGCGGCGGCGTGTCGGA\n") - f.write("CGAGTTCGTCTCGACTCGGAAGTCCGGCTTCGACCGCGGTTTCTCCGTGATTGCGAACATGCTCAAGAAA\n") - f.write("ATTGAGCCCCTCGACACCTCCGTTATCTCCAAGGGCGTTACGGATTCCGCCAGGGACTCCATGAAGCAGA\n") - f.write("CCATTTCTACTATGCTGGGGTTGCTCCCGTCCTATCAGTTCTCCGTCACCGTTAGGGTTTCCAAAGCCCC\n") - f.write("TCTCCATCGCCTCCTCACATCCTCGATAATCACCGGATATACACTGTGGAACGCGGAGTATCGGATATCG\n") - f.write("TTGATGAGGAATTTCGACAAATCCACGGAAAATTCTGTGCCGT\n") - f.write("\n") - f.write(">gi|226790269|gb|GO545898.1|GO545898 Mdas9005A07_e324.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S30151 polyubiquitin 6 - parsley emb|CAA45621.1| polyubiquitin [Petroselinum crispum] emb|CAA45622.1| polyubiquitin [Petroselinum crispum], mRNA sequence\n") - f.write("AAAACTAGAAATTATTTATTGATACCAAATTGAGTTTTGATGATTAAAAGTAAAGATAGAACAACCCATT\n") - f.write("CACCATCCCAAAGAACAAAACACGGTGGCAGACTGGCCACTCAACACAATTACACCACCATCAGAACCAA\n") - f.write("CATATCAAAACAAAACAAACCGAAACTAACTAACAAACTTTCTAGAAATCACCGCCACGGAGACGAAGAA\n") - f.write("CGAGATGGAGGGTAGACTCTTTCTGAATGTTGTAATCCGCAAGGGTACGACCATCCTCTAGCTGTTTCCC\n") - f.write("AGCGAAGATCAACCTCTGCTGGTCAGGTGGGATCCCCTCCTTGTCCTGAATCTTAGCTTTGACATTGTCA\n") - f.write("ATAGTGTCAGAGCTCTCAACCTCGAGAGTGATCGTCTTCCCTGTCAGTGTCTTCACAAAAATCTGCATAC\n") - f.write("CACCCCTCAATCGAAGAACCAAGTGCAAAGTTGACTCCTTTTGGATGTTGTAATCCGCGAGAGTCCTGCC\n") - f.write("ATCCTCCAATTGCTTACCAGCAAAAATTAATCTCTGCTGGTCTGGGGGGATTCCCTCCTTATCTTGGATC\n") - f.write("TTTGCCTTGACGTTATCGATCGTATCAGAACTTTCGACCTCCAGAGTAATTGTCTTCCCGGTCAGGGTTT\n") - f.write("TGACAAAGATCTGCATACCACCTCTCAATCGAAG\n") - f.write("\n") - f.write(">gi|226790245|gb|GO545897.1|GO545897 Mdas9005F17_e358.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TTTTGTCCGATAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTTTCCACGC\n") - f.write("TCAAATCCACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTCACTTTC\n") - f.write("CGGGAACAAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGCAAGGTT\n") - f.write("CTCCAATGGTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCCAACCTT\n") - f.write("CCATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCGTCAGCAAGACCCAATGGGTCGA\n") - f.write("AGCTTCCGCCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCCCTCAAC\n") - f.write("TGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGTTT\n") - f.write("CCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCACACGGCTTCGCCGAACT\n") - f.write("TAACACCGTTGCGGGACAAGAGCTCTGGGAAAACGCATCCAAGAGCTCCGAGCATGGCCCATCTGGAGTG\n") - f.write("GATCACTTCGAGCTCACG\n") - f.write("\n") - f.write(">gi|226790244|gb|GO545896.1|GO545896 Mdas9005M13_e382.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTGATGAAAAAACAGGAAGGCGCTCAATATATAAATGGTTTCACCTCGCACATTGT\n") - f.write("CTCTCGTGGCAATATAATCTGATGAGTACAGAAGCCCTACTTTACCTCCCAAAAAAGGAAGCATAAATAC\n") - f.write("AATTCATCAGACACAACTGAATTAGTTAACGGTAACTTTACCGACCATGCCAGCTCCCTGGTGAGGAGAG\n") - f.write("CAGTAGAAAGAGTATGAACCTTTTTCGGTCAAGGTGACGGCGTAGGTCTCCCCGGGGGCATTCAGGAGGT\n") - f.write("CCTCCTCGCTCATCGATATCTTTCCGGCATCCACACCGCTGGGAACCTCGTCCTCGTCGAAGACAATGTT\n") - f.write("GTGTGGGAATCCAGCATTGTTCTTGAACACAATCTTCTCGCCGGGGGCGACGGAGAAGCTGTTGGGGACG\n") - f.write("AAGGCCAAGCCCCCGTCATCGCTGCCGAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCGC\n") - f.write("TGGCTGCGGTGGCGGCGACGGCCACACCGACATCCTTGAGGGATGACTTGACGACGCACATCTGCCTTGG\n") - f.write("GCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790243|gb|GO545895.1|GO545895 Mdas9004M02_e308.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAATAAATTTCCTATTATTAAATTAATATATTGTATTGAATTAAATAC\n") - f.write("ATACTATTATTAAATTAATATATTGTATTGAATTAAATACATATTAGTTAATTAAATATTAAATAATATG\n") - f.write("AGACTCGAAATGAAAGTACCCTTCTCGCATACATTCCCCATTACGTTGTCGGAACAAAAATATTGCATGT\n") - f.write("ATCAATATGGATGGAAATATTTAGTACATGAAATATCGATTTGCTAGATATATAAATAGATATATAAGAT\n") - f.write("ATAACTAATAAAACGGATCTTGTGTTCTGGAATTGGAATCAAAGAAAGATATTTAAAATGGCTCGTATGT\n") - f.write("TGTGACTTGGAATAAATGTTTCCCGGTAAAGGAAGGGAATAGTAATTTATTCATTCCTAATTTATTCCTA\n") - f.write("TAGAACGTCTAGGAACAAGAAGATTAAATCGGATATATCGACAGATTCCCGCGTAGTCCAAAGAAAAAAA\n") - f.write("AGATCCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790242|gb|GO545894.1|GO545894 Mdas9005I19_e370.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB09799.1| hypothetical protein [Citrus x paradisi], mRNA sequence\n") - f.write("AGGGAAAATCCGTCGCTCCAAACGCCGAGATTTTGGAATGGCCGAAGAAGGACAAGCGCCGATTCCTCCA\n") - f.write("CGCCGTGTACCGCGTCGGCGATCTCGATCGCACCATCAAGTTTTATACGGAGGCTTTGGGGATGAAGCTG\n") - f.write("TTGAGGAAGAGGGACATTCCGGAGGAGAAATACTCGAATGCGTTTCTGGGATTTGGGCCCGAAGATTCTC\n") - f.write("ACTTCGTGGTTGAATTGACGTACAACTACGGAGTTTCTTCTTATGACATCGGCACTGGTTTCGGCCATTT\n") - f.write("CGCCATCGCTACTCCCGATGTTAAAAAACTGGTGGAAGATGTTCATGCCAAGGGTGGAAATGTGACGAGG\n") - f.write("GAGCCGGGCCCTGTGAAAGGCGGGACGAGCGTCATAGCCTTTGTGAAGGATCCTGATGGTTACACGTTTG\n") - f.write("AGATTATTCAGCGGCCCTCCACCCCTGAGCCACTTTGCCAAGTCATGCTCCGCGTTGGTGATCTCGAACG\n") - f.write("CTCTATCAAGTTCTATGAGAAGGCATTGGGGTTGAAGCTGTTGAGGACGATTGAGAGGCCCGAATACAAG\n") - f.write("TACACCATAGCCATTTTGGGATATGCAGAAGAAGACCA\n") - f.write("\n") - f.write(">gi|226790241|gb|GO545893.1|GO545893 Mdas9005E11_e347.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564507.1| expressed protein [Arabidopsis thaliana] pir|A96515 hypothetical protein F16N3.25 [imported] - Arabidopsis thaliana gb|AAD46039.1|AC007519_24 Similar to gb|X77136 HSR203J protein from Nicotiana tabacum and is a member of the PF|00, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTCGCTTCTCTATAAATTAGAATAGTAAATTCCAATAAAGCGTACAA\n") - f.write("TAATCAAGAAAGGGATCAAAGTACAGCAATGAAGTGAGAATGATCACTCTAAAAACGAGTGGTCGAATTG\n") - f.write("CTGAAAAGAGCAAATTCAAATTGCAGGTTTTTATTGCTTATTACAGAACTAAAGACTTATTAAAACTACC\n") - f.write("ATTAATTTAGAAATATAGAACCCAATTTCAGGCATTTATATATCCTGGTTAAGGAAGGAAGCAATTTTCA\n") - f.write("TGAGCAAAGCCACAGCATTGTCTCCAACGGGATTGTTCAAATGGAATACATGGTCCTCCTCCTTAGACTC\n") - f.write("CACAACCTCCACATTTCCTCCCCACTCACTTTTCCTCAATAAATCACTATAATACCAACCTCTTTGCCTC\n") - f.write("AACGCATCTTGCTCAGCAACACAAACCAGCACTCTCTCTGCCCCTAATTTCGACAGCTTCGGATCCTTTC\n") - f.write("CCGGGTTTATAAGCAGGTCATCCGCTCCGCTAGTAGTCGGATAAGCGAACCGCCATATACCCTCAGCCCT\n") - f.write("TGCCCTATTCTCAACCACATCAGTCTCACCCTCAATTGGTTCTGACCCCCA\n") - f.write("\n") - f.write(">gi|226790240|gb|GO545892.1|GO545892 Mdas9004K11_e301.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TGTCTAAGGAAAAACTTCATTGAGCTTTTCAACAGTGAAATGAACCCAACAATGGATACACATATACAGA\n") - f.write("GTAAGCTGTTGCAAAACCATTTTAGTGCCGAGACATATCTTTGATAAATAATACAAAAGGAATCTTGAGA\n") - f.write("CCTTACTTCCTCTTTCCTGTGCCGATTGAAAGGAGTTCAAAGCTCCGAAGTGTGTCATCACGGCCACCTC\n") - f.write("TTGCAGCGGATGCTCGGGTGAAAGATGTTTTGGGTTCATACCCAGGTTGAAACCTTTGGGTGGTGGACAG\n") - f.write("GCGGCCACTACTTGAGACCAGCCGGCTTGACCGACTCTCACTGGGCTCACCAAATGAGCTTGGCCGGCTG\n") - f.write("CTTGATATGACTGGCCTCCTTGAACTACTGCCATTTCTAGATGAACTACGAGCCCTTTCTGAATCAGCTT\n") - f.write("GGACGTCTTTGGACGATGGCGCATCATCGGTCGACCTATGTCTGGAGTGATCGCCATAACCATGACCAGA\n") - f.write("ACTATTCCTTCTAGAAAATGCCTCTACTGCACCTGAGAGTCTTTCTCGAAAATCTTGTGCCACTGCTGGA\n") - f.write("GGTCTTTCTGTTCTTTCTGCAGATGGTCCAGGGTTT\n") - f.write("\n") - f.write(">gi|226790239|gb|GO545891.1|GO545891 Mdas9005F14_e356.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179547.1| cytidine deaminase -related [Arabidopsis thaliana] pir|T51733 cytidine deaminase (EC 3.5.4.5) [validated] - Arabidopsis thaliana emb|CAA06460.1| cytidine deaminase [Arabidopsis thaliana] emb|CAA06671.1| cytidine deaminase [Arabid, mRNA sequence\n") - f.write("CTCGCCCCCCTTTCCCTTCTCCAATTTCCAGGTAGGCGCCGAAGGGTACGGTTCTTCGGGTCGAATCTTC\n") - f.write("TTCGGCTTCAACCTCAATTTCCCGGGTCTCCCCCTCCATTACTCGGTCCACGCCAAGCATTTCCTTGTCA\n") - f.write("CCAACCTCTCATTCCAATCGAAATCCAAGCTCCAATACTTCCCCGTCTCCGCTGCCCCCGGCGGCCATTG\n") - f.write("CCGCCATTTCATCCAAAAATTCCGCGAACCCCAGAATATCCAAATCCTAATTACTTCGGGGAAATCCGGC\n") - f.write("AACAACAATTCCGGAATAACCGTTTTCAACCCGCTCCAACACTTACTCCCCCACCGGTTCGAACCCAAAA\n") - f.write("ACCTCCGGGAACAGGACTTCCCCTGGTTCTTAAAGCACCTCAAAAACGGCCGGTCTTTTTTAAGCAAAAC\n") - f.write("CAAAAATTTAACCAACAATTTAAAACTGATTGCGAATTTAAAACCCGCGGCTTTAAAGGCCCCAAAAAAT\n") - f.write("TCACACCCGCCTTACACCGGTTGCCCTTCGGGGGTGG\n") - f.write("\n") - f.write(">gi|226790212|gb|GO545890.1|GO545890 Mdas9005I02_e366.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF26741.1|AF220527_1 chlorophyll a/b binding protein precursor [Euphorbia esula], mRNA sequence\n") - f.write("CTAGTATCACATTTGTTTTGCAATGGCAGCTTCCATGGCTCTCTCTTCCCCAACCTTCGCCGGCAAAGCC\n") - f.write("GTGCAACTTTCCCCGGGAGCCACCGAGCTTTTTGGAAACGGAAGAGTGTCCATGAGGAAAACTGCTACCA\n") - f.write("AAAAAGTCTCCTCTGGCAGCCCATGGTACGGCCCTGACAGAGTCAAGTACTTGGGGCCATTCACCGGTGA\n") - f.write("GCCCCCAAGCTACCTCACCGGCGAGTTCCCCGGTGACTACGGCTGGGACACCGCCGGACTCTCAGCTGAC\n") - f.write("CCAGAGACCTTCGCCAAGAACCGTGAGCTCGAAGTGATCCACTCCAGATGGGCCATGCTCGGAGCTCTTG\n") - f.write("GATGCGTTTTCCCAGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAAGCCGTGTGGTTCAAGGCCGG\n") - f.write("AGCCCAGATCTTCAGCGAGGGCGGTCTCGACTACTTGGGAAACCCTAGCTTGGTCCATGCCCAGAGCATC\n") - f.write("TTGGCCATCTGGGCCTACCCAAGTGGTGTTGATGGGCGC\n") - f.write("\n") - f.write(">gi|226790211|gb|GO545889.1|GO545889 Mdas9005A11_e325.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CGGCCCATGAACCGGGATTGGAAGCACAAAATGGGGGCCCCAACCTCTCCTCACAAAAAAAAAAAAAAAT\n") - f.write("TTCTAAAACCAAAGAAACAGGGTAATAAAATTTTGACACAAACCCCCCGGTAAAAAACACCCCTCCCCCC\n") - f.write("CTAAAAAAAACCCCCCGGGCCCCCCAAAAAAAAACTTTTAATTTTACCCCACCCTCAAATTTTTCTCCAA\n") - f.write("AAAAATCAACAACCCGAAAAGCCCCCAAAAACACCTTTTAAACCTTTTTTGACAGCCCCCTATCGGAAAA\n") - f.write("AAAAAAGAAATCCCCCATCAAAACCTAAAAAAGCAGCGCCTTAGAAAAAAAGAAAAAAAAAAA\n") - f.write("\n") - f.write(">gi|226790210|gb|GO545888.1|GO545888 Mdas9004O03_e318.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|B86212 protein F24B9.20 [imported] - Arabidopsis thaliana gb|AAF75084.1|AC007583_20 F24B9.20 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTAAGAAGCTGATTAGCTGAACACTGCAATAAGGTGTATAAGACAATTGCTTACAATTGCTAAAT\n") - f.write("TGAAGGAACATTGATTGATACGAGAAACTGATTTACGTTCTAATGAATGAAATCCATCAACTGAAACTTT\n") - f.write("ACATTCTAAAATATTAAGAGTGTCAATGCTGTGGTAACACCGGTCTCTTCTCCAACAACTCGTAATGCAC\n") - f.write("AATAAAATTATCCTTTCGGATAGTTTCAAAGGTATTGGGATCAAAGCAGTGATAAGATCCTCTCTCACAC\n") - f.write("GTGTTGGTCTTCACAAGTGGTTCCATGTTGGGTACTCTTATGAACCATAGGCGGTGTTCCTTGTGATAAA\n") - f.write("ACCAGCCTCTATTATTTAGTTCATTGGCAGCATATAATTGGGCCTCGTCTTTGGGCATGCTGTAAAAGAT\n") - f.write("ATAGAACAACGTTTCCACAGAAAACTTTGAAAAATACCCTTGATGTAGTACAGGCGGTTGTTTAGCATAG\n") - f.write("TAACATTGTGGAACAGTAAACTCTGGATCACCCTTAGCCGGCTCGTCAGACCATGGGGAACCAAAAGTCT\n") - f.write("TGTGAAGGTTTTCTGTTGAATTCAAGTTTAATCCAAGCGTTGTCAAATCAATTCCAAGTGCAAGAGATGT\n") - f.write("AAGATCAGGATCACTCATC\n") - f.write("\n") - f.write(">gi|226790209|gb|GO545887.1|GO545887 Mdas9005E03_e345.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849293.1| expressed protein [Arabidopsis thaliana] gb|AAL91159.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTCTATCCATTTTGATGAGCAGAAAGCAGAATGGGAAATTGGCAATCCTCTCTCTTAAAAGATCTGGCCC\n") - f.write("CGAGCTTCCGGATCTCCTGACGCAGTTTTCTGCCGCTATTGCTGGAACTGGCTTGGCTGTCCTCTTCTCT\n") - f.write("GTCCTCTGTAAAGTAGCTTCTGGGAGGGTACCCTTTTGTGCGTACAAACTCTTGAATACTGGAGTTGCAT\n") - f.write("TTGCATTAGTTTGGCTCTCTTGGGGGGTGAACAAACTGAGGGACACAATCGTTGAAACCAGCAAGAATTC\n") - f.write("ACAGAAGCGGGCTTTAAAAGAACAGGAAATCATGGAAAGGGTAGATAGAAGCGTGAAGGAGATTTACTTG\n") - f.write("AGAGCGGGAACATTGATGGCAGTGGCGGTGTTGAGGCTTGCTTGAGCATGAAATGAGAAGAGGAAAGAGA\n") - f.write("AAACGTAAAGATGGTTTGAAGAGCATCTGACCGGATGGTGAGTATAAATGTACATATGGTGTCCGATTTG\n") - f.write("GGTGATCGTCGGACAGATGAAGCTTGATGGGCATGAGGTGAAGGATCCTTCTTCGAAAGACATTGAATTC\n") - f.write("TGATTCCGAATCACTCCACTCCACGGCTGACGGGAACCGGAGCTCCCCTGAGCTCTGG\n") - f.write("\n") - f.write(">gi|226790208|gb|GO545886.1|GO545886 Mdas9004N04_e311.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA77604.1| plastidic aldolase NPALDP1 [Nicotiana paniculata], mRNA sequence\n") - f.write("CTCGAGTTTTTTTTTTTTTTTTTTCAACAAAAATAGTCTTTCATGGCTATAAAGCATTACACACATTAAA\n") - f.write("GATGCATGTCTGGTTCCTCCATTAACATCAACATCATCATCTTCCCTTTGTTCTTCATCATCTACAGCGT\n") - f.write("CGGTACAAATTACTTAGTACACATAGCCCTTGACAAACAATTCCTTCTTTGCCTCCTCTGACTCTCCCTC\n") - f.write("TCCGGTGTACTTGCCCAGCTGTGCAAGTGAGTTGGCCTTGGCACGGATGAACAAAGCATCCTGAGCTGCC\n") - f.write("TTCACGTTCTCCGGTCTGCCTCCCCATGTCTTCAGGCAGGTATTTTGGAAAGCTCTGGCGTAGGAAAAGG\n") - f.write("ACACGTGCCATGGGTTTGGTGATTGGTTCATCGCATTCAAGTTCAGGGTTGCCTCAACTTCAAATTGTCC\n") - f.write("ACCGGACAAAAACATGATTCCGGGGACAGCTGGGGGGATTCTCCTGTGGAGGAGCTTGAGGGTGTAGTCA\n") - f.write("G\n") - f.write("\n") - f.write(">gi|226790207|gb|GO545885.1|GO545885 Mdas9005B07_e330.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CGGGACTGAGATTCGCCGCATTCACTCTGGTGAAAGGAAGTTGGAGAAACCAAGTGGGAATGTGGTTTTG\n") - f.write("GAGAGGCGTAAAAACTTGCCCCCAAACTATCGAATCCCATATAGGAAATTCCAACCCAGACCTCGTCTCA\n") - f.write("GACAACATGTCTAAAGAGGCCAAGGGAATCAACAACCAGATAAAGAGGAGAAAGGTAAGCTAGTAGGGTC\n") - f.write("ATTTTTGTCTTTTCGATGCGTGTTCTTCGTGTACATATTGGTATGAAATGCAGAAATCGAGTACTGTCTG\n") - f.write("TCTGTCTAATACACGACGAGAAGAAGAAGAAGAAAAATAGGCCCTACGTTTGACGGGTAGTGTTGGGCCT\n") - f.write("AGGGTGGTAATTAAACCGTAAGCCCGGCCCATTTCTTTTTCCAAGAATTTTTCTTTAAATTTTTTGCCTT\n") - f.write("CCCTCCTAAAAATTGGAAAATTGTTGTGTATTTTGGTAAAATGTATGTAGATTCCATTGAGAAAAATGTT\n") - f.write("GGCTACATCAGATAAATGTTCTTTTGTAAAAAAAAAAAAAAAAAAACTCGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790206|gb|GO545884.1|GO545884 Mdas9005E10_e346.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTTTTTTTTTTAAAATAAAATACGGATCTCATTGAATTATGAATTTCTCATTCAACACCATCTTGAATC\n") - f.write("CGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAAT\n") - f.write("AGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCC\n") - f.write("ACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTA\n") - f.write("AGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGG\n") - f.write("TAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCT\n") - f.write("TCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATG\n") - f.write("CTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCC\n") - f.write("\n") - f.write(">gi|226790177|gb|GO545883.1|GO545883 Mdas9004K07_e299.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM66084.1| thioredoxin [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTAAACCTTGACGATTTTTCTACATCACGAGATTATACAAAATTACATACTTATGAATGTTTATGC\n") - f.write("TGGCTGAGGGAATTGAACACCCTGAAAGGGCTGTGGTATCAGCGGTGAAGCTGAAGAACCTACACATTGA\n") - f.write("CACAATCCAGCAAGCATACAGTCCGAGTCTCCGAGTCTCGGGGAGATATGAATATGGTTCCCTTTTATAG\n") - f.write("CGTACAATATATGCATTGGCACAAACACTAGCAGGAAAGCTTCCATAGCATATGAGGTCTTACCAATTAA\n") - f.write("AACTGCAAATGTAAAACACAAACTCTGATCTTAGACAGAGCGGCATTTCTCGACCTTTTTCTCGAGCTCA\n") - f.write("TCCTTTTTCGCTCCGATCACCCGATCCACTTCCTTCCCCTTCTTCAACAGGACGAACGTTGGCATTGCCT\n") - f.write("GCACACCGAATTCCCGCGCCACTTCAGATAGCTCGTCGACGTCGATCTTGGCGAACTGGACGTCGGTGAA\n") - f.write("CTTGGCGGCCATGGCGCGGATGGCGGGCTCTATGAACCGGCAGGGCCCGCACCACGACGCCGAGAAATCG\n") - f.write("ACCACCAGCAGCTGGGAGGATTCCTCATGGGTTTTCAAGTGAAGCTGCCATCTCTCCGACGAGTGAAACG\n") - f.write("ACGTCACTCCGGACTCCTCCCCTGCCGAGTCGTCTGCCGGCGCTCCGCCGGCGCCCATCAAGCTTGACAG\n") - f.write("AAGGGCCCCCCATCTCTCTCTCTCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226790176|gb|GO545882.1|GO545882 Mdas9004O18_e319.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA33810.1| phi-1 [Nicotiana tabacum], mRNA sequence\n") - f.write("CTGAAAAACCTCTCCAAAATCTAATAATTTTTCAGAAGAAACAATGGGTTTGAATTCTAGTCAGTGGCTT\n") - f.write("ATGAAGCTGTTTGTTGTGGCCACCTTGTTCCAAGTTTCATTCGGTTCCAGCAGGTTGTTCCAAGTCTCGT\n") - f.write("TGGCAACAAGGAAGCTGAGCGAGCTTGTCCAAGACCAAACCCAGCTCCTCAAATACCACAACGGCCCTCT\n") - f.write("CCTCTCCGGTAAAATTGCCATCAACCTCATCTGGTACGGTAACTTTAAGCCCTCCCAGAAAGCCATTGTT\n") - f.write("TCCGATTTCGTCTCCTCCTTGTCCTCCTCCTCCCCTTCCAAAACCCCCCAACCCTCCGTCGCCGCCTGGT\n") - f.write("GGAAGACCACCGAGAAATACTACCACCTCACCTCCAACAAAAAGTCCTCCAACTCCCTCTCCCTCTCTCT\n") - f.write("GGGGAGACAGATTCTCGACCAAGGCTACTCCCTCGGCAAATCCCTCACCACCAAACAGATTGTCGCATTG\n") - f.write("GCCGCAAAGGGTGACCAAAAGAACGCCATCAACGTTGTCCTGACATCCGCCGACGTGGCTGTCGATGGCT\n") - f.write("TCTGTATGAACCGGTGCGGTACCCACGGGTCTGCATCCGGCTCTTCCAAGCAGGACACATCAAAGGCG\n") - f.write("\n") - f.write(">gi|226790175|gb|GO545881.1|GO545881 Mdas9005H12_e365.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n") - f.write("TTTTTTTTTTTTACGGATCTCATTGAATTATGAATTTCTCAATCAACACCCTCTTGAATCCGATTACCAC\n") - f.write("CAAATTCAAAAACAAACGACAGTGCCTCGAAAAGGGGACAGAGAATTAAAGAAACAAATACACAGTATGT\n") - f.write("CTTGAAAGCCCTATTCATCTACCAACTTGTTCAGACCACCTGGACCCTTGGCTAAGAGCCACATATGGTA\n") - f.write("CATACAAGAACAACATTATTTATGAAAATTGTGGAACAACTTAAACGCCTGCAGGCTTGTTTTCGATGTA\n") - f.write("GACTGATGCACTGCACTTGACGGACATTGTCCAATCCGATGATCCGGATGAACGATTGGGGGTAG\n") - f.write("\n") - f.write(">gi|226790174|gb|GO545880.1|GO545880 Mdas9005C09_e334.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_197770.1| amino acid transporter family [Arabidopsis thaliana] dbj|BAB10054.1| amino acid transporter [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAGGATGAATACATACATATATATATATATATGTGTATATTATATT\n") - f.write("CATTTGTTTATGGAGGATATTACAATATTCTTTGTACTTCCCTAGCTCAGTTTGGCACTTATAAGTCCTT\n") - f.write("CAACTGATCCAATCACACCCACAACTGTCACAATAAAGCAAGCTATACTAAATGTCCTCAGAACAACCCA\n") - f.write("TGTTTTTGTCCAAGCCCCAATTTTCTTCTGTACAAAGTACATTTCTACAGGGAAATATATGGCCAAAGGC\n") - f.write("CAAAAGTTCAAGGCCCCTAAAACTCCCAAAACCTGGTTGAAGTAAGGAAACATCATCGCAATTGCGGTAG\n") - f.write("TTGACACAACGTAAACAGTACGGAAACAAAGCCTGAAGGGATTCACTTGAAATCTCGGTAACAATGGGAC\n") - f.write("TTTGATAGAGTAAAAGTTGTTCACAAATCCACTGCTCGGGTATTTCTTCCTAGACCATCTCTCAGCAACT\n") - f.write("GCAAATACTGGTTGACTGAAGATCTGATATCCTCCCACCAAATGAAGAACAATGCAAGCATTGGCAAAAT\n") - f.write("CAATGAGCCAGTAGGGTTCGTAGAATCCAAATCCTGTACAGAGGTTCCCTGGCGTGTCATCCCCCAAGGC\n") - f.write("GGCATATT\n") - f.write("\n") - f.write(">gi|226790173|gb|GO545879.1|GO545879 Mdas9005A12_e326.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGGTATGAGGCATACATACCTTTGAACGCCACATGCGTGGCCATTTACCCCAGCATAGCACACTTGA\n") - f.write("TACCGAAGCCAAAGCCGAGGCACCCGGATTACAAGCCTACGAAGAACACGGGCAGGTTTTGCTGCTACCA\n") - f.write("CGAGCATAACAGCCGTGACGGTGAGAAGTGTATCACCCTTCGTGATCATATTAAAGCTTTGGCACATGAA\n") - f.write("GGAAAAATTGATCAATTCCTCATTCACCCTCCAAAGGGTAACCGTAACCAACGCCAGGTAAATGTGATAT\n") - f.write("ATTTCATAAGTGGTGGCACACCCATATCTAAATCTTCCAACAGGGCCATGAAAAATAGTGAACGAGTTTT\n") - f.write("AAGGTTTGGCCATCAAGTGTTTCACGTGAAAGACATCAAGGGAGGTAAGTATCAAAAGCCTAACTAGGAT\n") - f.write("CTAATATGTTTCTACCCTGAGGAAGAAAGATGTATCATCTACCCTTACAACGACCCACTGATCGTGGAAG\n") - f.write("CTCACATAGCCAACTTTAAAGTACGATAAATCTTGGTAGACACGGGGGCTTCAGTCAATATCATGTTTGC\n") - f.write("TGAAGCTTTTAGGGCACTTAATGTAGCTGAACACTTGCTCGACCGCTCGATTTCCCATCTGATAAGCTTC\n") - f.write("TCCGGTGATATCGTGCAACCTTTGGGGGGCATACACTTACCTTT\n") - f.write("\n") - f.write(">gi|226790172|gb|GO545878.1|GO545878 Mdas9005H09_e364.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTAGCCACTATAAATAATACATTAATATTTATTTTATGAACATGCGTAACAGGAG\n") - f.write("TAGGTATCAAATAATAATGCCGAAAACCAAAAACAAAAGACTACTAGCAAAAATTAAAAAAAAAAAAAAA\n") - f.write("CTGACTGAACAAGAACATATCTGAACCCGAT\n") - f.write("\n") - f.write(">gi|226790171|gb|GO545877.1|GO545877 Mdas9004O02_e317.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL11502.1|AF367442_1 NAD-dependent malate dehydrogenase [Prunus persica], mRNA sequence\n") - f.write("TTAGAATCAAGGCAGATATGGATTATTTTACGTCAATGGGACAATCCCATTCAAATATGCAACTAAAAGA\n") - f.write("AGAAAAAAGTCGAAGTGTCCGAATAGAATATTGGGCTCAACAACTGTAAAACCCACAAAAGCAGCTTCTG\n") - f.write("CATCATTAACATATCTCTCTATCTTAACAATGGCATTATTCAAAACTTCAGCTGCTTTTCTCACACATTG\n") - f.write("CAGGGAGGCCAACTTACAACCACACCAAGGAAAGGCCAAGAGCATCTAAGAGAGGCAAGAGTATGCCAAA\n") - f.write("GCTTTCTCCTCACTGAGCTCCTCTGCAGTTGCATCCAACTTCTTCCTCGAGAACTCGTCAATAGAGAGTC\n") - f.write("CTTGAACAATCTTCCACTCCCCATGTTGGCAAGTGACTGGGAATGAGAAAATGAGACCAGAAGGTACATC\n") - f.write("GTATGAGCCGTCAGAGTAAACACCCATGGAAACCCAAGTGCCCTCCGGGGTTCCAAGTACCCAATCACGA\n") - f.write("ATGTGATCACAAGCAGAACTTGCAGCAGATAATGCACTTGACAGCTTACGGGCCTTGATGATTGCAGCAC\n") - f.write("CACGTTGTTGAACAGTGGAAATGAATTCTCCATTTCACCATGCATCATCAGCAACAAGCTCACGGACAC\n") - f.write("\n") - f.write(">gi|226790170|gb|GO545876.1|GO545876 Mdas9004O20_e320.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCTGTCTCATTCTTATTGAATCTTTTGAAAGCATCTCGGAACTTCCTGCATTTGCTTTATATTGCTACAT\n") - f.write("AATCACTTTCTATCAACTTTTCAAAGCAAGAGAATCTCACTTGTGAGATTCAGTGTTCACTTGTAGAGCC\n") - f.write("AACATTGATTAATACTAGTTAAAGTGATCGATCATTCACGTCCCAAGGCACAGGTGCAGG\n") - f.write("\n") - f.write(">gi|226790051|gb|GO546188.1|GO546188 Mdas9009O17_e711.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("AGTTCCCATGAAAAATCTGGAGTTGTGAACTGTAATAAAAAAATAATAAATATGACAGTAAATTGTATAA\n") - f.write("TCTAACTTCCATGGATGTACAAGTTTTCAAGATCAAGTTAAAATTCCCCATTGATGCATTTTTTGAAACT\n") - f.write("TAATTTTACATACAAGTAGGTAGCTTAAAAATCCTCTATTGTACACACTGATTAAGTGTCCTCCCTTCCC\n") - f.write("GGGCACCAAATTGGTGGCATAAACCCCAGCGTTGTTGGTAACAGGGTCAGCCAAAAGATCAGCAAGGTTC\n") - f.write("TCAATGGGGCCCTTTCCGGTGACAATAACCTGCACAAAAAAACCCAACATTGAAAACATGGCAAGCCTTC\n") - f.write("CATTCTTGAGTTCTTTGACCTTAAACTCTGCAAATGCCTCTGGGTCATCTGCAAGTCCCAAAGGATCAAA\n") - f.write("GCT\n") - f.write("\n") - f.write(">gi|226790050|gb|GO546187.1|GO546187 Mdas9001P02_e83.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD37374.1|AF145348_1 peroxidase [Glycine max], mRNA sequence\n") - f.write("TTTTTTTTCTATATAACCATCATCGTTGAAATCCATACATCAGCATACATGTTCAAAGTTCAAATCATCC\n") - f.write("ATCCATACATACACACATCCCGACATATCCACCATGCCCATCTCACCCAAAGAGAAGAAGCCAAAAGATA\n") - f.write("AAATCGAAACCCTAAATCAGACACAGTGCATCATGAACAAGGGCCACATGAACAACTGACCACATGCATG\n") - f.write("CCTTTTAACCCTAGCACTGACCAACTTCCATAAAAACAAAACATACATATTGGTTAAAAAAAAACCCTTT\n") - f.write("TATTATCCAGCAACTTGCCCCACACACATTTTCTCCCCTAATTACATAACTAAAGAAGAAAAGTGCTTCC\n") - f.write("TGACAAGGCTGCTTTTTGCTCTAGTCCCGGATCTTATTGGCAACATTGCACTGCTGTCGGATCTCGCCCT\n") - f.write("TGTTTCCGGTGAGAGGGTTGTTCTCGGAGAGAATGGTGAAGGCTCTCGAAAAC\n") - f.write("\n") - f.write(">gi|226790049|gb|GO546186.1|GO546186 Mdas9001G06_e33.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGCTGCTCCCGCGGCGAGAGCGGGCCGCCGCGTGCCGGCCGGGGGAAGGACCGGGAACGGTCCCCTC\n") - f.write("GGGGGCCTTCCCCGGGCAGCGAACGTTCAGCTCATAACTGGTACGGACAAGGGGAATCCGACTGTTTAAT\n") - f.write("TAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCCGTGCTCTGAATGT\n") - f.write("CAAAGTGAACAAATTCAACCAAGCGCGGGTAGACGGCGGGAGTAACTATGACTCTCCTACAGTACCCAAA\n") - f.write("TGCCTCGTCATCTAATTACTGAAGCGCATGAATGGATAAACGAC\n") - f.write("\n") - f.write(">gi|226790048|gb|GO546185.1|GO546185 Mdas9001J10_e56.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CCTTTTTAATTTAGAGCAAAATCTGAGATCCCCGAATCACATTAATTTAATAC\n") - f.write("\n") - f.write(">gi|226790047|gb|GO546184.1|GO546184 Mdas9001H16_e42.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB64719.1| AKIN beta2 [Arabidopsis thaliana] gb|AAK25958.1|AF360248_1 putative kinase [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTGCAAAAGCGGATGGATCAATGGTCATTAAGCAATGGAATTGTGTGAAAATACAATCCTGAAGTTTC\n") - f.write("ACCTGAAAAATTCTTCCTGAACATAAACCGACGCCATGGAAATGGCATTTGACTTTGAAATTGATATAAA\n") - f.write("ACTAACTACATAATGGGAACCGTGGAGTCCAGACAGACACTTTGTGTGTGTATGTTTTTTTATCTCTGCA\n") - f.write("AGGACTTGTAGAGAACCACTGTAACATACTTCGCTATAAACCTCTCTGTTGTACCGAGTGCCACCACAGA\n") - f.write("TGGTCCACTCTTCCCTCTCTGCATGTAAAGATGATTGAGTACCACATGTTGAGGTCTTGACAAAGGAGGC\n") - f.write("GGCATCTCCATGTAAGATGAAGGTGCATTCAGCAGTGTCATTTGTAGGTGTGGAGGAACCAATGGGGGCT\n") - f.write("CCTTCGCGAAATCTTCAGATCCAAGCTGCAGGTTGTTATAACTTGATTCCGGCGACTGGGGAGGTTTCAA\n") - f.write("ACCAGAAATGCTGCCGATGTCTTCTGGGACGTAATCCTGCAAGTCCAAAAGGTTGTAAGAATTGCCAGCA\n") - f.write("TCA\n") - f.write("\n") - f.write(">gi|226790046|gb|GO546183.1|GO546183 Mdas9001D24_e23.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P52765|NU3C_LUPLU NAD(P)H-quinone oxidoreductase chain 3, chloroplast (NAD(P)H dehydrogenase, chain 3) (NADH-plastoquinone oxidoreductase chain 3) gb|AAB86905.1| NADH-plastoquinone oxidoreductase [Lupinus luteus], mRNA sequence\n") - f.write("TTTTTTTTTTATTGTTTGATGACTATTCAAGAGCTAAGACCATTCCAATGCTCCTTTTCGCCATGCATAA\n") - f.write("ATTAAACCAACAATTAGGATAAGCACGAAAATTAAAGCTTCTATAAATACGGATACTCCCAATACATCGA\n") - f.write("AACTCATTGCCCATGGATAAAGAAAAACCGTTTCAACATCAAAAACAACAAAAACTAGAGCAAACATATA\n") - f.write("ATAACGGATTCTAAATTGTAACCAAGCATCCCCCATTGGTTCTATTCCCGATTCATAACTCGAAAGTTTT\n") - f.write("TCTGGTCCTTTGCTAATCGGGGCTAAAACTCCGGAAATTAGAAATGCCAAAATAGGAATAACACTTGATA\n") - f.write("CTATCAGAAATGCCCAGAAAAAATCATATTCGTAAAGCAGAAACATAGACGTACTCCTATTAATGTGGAA\n") - f.write("AATATACCGTACTAGTCGATTCGAATTAGAATAAATTGTAAAATAATCCATAACTGTTTAGTCAAAACAA\n") - f.write("CAATTTATTTTGATCGAACCGCCCAGTTTCTTTTGTTTGCTGCGGTACATGTCTTGTTTCAAGAAT\n") - f.write("\n") - f.write(">gi|226790045|gb|GO546182.1|GO546182 Mdas9001D05_e20.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL36317.1| unknown protein [Arabidopsis thaliana] gb|AAM20042.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("AAACATTAGCATTCACCATTTCATGAAAATTTCAAGTTGGAGTTTGGATTTAATCCAATCTATTACACAG\n") - f.write("ATTTCACACAATGAGATACAGAGCAAGTCTATTATCTGACTAGCGAGTACCAACGACGGAACACAAAAAA\n") - f.write("TACACCGAGGTGAAGACGAACATTTAGCATTAATAAGCTGGAGCCGGAACTTTAAAGTACGATCGACACA\n") - f.write("AAACCCAAATGTGGGGAAAATAAAACCCTAATAGAAACCTAACGATTGTATTTGTATCTTTCGTTGTCGA\n") - f.write("AGCGTCAAACACATCCAAAGAACTGTTCCAAGGATGGGGCGTTGAACACATTAGAAGCAGGTCGTTCTGT\n") - f.write("TCTGGTAGGAGAGATGTGAAGCTGATACTTGATGAACCTAGATAATTGAAATATGATGTCAGGATTTGTG\n") - f.write("TCGATATGCCAATCTGGTT\n") - f.write("\n") - f.write(">gi|226790032|gb|GO546181.1|GO546181 Mdas9001A11_e2.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTATGTAACCCTGCTTAACATTATCAGAGACAGCAACATAACACAGCAGAATTATAGATACTCGATGG\n") - f.write("AAACAAAAGATAGCACTCTGCCACAATAATAACCTCAAATAAACACATAGGAGCGCACCGATGGCCAGCC\n") - f.write("ATTATCCGTTCAAAGATCTAATAGACAAACTAAGCAGCTAAATGCTACAGAATTCTTAATTAGCAATTAC\n") - f.write("TAAAACCTTAAGCATGGTCTTTCTAGACATCAACACAAGCATCTCGACTTGCTATACCTGATCCAACGTT\n") - f.write("CTAATGGTCGGATGACTTTAAAGCCTCCAGAATCACCTTCGTCTGATCTCTCATTAACTCGGACCGCTTC\n") - f.write("ACAAAAAGCTCCAATTCCGCAACATGCAGCTTCCTCCATTTCTCCTTCAACTCAGCTCGCTTGGGCCCTC\n") - f.write("CAATCAACTCCAAACCCTGTTTCACCACACCCTCCGGCAACCCCAGCTTGCCGAAACCCTTGTCAAACCC\n") - f.write("AATCACCTCACTCAAACTTTCCGAAGAGCACGGGTTCAGACCAAAATCCACCTTCGCAGCCTCCTTTGGC\n") - f.write("GGCTCCGGTGAGCTCAAACTATCAGCTCTTATCGAAGCGAGAGTCTTGGTATTTCTAGCTTTCCCATTAG\n") - f.write("ACTTTGGCTGTTCAGACACCCCGCTGACACCACTCGACCCCTCCCCGCTACTGCTGCTACCCCAT\n") - f.write("\n") - f.write(">gi|226790031|gb|GO546180.1|GO546180 Mdas9009P23_e715.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK50586.1|AC084404_11 putative translation initiation factor [Oryza sativa], mRNA sequence\n") - f.write("TCGAGCAATCAAATTATTAGTTCTTGATGAATCTGATGAAATGTTGAGCAGAGGATTCAAGGATCAGATT\n") - f.write("TATGATGTCTACAGATATCTTCCTCCTGAGCTCCAGGTTTGCTTGATTTCTGCTACACTTCCTCATGAAA\n") - f.write("TTTTGGAGATGACCAACAAGTTTATGACTGAACCTGTAAGGATCCTTGTTAAACGTGATGAGTTGACGTT\n") - f.write("GGAGGGAATCAAGCAATTTTTCGTGGCTGTCGAAAGAGAGGAATGGAAGTTTGATACTCTTTGTGATCTA\n") - f.write("TATGATACCCTTACGATTACACAAGCTGTTATTTTCTGCAACACCAAGCGAAAGGTGGACTGGCTCACCG\n") - f.write("AAAAGATGAGGAGTAATAACTTTACTGTCTCTGCAATGCATGGAGATATGCCTCAGAAGGAAAGAGATGC\n") - f.write("TATTATGGCTGAGTTTCGTGGTGGTAATACTCGTGTCCTGATCACAACCGATGTTTGGGCCCGGGGCCTT\n") - f.write("GACGTTCAGCAGGTTTCTTTGGTTATCAATTATGATCTCCCAAACAATCGAGAGCTATACATTCATCGAA\n") - f.write("TTGGTCGTTCTGGACGTTTTGGGCGCAAGGGTGTGGCAATAAACTTTGTGAAAAGTGATGATATTAAGAT\n") - f.write("TCTAAGAGACATTGAGCAGTATTACAGTACGCAGATTGACGAAATGCCGATG\n") - f.write("\n") - f.write(">gi|226790030|gb|GO546179.1|GO546179 Mdas9001C04_e13.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567130.1| membrane protein -related [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTATTACAAAGTCATTTTTATTCATCACTAAAAGATGCTATTGGTGGCAAGAACAAATTTTCGAT\n") - f.write("AGCCATATAATGTCTTTGAATGAGCGGAACGGACTCAACAATTGCCTACCAAAACAAGAAGCAAGTATAC\n") - f.write("ATCATCTTAAGTGTGTTGTTTTTGGAAACCGAGAAGAAAGCCCCCATAGAAAAGGGGAAGTTGGGGTTTT\n") - f.write("ATTTTCTTAGAGATCAAGTCTACCAGCCAAGTACCACGAGTGCATAGCAAGGCTGCCAAATGCGAAGATG\n") - f.write("TTGGCAAGAGATGATAGCCCGTGAATCATACCAAACTTCTTATTCATGGCTGCCAGTTTTGGGTTTACCT\n") - f.write("TTGCAACTTGCACATTCTTTGACCATCCAACTTCTTCCCCAATGTTCTGCTCCCTCTCCACCTTATGCCT\n") - f.write("TTGCTTCATCATCTCGATGGTCATGGGAGTGAAGACGAAGAGATTGGTGAGATTGAATGCAAAGGCAGAG\n") - f.write("AGCAAAAAGCCGAGCTGGTACTTGTCGGCAACAGAGGAAGAGCTCCACGGATGCAAATACCCAAACGACC\n") - f.write("CAGCTGATACTGCAAGGCATATCCCCACCATCGTGAAGTACGCCGGAAACATCTTGCTCTGAAGATTCCC\n") - f.write("GAACTGATGCCGCGGAAGATTCTTTGACATGATGATGCCGCCTATG\n") - f.write("\n") - f.write(">gi|226790029|gb|GO546178.1|GO546178 Mdas9001M08_e69.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC77927.1| similar to chloroplast 50S ribosomal protein L31 [Medicago sativa], mRNA sequence\n") - f.write("ACAATGTAATTATGTAAATTAAATTAACAAAAAGGCAGGTATTAACGTAATAAACACAGATAGGCACTGA\n") - f.write("ATTCTACTCAATTTTCATGCTTCACCTATAATCTTACATTGAGTAAGCAAAGCATTGGCCTTTTCTACTT\n") - f.write("CTTCTTGCCCCCTTTACCGGCGGCGGCCTTGCGGCGGGAGGGCAAAACAATCTCTCCCTTGAGGACAGGA\n") - f.write("ATCCCCATGATCTGGGTGAACTCGCCGTACTTCTTCCTGAACTTCTCCACCTGGTCGTCCTCCACGAACA\n") - f.write("TGCCCGACCGGTTTCCGAAGTAAAAGGGGTGGTTGCCCGACCACACGTCCACCACGTACTCCTTCTGGGT\n") - f.write("CCCCCCCGGGCCGAA\n") - f.write("\n") - f.write(">gi|226790028|gb|GO546177.1|GO546177 Mdas9001L01_e64.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_567980.1| protein kinase family [Arabidopsis thaliana] gb|AAL27496.1|AF439824_1 AT4g35230/F23E12_210 [Arabidopsis thaliana] gb|AAM98327.1| At4g35230/F23E12_210 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTGCAACAAAAGGCGTTTCTGTGTAAATACATTCTCAACGGTAAAGACAATTTGGATTCCCAGCTC\n") - f.write("AGATTTTATACAAATTACGTGTAGCCTCAACAACAATTGTCAACTGGCAATGGTAAATTATGGACTATCA\n") - f.write("CTCATTAGTTATTAAAGAGTTGATCCTCATGATCCCCGGCCTCCTCGCTGCTTCTTTTCTTCTAGCGCAG\n") - f.write("TCGCTTCGTTCAACATGTCAGCGGCATCCTTGTGCATGTCCAGCTTGGCTAGAGCAACTGACTGCATGTA\n") - f.write("GAAGGCTGTGGGCCACTCAGGATAGACACATTGCGCTTGCATTGCATCTCGAAGGGCAGCATCTGGTTGC\n") - f.write("TCATTTAACAGGTAGCATAAACTGCGTCGGGCAAAAACAGTTGGCGAAACCATAGTTCCAACATCTATGA\n") - f.write("ACTGGGAGTAACACTCAATGGCTGCTTTAAAATCTTTGTCCCGAAATGCATAATCCCCTCGTTTCCTTGC\n") - f.write("CTCCAACATGTCTCTCATCTGTTGAGTCCACTCTTGGAAAGATAACTCATTGGTTCCTTCATCATCTCTG\n") - f.write("TAGTGCGTCATAACCAAGATCTGATGGATTGCTGTGAG\n") - f.write("\n") - f.write(">gi|226790027|gb|GO546176.1|GO546176 Mdas9001J09_e55.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTACTATGCGGTTTTTATTATCAAAATAAACAGCAGGAACTTGTAAGGGAAAATTAGACACTCTCTTTAC\n") - f.write("AAATAACAGCAGAGATTATGCAGACTTAGCAACATGGAAACCCTAGCAACTCGGAACGAGCACACCCGAA\n") - f.write("CCCTAGCAACAGCGGAGATTCAACCACTATACTTAGATAGTCGCACATGCACTAGATTGCAACTCAGAAC\n") - f.write("AAACAACACCCAAAACCCTACGTGGAAACCCTAGACAGTTTCTTTTTTCCTTCCAGCCATGGCTAAACCG\n") - f.write("TCCGCAGAAAACATGTACATCTCATCGCATGCCGTGAAGAGGGCTCGCATCTCAAATCTCACGGATGAT\n") - f.write("\n") - f.write(">gi|226790026|gb|GO546175.1|GO546175 Mdas9009P04_e712.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n") - f.write("ACTCATTTATTAAGTACCAAAAAAAATACAAGGGCCGTTTATTATATTTTCCTTTGCAAGGCCTAATGCA\n") - f.write("AAGGGCAAATAATGAATTTTTCAAACTACCAAATAAATGACCTTCTGGAAAATTATATGAACCTCATTTT\n") - f.write("ATTGTAAGTAAAATTCACAAAATTTTCCATTTCCCTTCCGTTAAACACCCTTGAAAAAATTTGCGAAGGC\n") - f.write("ACCAATTCAAAGGTTTTTGAATGGCACGCTTATGCATACACGTCTAACCCCCAAGTCTTGAAAGGAAAAC\n") - f.write("TGGAACAATACTTCCTGTCAATACTGAAAATGACCTGCATGTCTTCATCCCTCACCTGGAATTCAAAAAC\n") - f.write("CTCCAAATTCTCTTTCAATCCCTAAATTTTCAATGATTTTGGAATCACTGCTGTTTTCCTCTGAATTCCC\n") - f.write("CACCTCAAACAAATTTGTGCCACGCTCTTTCCGTATTTCTTACCCCCATCATTGAAAACTGGATCATCCA\n") - f.write("AAGGTGAAACAAAACCAAACATATCCTTGTTGGCACCACCCCCTC\n") - f.write("\n") - f.write(">gi|226790011|gb|GO546174.1|GO546174 Mdas9001B10_e8.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTACCCGCCGCTCGGTGGGAATTACGATTCAAGGCGGCCACCGCGGCTCGTCCGCCGCGAGGGCCAGACC\n") - f.write("ATCGACATGAGCCTTTGGGGGCCGGGGCCCCTACTGCAGGTCGGCAATCGGGCGGCGGGCGCAAGCGTCG\n") - f.write("CTTCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCACGGTAGCTTCGCGCCACTGGC\n") - f.write("TTTTCAACCAAGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGAATTACTATTG\n") - f.write("CGACGCTGTCATCACTAGGGTA\n") - f.write("\n") - f.write(">gi|226790010|gb|GO546173.1|GO546173 Mdas9009N17_e707.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTTAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAA\n") - f.write("ATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGGTCTTG\n") - f.write("AAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTACATAC\n") - f.write("AACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGACACTGA\n") - f.write("TGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGC\n") - f.write("CTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAG\n") - f.write("TACCTTCCATCATAGTATCCTGCGGATCTGTGGTTCTCACGGTACACGAA\n") - f.write("\n") - f.write(">gi|226790009|gb|GO546172.1|GO546172 Mdas9001L14_e67.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAB87573.1| chlorophyll a/b binding protein of LHCII type I precursor [Panax ginseng], mRNA sequence\n") - f.write("TCAGCATCTCCTCTCTCTCTCTCTCTCTGTCTCTCAGCCTCTCTCTCTCATCCCCAATGGCAACTATGGC\n") - f.write("CCTCTCATCCCCATTCACTGGGAAGGCCATTCCTCTTAACACACAGACAGAGTTCTCAGCTGTCCAAGGA\n") - f.write("AATGGTAGGGTTTCTATGAGGAAGACGGGCAAAAAGCCTGCTGTCTCATCAGGGAGCCCCTGGTACGGCC\n") - f.write("CTGATCGTGTCAAGTACCTCGGACCATTCTCCGGTGAGGCTCCATCTTACCTAACCGGTGAATTCCCCGG\n") - f.write("TGACTACGGGTGGGACACTGCTGGGCTATCAGCAGACCCCGAAACCTTTGCCAAGAACCGTGAACTTGAA\n") - f.write("GTCATTCACTCAAGATGGGCAATGCTTGGTGCTTTGGGCTGTGTTTTCCCGGAGCTCCTCTCCAGGAACG\n") - f.write("GAGTCAAGTTTGGTGAAGCAGTGTGGTTCAAAGCCGGAGCTCAAATCTTCAGCGAAGGTGGCCTTGACTA\n") - f.write("CCTTGGAAACCCAAAGCCTGGTTCATGCACAGAGCATTCTAAGCAATCTGGGGCAACCCCAGGTGGGCCT\n") - f.write("CAAT\n") - f.write("\n") - f.write(">gi|226790008|gb|GO546171.1|GO546171 Mdas9001A24_e7.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AATGGTCGAAACGGACAGAAAACAAGAAAGAGGCCCCACAACAATGAAGCCCAAAAAAAAACACAGAACA\n") - f.write("ACCCACCGAGAAGCTTCTGCTCAAATCTCCTCCACCGACAGAGATCCAAGCCAGCCACCGGAAACGTCAT\n") - f.write("CCATCACCGAGCATCGCCGCCTCAGACAACACCGCCAACCCCGAACAGCAACCAGATCACATC\n") - f.write("\n") - f.write(">gi|226790007|gb|GO546170.1|GO546170 Mdas9001O20_e81.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GGCAAAAATTAAAATTTGGTTGGAAAACAATAATATCTTAAAAAGCAAAAATATTTGACTACTAAAAAAA\n") - f.write("CATAGGAAGAGGGGAATAAGGCCCTGAATTTACAAAAGGGCGGATTCGGCTCCCAATTCCCCCAACTTTT\n") - f.write("TTGCCATAAATTACAAAGGACTCTCCCTCTCTCTATCACCTTAACACATCCCTTGCTCTCCATGAAGGAT\n") - f.write("TAAAACCAAAACAAAAAGATTAAAACTAAATTTAAAAAACAGACGGCCCCGGCAGACACACCGACACCAA\n") - f.write("ACTAAAG\n") - f.write("\n") - f.write(">gi|226790006|gb|GO546169.1|GO546169 Mdas9001I10_e47.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO72532.1| aldehyde dehydrogenase 1 precursor [Lotus corniculatus], mRNA sequence\n") - f.write("TCCCACAAAACAGTATAACATCTTTCTATCACCACAAACTAGTCAACTTCTTTCGATTACGGATTACAGA\n") - f.write("CAGACTTTTTGTATCTTTATTATTTGAAACCACACAGATCGGAGCATATGGTTCGGTCGAGAGATTTTAC\n") - f.write("AGCCATGCCGGATTCTTCAAAGGAGTGACAACAGCCTTCACCTGCAAGTAGTTGTGAAGGCTGTAGATTC\n") - f.write("CCTTTTCTCTGCCTATTCCACTCATCTTGTATCCGCCAAAAGGAATCGCAGCATCAAACACGTCGAAGCA\n") - f.write("GTTCACCCAGACTGTCCCAGCCCTCAATGCCCGTGTCAAGTAGTTGGCGGTGTTAATGTTCTTTGTGAAT\n") - f.write("ACTCCGGCAGCTAGACCATAGCGCGTTGCGTTTGCCCTTCGTACCACTTCATCGAGCTCCTTGAATTTCA\n") - f.write("\n") - f.write(">gi|226790005|gb|GO546168.1|GO546168 Mdas9001N03_e74.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AGACCGACTTCCCTTCTCTCTCTCTCTCTCTCTCTCTTCTCTTTCTCTCTCTAAAATCTCAGACACCAGA\n") - f.write("AGTGAACTGCTGCTGCTGCTGCTGCCCCCGCCGCCGCCGCCGCCGCCGCCGCCGTATACATATAAATGTA\n") - f.write("TCCCACAAACTCATCCTCCTCGCCTCAAAAGCCCATGGCCCCGAGACCAAGCACAACGGGCCTGACCCGC\n") - f.write("TACGGCTCCGCCCCGGGATCCCTCCTAAACTCAGCCGTGGACTCCGTCATGGGAGCCGCCGCCGACCGCG\n") - f.write("AATTCTCATCCCTCCGACCGCAGCACCTACGAGGCCACTACTTCTCCGGAGACGGTGGCGGCGACTCTCC\n") - f.write("CTCCCTCACTGGCTCCGAGTCCAGCTTCAAAGTCAACTCATCCAACGGCAGCCACAGGGACACCAGCACC\n") - f.write("ACCAAGCCATTGCTCCAATCGCACGGACGGAACGAGATTGGATCTTC\n") - f.write("\n") - f.write(">gi|226790004|gb|GO546167.1|GO546167 Mdas9001H13_e40.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CCGGATTTTATATTCCTTTTTTATAACTGCAGAGACGGAGAGATTTACAAGACTACCCCTACAGACCAAC\n") - f.write("TAGACTCTCTTCCTCTCTAAACTCTCTCACTTCCTTCCTCTGCGAGCTGGAGCTTTCCTCGCCGGCGACT\n") - f.write("TCACGCTCCGCGCAGGAGCCTTCTTCGGAGCCGACGCTTTCTTAGGGGCAGGCCGGGGGGTCGGAGCTTT\n") - f.write("CCTTCCGGGAGACGACCTCGTCAGCGTCCTCGACACCTTGGCTGGCTTCTCCTTTGGCTTCGGCTTCGGA\n") - f.write("GCAGCCGCCTTGGGCTTGGCAGCAGCAGCTTTTGGCTTGGCGGCCGCGGGTTTAGGCTTGGCGGCGGGTT\n") - f.write("TAGGCTTGGCAGCAGGCTTAGACTTAACCGGAGCAGCCGCTTTGGGCTTCGGAACAGCAGCTTTTGGCTT\n") - f.write("ATCTGCGGGCTTTG\n") - f.write("\n") - f.write(">gi|226790003|gb|GO546166.1|GO546166 Mdas9001I19_e50.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26889.1|AF317062_1 abscisic stress ripening-like protein [Prunus persica], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAACACCGAGTAAACAGTATTATTATGAACAATAACAATGACATACAT\n") - f.write("ACATACATACATACATAGATGGCATGCTAAAAGAAAACCAGATAGCACCCATTAATTGAAAAGGACATTT\n") - f.write("AACCACTCAACTATTGTAGCGATATTGTTGAGATTAAGCATCACACTCTCACTGATCACACCACATGATA\n") - f.write("ACTAGTAAAAACACAACATTGCATATGTAGTCAAAAGATGATGTTCCACAATCCACATAGATCTAGAAGT\n") - f.write("GGTGGTGCTTCTTCTTTCCATAAGCCTCTTCCTCTTCTTCCTTTGTCTCTTTCTTCTCATGATGCTCATG\n") - f.write("GAAGGCAAATCCACCCGAACCAACTGCAGCTGCTGCAGCAATCTCCTCTTCTATCTTGTGCCTGTGGGCA\n") - f.write("TGCTCTGGGTCTTTCTTTTCATTGTGCTTCTCATGCAAGGCAAAAGCGCCGGCAGCAGCTACACCGGCCT\n") - f.write("CGCCGAGGTGCTCGAGA\n") - f.write("\n") - f.write(">gi|226789990|gb|GO546165.1|GO546165 Mdas9001G03_e32.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTTGAATCCGAACCGTGCACTTGTAGAATACATTTGAAAGTAGTGTGAAAACGAACAGAAGCCTAATTCG\n") - f.write("TTATGAGCAAACGATAACCCGCTGGGCCAGACAACCGAAAAAGAATGAAAGAAAACCCTAACTTGTATTA\n") - f.write("TACACAAACAATAAGCCCTTGCCATACAAAACACACATTTTTACACTCACTCTCTCAAACCAATCTTATT\n") - f.write("GAAAGCTCATTCTTGTTGGATCATCTTGAAACACCGTCACGACTCA\n") - f.write("\n") - f.write(">gi|226789989|gb|GO546164.1|GO546164 Mdas9001K13_e62.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB64115.1| putative aspartate aminotransferase [Oryza sativa (japonica cultivar-group)] dbj|BAB86539.1| putative aspartate aminotransferase [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("CAACAAAACAAACACCCCTTTGTTTACTTTACGGTTAAATACAACGCCAAAAAAATTATTTTCCACCTTC\n") - f.write("CCAACATGACCAACTTATTCGTACCTTCAACTCAAATACTAAAATACGGATTTACCCCAAGTAAAACAGG\n") - f.write("GGCAAAACCAAAAACATTTTAGTTAGTAACACCGGCCACAGGCTTTAATTCAACAAAAGCTTTCTTAATT\n") - f.write("CCCCCCACACCTGCCTGTACGGGGGGAAGGGATGCTGCGAAGGAAATTCGAATGCACGTGTCATCCCCAA\n") - f.write("AGGCATCCCCCGGAACTAGGGCAACCTGACCCTTGTCAAGTAGGTAACGGCATAGGGACTCTGAATTCTC\n") - f.write("AATTTTACCAAATCCTTCACCCTCGGTTCCATAGTAAGCGCTGAAATCTACAAAAAAATAAAAAGCTCCC\n") - f.write("CTGGGTTCTGAAATCTTGACACCGGAAAGTTCGCCAAAGCTTTTGACCAAAAAATCCCGTCGCTCCCGGA\n") - f.write("ATGCTTTCACCATAACAAAAACGGCCTCCCCACCA\n") - f.write("\n") - f.write(">gi|226789988|gb|GO546163.1|GO546163 Mdas9001N13_e75.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_683478.1| RRM-containing RNA-binding protein -related [Arabidopsis thaliana] dbj|BAC41896.1| unknown protein [Arabidopsis thaliana] gb|AAO63346.1| At1g67325 [Arabidopsis thaliana], mRNA sequence\n") - f.write("CACCGTTGTTTCTGCTAGGGCAACTTGCCTTCCTCTCTGGCATTCGAACCCGGACTCTCATATCTCGCCG\n") - f.write("CCGATATGTCTCAGGTTGACAACAGAAATTCTTCAGCAGCCAAGCGTGCTAGAACCGATGGTAGTCGAAG\n") - f.write("GGAAGATGATTGGACCTGCCCTAGCTGTGGGAATGATAATTTTTCATTTAGAACGACTTGCAATATGCGT\n") - f.write("AATTGCACTCAGCCGAGGCCTGCAGATCATAACTCAAAACCCGCTGCTAAGCCTTTCCCAGCCCCACAGG\n") - f.write("GTTACACATCTGCTCCTCCTTATCTGGGCTCTGCTGCACCCTCTTCAATGTATCTTGGTGTGCCACCCTA\n") - f.write("TGGTTCTTCTATCTTCAATGGATCATCCATTCCTCCCTATGATGTCCCATTTTCAGGGGGATCAGCATAT\n") - f.write("CATTACAACTACGGCAGCCGCCTCTCTACGGGCAGCCCCTACAGACCTCTGCATTTGTCTGGACCAACAC\n") - f.write("CCATATT\n") - f.write("\n") - f.write(">gi|226789987|gb|GO546162.1|GO546162 Mdas9001O10_e80.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566406.1| ethylene-responsive protein -related [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTCTTCACGACGAGGACAGGGCAATTGGCGTGCTGAACACAGTAGTCGCTGACACTACCAAGAATTGCC\n") - f.write("CTTTTGATTTTTCCGAGCCCACGCTCGCCTACAACTAGCAGCTTGATGCCGTGTTTTTTGACAGCATCAC\n") - f.write("GTATGGCTTCTTTCGGATCTCCAACTTCTGTGACTGTCTCAGCATTTACCCCACGACTAGCACAGATCTG\n") - f.write("TTTAGCTTTCTCCAACAGTGCCAACGCAAACTTCCTTTGATTTTCTTGGGAAGAGTTAACAAACTCCTGA\n") - f.write("CTGGAAGACATAGGACAGTACATGCGAGCAGCGCCGAGCGACGCCGAGAAGGTGATGTTGCCCCTCTTGC\n") - f.write("CGAA\n") - f.write("\n") - f.write(">gi|226789986|gb|GO546161.1|GO546161 Mdas9001P03_e84.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK93649.2| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTACATTGGCAATCTACGGCACGCTTTATTTCACCATTTCGTTCTGCACATTACAAGCCAATA\n") - f.write("AACTTCGGTTCTACATAAGAGGTTTTGCATCCAATTACACTGATAGAAAGGTAAACTCATATATCTGCTA\n") - f.write("ATTGCTTGCTCACGGTGCATATTAAGCTTTAAGCAATTTATTGGCCTTTTTCACCCAAACATCGTAAATA\n") - f.write("TCGTCTGCGAAGAGAACAAAGTGCACCTCCTTTAGGCCATCCGCAAACTCCTTAATTGTGGATATAGATA\n") - f.write("CTGTGGCTGCTTCATCATACGGATATCCATACACACCACAAGAAATAGCAGGAAACGCGATATGCTGAAG\n") - f.write("GTTGTTTGATTTGGCTAAGGTCAAGCTATTCCTGTACGCAGCACTCAGAAAGGTTTCCGGGTTGCTGCCA\n") - f.write("GAACGGTACACGGGTCCAACAGTATGAATTACATGAGATGCAGGCAACTTAAAACCCGGGGTGATCCTTG\n") - f.write("CTTCTCCGGTGGGACAGCGAACACGTGGCCTGACTTCTGGGACACTATAGCATGCTTGCAGAAGATCTGG\n") - f.write("GCCAGCAGCCCTATGTATAGCTCCATCTGCACCACCACCTCCAAGCATCCCCTC\n") - f.write("\n") - f.write(">gi|226789985|gb|GO546160.1|GO546160 Mdas9001L22_e68.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P13869|CB12_PETHY Chlorophyll A-B binding protein, chloroplast precursor (LHCI type II CAB) pir|S00442 chlorophyll a/b-binding protein precursor - garden petunia gb|AAA33711.1| chlorophyll binding protein precursor prf|1503272A chlorophyll bi, mRNA sequence\n") - f.write("TTTTTTTTTAGGTCGCCAGCTGATTTCATACATATTGGAATGAAGGTTCCAAATAGATTTTTGTACACAA\n") - f.write("GGCAAGCAGATAAAATTACAAGTTTTTAGTCCTACAAACGTTGCCCCTTCTCCTCCCGCACTTGAATCCC\n") - f.write("AATTAGAATTCTCCTTCTTTCCTCACTTCGGGGAAAAAGAAGCAAAAATGGTGGCATGGCCGGGATCGGC\n") - f.write("GAGGTGAGCGAAGAGGTTGTCAATGGGGCCAGTCCCAGTGTAAATGTGTTGGAACCAAGCTCCCATCACA\n") - f.write("GCCAACATAGCCAGCCTTCCGTTCTTGATCTCCTTTGTCCTCAACTCCTTGATCTTCTCAGGCGAGCCGC\n") - f.write("TTCCCCATCCAAGTGGGTCGAACCAGAG\n") - f.write("\n") - f.write(">gi|226789972|gb|GO546159.1|GO546159 Mdas9001H05_e38.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTCCCCCCACGGTTTTTTAAACCAAATTCAAAACCAACACCTGTACTTCGGAA\n") - f.write("TTTCCAAACCAGGGTTAATTTATTTATCCAAAAAAAAAAAAAAAAAAAAAACCTTTTTACCAGGGTTCTA\n") - f.write("CAAGGATATAAGGCCCTATTTGGTTTTTCACATTTAATGGCCAAAAATTTCAAAACAAAAAATGGTTTCA\n") - f.write("ATAGAACAAAAATAATTTCAAAACAAATGGCACCCAATTTCATTTCCTGGGAACAAAATCAATAAACACT\n") - f.write("TCCTCTTCAAAAACACTGCATACCCAAAAAACCCAACCCTTGCCGCCCCTAAATTGAATTTCTCAACTTC\n") - f.write("TTTGTACAAAAAACCAAAGGAAACCATAATTTGAAACCTCACACTTCACGTGCAAAAGGCCCCTACCCCC\n") - f.write("CTTCAGGCAAACACTTTGTTTCGTTCACCTGGAAACTTTGGGGGCAACCTTTCCTTGAAACCTATCACCT\n") - f.write("TATTCAAGGCCCCGATGTAGGCCTTG\n") - f.write("\n") - f.write(">gi|226789971|gb|GO546158.1|GO546158 Mdas9002D15_e108.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40519|PSBR_TOBAC Photosystem II 10 kDa polypeptide, chloroplast precursor (PII10) pir|S32021 photosystem II 10K protein - common tobacco emb|CAA49693.1| NtpII10 [Nicotiana tabacum], mRNA sequence\n") - f.write("CCAGCTCAATATTACACCCATCAAATTGAATCCATGCCAAAACAATTACAATTAAGGTTTGCACAAAATA\n") - f.write("TTTCTTTAATGTTCTTGTTTACGGCAACTAATTGGGACAGGCTACATAAATTACAACAACAAAAGAATAA\n") - f.write("TCAATAATTTTACTGTGACAAAACACTTGTGTTGTAAACAAAAAGGGCACCCCCTGCAAAAATGCCAAAA\n") - f.write("AAGGTAACTGCCCAAATGGCCAAGCCAGTAAAACCCCCAACATAAACATCACCAAATGGAACCCACTCAT\n") - f.write("CTTTGTTGTAAATGGGACTGTATCCATCAACATTAACACCGTACTTGTCTACAAACTGGTAAACACCCTT\n") - f.write("TCCCGTAAGCTTCCTCCCGGAAGCATCAACACCGTTCCTCAACTCCATGCCGCCACCAGTTCCATATGGG\n") - f.write("GTGGCAGTCTTGATTTTCTTGACGCCACTGGCTTGCACCTTGAATGAAACAAAAGACCTGGAAAGAGAGG\n") - f.write("GAAGGCCTCTCACTGCTGACTTCTGAA\n") - f.write("\n") - f.write(">gi|226789970|gb|GO546157.1|GO546157 Mdas9010B13_e722.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n") - f.write("AACACCACCAAAACTTCAAACAGAAAAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCA\n") - f.write("TTTGCTGGCCAGACTGCTTTGAAGCAGTCCAGTGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCC\n") - f.write("GCTTCTCCATGCGGCGCACCGTCAAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTA\n") - f.write("CTTGGGACCATTCTCCGAGCAAACTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGAC\n") - f.write("ACTGCTGGACTATCTGCAGACCCCGAAACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGAT\n") - f.write("GGGCCATGCTTGGTGCACTGGGATGCGTCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGA\n") - f.write("GGCTGTCTGGTTCAAGGCTGGATCGCAAATCTTCTCTGAGGGCGGCCTTGACTACCT\n") - f.write("\n") - f.write(">gi|226789969|gb|GO546156.1|GO546156 Mdas9002B06_e94.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("CTTGGTACCAAATTTACATCACCGACAACAATACAAACAAAAGTACGAGACAACTCCTGAGCTCTCACTT\n") - f.write("TCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTGGCGACTGGGTCTGCAAGGTGGTCGGCAAGA\n") - f.write("TTCTCCAATGGTACCTTTCCGGTGACGATGGCCTGGACAAAGAATCCGAACATGGAGAACATGGCCAACC\n") - f.write("TTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGCTTCTGGGTCGTCAGCAAGGCCCAAGGGGTC\n") - f.write("GAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCGAGGGGTCCGCCGGCAATTCTGTATCCCTCA\n") - f.write("ACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCTAGGGT\n") - f.write("TTCCCAAGTAATCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAACCACACAGCCTCGCCGAA\n") - f.write("CTTGACAC\n") - f.write("\n") - f.write(">gi|226789968|gb|GO546155.1|GO546155 Mdas9002I06_e129.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|G86149 hypothetical protein T1N6.22 - Arabidopsis thaliana gb|AAF78417.1|AC009273_23 Contains similarity to a retinal short-chain dehydrogenase/reductase retSDR4 from Homo sapiens gb|AF126782. It contains a short chain dehydrogenase PF|00106 do, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTTTGTCACCTAAAACAAGAGATTTATAATTGAAACTTCATTAAAACTTG\n") - f.write("ACATATATTTTTATTAAGAACACATTGTGCTTAAGAGTACATGTCACATGTGCATATAGATATATTAAGA\n") - f.write("GACGAAAAATAGACCAATTATTTCACAATTTCAAATTTTCATTCCAAGGTTGACAATTCAGTCTGTTCGA\n") - f.write("AAAAAAGGCCAGAAACTCCATTATCAGGCAGCAAAGCCAGCTTCACAGGACCTTTTGCAGCTTCTTCAGT\n") - f.write("TGTGAAGACTCCAGTGTGATTGTTCATGTCCGTGTCAGTAAAACCCGGACACACGGCGTTGATAGCAATT\n") - f.write("TTGTTGGAATACTTCTTAGCCAAAACTCTTGTATAAGCATTCAGAGCGGCTTTGGATACAGTGTAGGCAG\n") - f.write("AGAAATTGGTTGGCCAGCTTTTGGCTTCAACCA\n") - f.write("\n") - f.write(">gi|226789967|gb|GO546154.1|GO546154 Mdas9002B04_e93.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565889.1| expressed protein [Arabidopsis thaliana] gb|AAC28759.2| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTCAAACTAAATTTTTGACATGAAATTGCAATTAACAAATGATTGTCTTCCCATGAAAATAAAGGC\n") - f.write("TTAGGTACATTGATACGTCCGGAAAATAAACAAAATTAACTGAAGAAAGTATAAATCTTGTTACAGGCAC\n") - f.write("ATCCATGATGGGCGAGGGTCAGCACGATTCCAAGCACAGCCTACGACATCCAGCTCAAAATTTGATCGGA\n") - f.write("CACGAAGGACAACTTCGTCGTGCTAAGAATCACCCTTCAGTTCATCTGAATCTGAGTCACTTGCATTATA\n") - f.write("ACCTGGCTGCTTATCACTAACTTTCCAAACCGAAGATCGAGTCCTCGAGGCTCTTGTAATCCATACTTCT\n") - f.write("TCCCATGTGGTCATCTCTGGGGACGCCATAACCGGTGTAATACATCTGTCCCCACCAAAAACCTGCATGT\n") - f.write("TAATATCGCCAGCTTTGGCCTCCTTGAGCGTGTCCTTGAACCACCGC\n") - f.write("\n") - f.write(">gi|226789952|gb|GO546153.1|GO546153 Mdas9002J04_e135.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTCCAATGCCACTTAGCTGATTGCCTCCACAAACACAGGGAGGAGGAGAAGGCAGACGTCTCCAATGGCG\n") - f.write("GTTTTGGCTCATGGGTTTTATCTACCCCCACCCACACGGACACCCAAATCGTCAAATCGGAAACTTGTTG\n") - f.write("GGTATTCGAGCTCTATCATTGTCAGACGCAGATTGCTGACGGACGGGAACGAATGCGTGCAGGTTTCCGA\n") - f.write("ACTCTTCACTCCCAAGACTTTCAGGATCAGAAGCTTTTATGAGGAGGATGCAGGAAATAATGAGGTTGAA\n") - f.write("ATATCTAAAGACATTCTGGATGGGGAAGATGGGATTTCGGATGATCTGCTTGAAAATGTTGTGAATACTG\n") - f.write("AAATTAGTACAGAAAATT\n") - f.write("\n") - f.write(">gi|226789951|gb|GO546152.1|GO546152 Mdas9002I12_e130.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("GCAGAGAGAGATAGCAATGGCTTCCTCCATGATTTCCTCCGGTACCGTGGCTACAGTTTCCGCCCCCGCT\n") - f.write("CAAGCCAGAATGGTTGCTCCATTCACCGGCCTCAAGTCCTCCTCAGCTTTCCCTGTCACCAGAAAAAGCA\n") - f.write("ATGACATTACCTCTATTGCAAGCAATGGAGGAAGAGTGCAATGCATGCAGGTGTGGCCTCCACTTGGACT\n") - f.write("GAAGAAGTTCGAGACCCTCTCTTACCTTCCTCCCCTTTCTACCGAGTCCTTGGCCAAGGAAGTTGACTAC\n") - f.write("CTCCTCCGCAAAAACTGGGTTCCCTGCTTGGAATTTGAGTTGGAGCATGGATTCGTGTACCGTGAGAACC\n") - f.write("ACAGATCCCCAGGATACTATGATGGAAGGTACTGGACAATGTGGAAGCTGCCCATGTTCGGATGCACCGA\n") - f.write("CTCTTCCCAGGTGATGAAAGAGCTG\n") - f.write("\n") - f.write(">gi|226789950|gb|GO546151.1|GO546151 Mdas9002F08_e116.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK55780.1|AC079038_14 Putative 40S ribosomal protein; contains C-terminal domain [Oryza sativa], mRNA sequence\n") - f.write("TCGCCGAGCTGAACGAGGTTCTGACCAGAGAGCTGGCGGAGGACGGCTACTCCGGCGTCGAAGTTAGGGT\n") - f.write("CACCCCTGTCCGGACTGAAATCATCATCCGAGCCACTCGCACTCAGAACGTCCTTGGCGAGAAGGGAAGA\n") - f.write("AGGATTAGGGAGCTGACATCTATTGTTCAGAAGCGGTTCAAGTTCCCGGAGAACAGCGTCGAGCTCTATG\n") - f.write("CTGAGAAGGTGAACAACAGAGGACTCTGTGCCATTGCTCAGGCTGAGTCTCTTCGTTACAAGCTCCTCGG\n") - f.write("AGGCCTTGCTGTTCGCAGGGCTTGCTATGGTGTGTTGAGATTTGTCATGGAGAGTGGTGCAAAGGGATGT\n") - f.write("GAGG\n") - f.write("\n") - f.write(">gi|226789949|gb|GO546150.1|GO546150 Mdas9002G22_e123.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL11502.1|AF367442_1 NAD-dependent malate dehydrogenase [Prunus persica], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTATTTTGCGTCTCTATGCCATTGATGTTCAAATATGCAACTGAAAAAGAA\n") - f.write("AAAACAGTCAAAGCGTCCACATATAATAATGGGCTCAACAACTGTAAAACCCACAAAAGCAGCTTATGCA\n") - f.write("TCATTAACAGATTTCTCTATCTTAACAATGGCATTATTCAAAACTTCAGCTAATTCCGTTTTTCACACAT\n") - f.write("TGCAGGGAGGCCAAACTTACAACCACACAAAGGAATGGACGAGAGCATCTAAGAGAGGCAAGAGTATGCC\n") - f.write("AAAGCTTTCTCCTCACTAAGCTCATCTGCAGTTGCATCCAACTTCTTCCTCGAAAACTCGTCAATAGAGA\n") - f.write("GTCCTTGAACAATCTTCCACTCTCCATTTTGGCAAGTGACTGGGAATGAAAAAATGAGACCCGAAGGTAC\n") - f.write("ATTGTATGAGCCGTCTGAGTAGACACCCATGGAAACCCAAGTGCCCTCTGGGGTTCCAAGTACCCAATCA\n") - f.write("CGAATGTGATCACAAGCAGAACTTGCAGCAGATAATGCACTTGACAGCTTACGGGCCTTGAATGATTGCA\n") - f.write("GCACCACGTTGTTGAACAGTGGA\n") - f.write("\n") - f.write(">gi|226789948|gb|GO546149.1|GO546149 Mdas9002C13_e101.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P17067|CAHC_PEA Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) pir|S10200 carbonate dehydratase (EC 4.2.1.1) precursor, chloroplast - garden pea emb|CAA36792.1| precursor peptide (AA -104 to 224) [Pisum sativum], mRNA sequence\n") - f.write("TCGAGTTTGCCCATCACATGTTCTGGATATGCAGCCGGGAGAGGCTTTTGTTGTCCGCACAGTTGCTAAC\n") - f.write("TTGGTCCCACCCTATGATAAGGTTAAATACGCTGGGACTGGGGCGGCCATTGAGTATGCTGTCTTGCATC\n") - f.write("TCAAGGTTTCATACATAGTGGTGATTGGGCACAGTGCCTGTGGAGGAATCAAGGCACTCTTGTCTATTCC\n") - f.write("AGAAGATGGGTCTACCCTCGGCACTGACGTCATAAAAGACTGGATTCGTATCGCATCTCCGGCAGCGAAG\n") - f.write("AAGGTGAAGGCAGATCACGGTCCTGATACTCCTTTCCCTGAACTATGCAGTCGTTGCGAAAAGGAGGCGG\n") - f.write("TGAATGTATCGATCGGAAACCTGCTGAGCTATCCGTTTGTGAGAGATGGTTTGCTGAAGAAAACCCTAGC\n") - f.write("AATCAAGGGAGGATACTATGACTTTATCAATGGACATTTTGAGCTCTGGGATGTTGATTTCAGCCTCAAC\n") - f.write("CCCAACTTCTCCGTATGATCGTAATCACATAATTCCCATGCAACTCAATTGCTTCCTAATTAATTATCAT\n") - f.write("TAAGTACTTCTAATTTATTTCTTAATTTCATCTGCAATGTCCCCGGAAGCACGTCTG\n") - f.write("\n") - f.write(">gi|226789947|gb|GO546148.1|GO546148 Mdas9002C03_e98.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA93004.1| nonclathrin coat protein zeta2-COP [Glycine max], mRNA sequence\n") - f.write("CGGAAACTCCGTGTTATTGAAAGTTTATAGCTCAATCAAAACAACATCGCATATGGTACACAATTAATTA\n") - f.write("CAAACGGAATCTCGAACATCCCCGTGAGTTCATATGGCATTCAATTCATCAAAATATGTAAACGTATATA\n") - f.write("TCTCGAATACTAAACCTTTGGCATCAACTGTTCCAATGTCCAAATTAACCGAGTTCTGCAAAAGTAATCA\n") - f.write("AACTTGATAATATCGCAGCATCTGATGAAACAAAAACATATAAAACTGATGTCCTCTCTCCTTGCTTTTC\n") - f.write("CTCTTTCAACACATCATTTAAGGAGTTGTCTCGCTAGATGTTCGCGGGCAGTTGCCAATGCTTGACTTAT\n") - f.write("TGTCTGCTCGGACAACGGAGCTCCAGCATCAATACTGTGACTTGCAACCTTACTTGCTATAACATTTGAA\n") - f.write("TCGGTCTCAAAAAAAATACCTCCGTCAACAATTTCATCAAGGCATAATAAAATGAAATCCAAATTTTCAA\n") - f.write("GTGCCTCCTTCTTGT\n") - f.write("\n") - f.write(">gi|226789946|gb|GO546147.1|GO546147 Mdas9002N08_e153.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("TTTTTTTTTTGTCCGAAAAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTT\n") - f.write("TCCACGCTCAAATCCACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACT\n") - f.write("CACTTTCCGGGAACAAAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGG\n") - f.write("CAAGGTTCTCCAATGGTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGC\n") - f.write("CAACCTTCAATTCTTGAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCGTCAGCAAGACCCAAT\n") - f.write("GGGTCGAAGCTTCCGCCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATC\n") - f.write("CCTCAACTGCGCCCATCAACACCACTTGGGTAGCCCAGATGGCCAAGATGCTCTGTGCATGGACCAAGCT\n") - f.write("AAGGTTTCCCAAGTAGTCGAGACCGCCCTCGCTGAAGATCTGGGCTCCGGCCTTGAAC\n") - f.write("\n") - f.write(">gi|226789932|gb|GO546146.1|GO546146 Mdas9002M20_e151.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAA10766.1| cyclophilin [Pseudotsuga menziesii], mRNA sequence\n") - f.write("TTTGAACAAAAGGATCCTTCATCTTAAGTCAGAAGTCGGAACAATATACTGTATTAGAATTACACCCATA\n") - f.write("GAATGCTTTTATGGGAAAATTAAGATTCTATTGGTTACAAGAGTTTTTATAGTTAACCATCAATAGGCGG\n") - f.write("CTTACAAACTCGGGTTTTACATCTCTCCGCATTCAGCAATAACACAGGCTAGTTTAGGGCGATTGTTGGG\n") - f.write("TCCCGTAGCCACATTCTCAATCTTCCTAACAACCAAGAGACCATCTCCAAGCACTCTCCCGAACACAACA\n") - f.write("TGTTTATTGTCAAGCCAGTCACATTTCGCGCACGTGATAAAGAACTGGCTCCCATTTGTATTTGGTCCAC\n") - f.write("TATTTGCCATTGACAATAGGCCGGGACCAGTGTGTTTGGCATCAAAAGTCTCATCATCAAACTTAAGTCC\n") - f.write("ATAGATGGAAACACATCCACTACCATCACCCTTGAGAAAATCACCAGCTTGAATCATGAAATCCTTAATC\n") - f.write("ACCCTGTGGAACTGGCACCCCTTGTACCCAACTGGCAATCCAGCTTTTCTGTACTCGCCGGTGCAGAATT\n") - f.write("GCCTGAAATTCTCGGCGGTTTTGGGGGC\n") - f.write("\n") - f.write(">gi|226789931|gb|GO546145.1|GO546145 Mdas9002I14_e132.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD37374.1|AF145348_1 peroxidase [Glycine max], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTCATCAATAATTATTGAAATTCATACATCATAATACATTTTAAAA\n") - f.write("GTTCAAACCATCCATAAATACATACACACATCCCGACATCCATCCACCATGTCCATCTCACCCCAAGAGA\n") - f.write("AGAAGCCAAAAGATACAACGAAACCCTGCATCACAAGCAGTGCATCACGAACAAGGGCAAACATGTACAA\n") - f.write("CAAACCACATACCCTTTAACCCTAGCACTGACCAACTTCCATAAAAACAAAACATACATCTAGGTGAAAA\n") - f.write("AAATAAAGCATCTTATTATCCAGCAACTTGTCGCACACAATTTCTCCATTAGTTGCATAACTTAAAAAAA\n") - f.write("TAAGTGCTTCTTGGAAAAGCTGCTTTTTTCTAGTCGCGGATCTTGTTGGCAACATTGCACTGCTGTCGGA\n") - f.write("TCTCGCCCTTGTTTCCAGTGAGAGGGTTGTTCTCGGAGAGAATGGTGAAGGCTCTCGAAAACTCCTTGAA\n") - f.write("GAAGTAGTCTTGGCTCTTGGCCAT\n") - f.write("\n") - f.write(">gi|226789930|gb|GO546144.1|GO546144 Mdas9002F24_e118.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("GCATTCAAAGCTCTTAAAAAGCGTTATACATCAGGTACATTAATCCCTTTAAGGGTTTTAACCAAGCTTT\n") - f.write("TGAAGACCCT\n") - f.write("\n") - f.write(">gi|226789929|gb|GO546143.1|GO546143 Mdas9002K02_e140.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAO88964.1| sorbitol transporter [Malus x domestica], mRNA sequence\n") - f.write("GTCGGGTTCTTCTCGACTGGGATTGGGCCCATTGCCTGGGTTTACAGCTCTGAGATCTTCCCATTGAGGC\n") - f.write("TGCGGGCTCAAGGGTGTGGTATGGGAGTGGCCGTGAATAGGGTGATGAGTGGCGTGCTCTCAATGACTTT\n") - f.write("CATTTCGTTGTATAAGGCCATCACAATGGGTGGTGCCTTCTTCCTTTATGCGGCAATTGGCGCTGTTGGT\n") - f.write("TGGATCTTCTTTTTCACAATGCTCCCGGAAACACAAGGCAGAACCCTTGAAGACATGGAGGTCTTGTTTG\n") - f.write("GTAAATTCCACAAGTGGAGAAAAGCCAATAAACTGCTCGAAAAGGAAAGGCAAGTTGCTCGTGGTGATGG\n") - f.write("TGGCACCAGTGATCCGGACAACAGGGTGAACCTCTTGGCTTAGTGAGCGAATATAAACAACTAGTAGAAC\n") - f.write("TGCAGAACAATCTCTTGAATTATAAAAATATTTATTGTACGCACCGGTTATATATGAGGGTGATTCCGCC\n") - f.write("CAT\n") - f.write("\n") - f.write(">gi|226789928|gb|GO546142.1|GO546142 Mdas9002N20_e156.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n") - f.write("TTTTTTTTTATCAATAGCTTGTTTAATAATTAAAACAAAATAATTGCAAGAATTTCCATAGAAATACAAG\n") - f.write("CGCAAATTACAAAGAAAATATCAATAACCCAGCAAACAGAATATTTATTTTCTTCAGCTCCAATTACTCG\n") - f.write("TACTGACAGCTACCGTCGTCACTCCTTGCTGCTGGGTTGAAGTTTGCAGCTGTTCGATCAGTGCAGCCTT\n") - f.write("CTGGGACTGGTACATTAACTTGTTGGGCTGCCTTTCCATAGAATTCTCCTCGGTTAATGGAGTCCTGGTT\n") - f.write("TGCATCTCCAAGGGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCTCTTCACATTGTCCTGATCC\n") - f.write("TGAACAAGCATTTGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGTTGATCGAAAGTCGGGGGAC\n") - f.write("CTTCTTTTGAGTTCACAAGCTTCTTCCCAATCCCGTCAATTCCAACACCGGAAAATCCACTTCCTCACTT\n") - f.write("CATCGTCATAAACTCGAGCCCTTAGGGCACCGAAGAATCAATGGATTGACGGGGGAATGTGTCAACAATC\n") - f.write("TTGACAACATCTTCCT\n") - f.write("\n") - f.write(">gi|226789927|gb|GO546141.1|GO546141 Mdas9010B19_e724.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAM65322.1| unknown [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTCAGATACTAAAATTGCACGGATACAATATGTACATAGTTTCGTTTTCGACTTTATATACGTAT\n") - f.write("ACATTATTTGGGAATATCTGCAAAGAATCTGCTCTGTAATTTACAAATTTTATCCCCAGACTAGTAAAGC\n") - f.write("TCCACAACTTATTCTACTTCTTTCCTTCTACTTTAAGCTGCTGGATCCTCTGGCGTAGTCTTTTCCGATG\n") - f.write("ATCGTGTATCTTCCAAAGGCCATGACCCAATATCACAGCAGAGTATATGCCGTGCGTGATCATAGGCGTA\n") - f.write("AGCATATTGTTCGTCTGGATCCACTCAAAACCAAGATATAGGGCAAGAAGTCCTTCAAGCAGGGGAGAGT\n") - f.write("AAATCTTCTTCATTTGTCTCCTCTGATACCAAGCTGCAAAAAGCTTTTTCATGTCTTCACGACCAGAGCG\n") - f.write("AGATTGTAAAACTGGTGCAACTACATAAGCAGGATCTTTTGGAGAAGCTGCCACATAGTACAGAGAACCT\n") - f.write("GTGAGCGCAGCTGTAATCACCGCTGC\n") - f.write("\n") - f.write(">gi|226789926|gb|GO546140.1|GO546140 Mdas9010B11_e720.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC22214.1| putative plastid protein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTAACCTTAATAAATAGTCTGAAATTGCACAAAACAACTAATACTGTTCAAGGT\n") - f.write("TTAGAATAGTTTATAGCCTTGAAGGTTCATCACGAACTCAAGGGTTTAACAACAGACAATGATAAAAAAA\n") - f.write("AACGTTCAGCTACTAAGCAAACTTTGGCATAATCGCCTTTTCACCAAGATATTTACATTGCTAGCCTTCC\n") - f.write("GTTTATTTCAACGGACATTTTCCCTTCGGCGCACATAACGGGTTCTGTCATTGTATCTTGGTCTGTCCTG\n") - f.write("AGCTCTCGAGGGCTGCGGCTCCACCCTCCTCTGCCTCTCAGGTGATCTTTGAACAATTTCTCCATTCACA\n") - f.write("TACAACTCAGCACCGTAGTCTTTGTACTCAGGATCAACATACGAATCCGGAAGAACAAAAAGAACACCGG\n") - f.write("GCAAGCCTTCAAGCTTATTCGAGGTCTCCTCATCAATCTCACAACCAAAACCAAAATACCTCTCACAAGA\n") - f.write("GACATTGTATATCTT\n") - f.write("\n") - f.write(">gi|226789925|gb|GO546139.1|GO546139 Mdas9002E23_e114.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTAAATAAGTTCCCTTTTTTGGATCAATACTTTCAGAATTCGAATATTAAATCACAAGATGAA\n") - f.write("CTAACTGATCTTTTTGTAGAGTCCAAGAACCTGGGGACTAACTACTCTCAGTCCTCATCGACTTTTGTTC\n") - f.write("ACCATAGGTCAAATAGTACACTCTCTTCTCGCTCCAAAAACATCGAACTAATGCACACGTTCACTGATAT\n") - f.write("CGCATTGATTGCATCTCAAAACAGGCGTTGTAATGTCCCAACTGCGATCCATGAAGATTGCCACTCAGAA\n") - f.write("AATTTTGCTCCTCAAGCTTAGGTACATGTGAAGACATCCCACAAAACGGTCCCAAGAAGTTGTTCCCATT\n") - f.write("TGCAGAACCGAAAACCATTTGCTGTCCCTCATCGGGCGATTTCCAGTCAATGCTCACGCTGGCCAACTTC\n") - f.write("TGGTGCTGGTGTGGCTGCTGCACCAGGGTTGAGGAGAGATCCGATGATGGT\n") - f.write("\n") - f.write(">gi|226789911|gb|GO546138.1|GO546138 Mdas9002N18_e155.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_198818.1| thaumatin family [Arabidopsis thaliana] dbj|BAB10226.1| thaumatin-like protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTCCACAACATTATTTGTGGTGTTGATTATCAATTGTACATTAGCCTTTACACCCGAATTTCAAA\n") - f.write("GTAACACAACATGGGGCAAACTAGTCTTTAACCTACATGGAGATATACCCAGCACCAGCAGCACCCCACC\n") - f.write("CCGCAGGACAAAATGTGATCACATACTTACTCGCCTTGCAGGTCACCAATGGAGGTGGTGTATCATAAGC\n") - f.write("ATAGCTGTAATACGAAGGGCAAGCATCTTTGAATAACTTTGAGTACACACTCGGCTTGCATTTTTCTGGG\n") - f.write("GTTCCATACTCTTTCCGGCAACAATACGCGTCCGTATTAAACGCCAAGCAAGCGCTTTTGCACGCCACAA\n") - f.write("CTTCCCCTTTCTTGTTTAAAACCTTAAGCTCTTTGGGGCACCGAGTTTTCAAATCTTTCAAACACCCTCC\n") - f.write("GATAGTGCAATTGGATGCTACTGGATTTGATAAGACCACGACCGGAAGATTGTATCCATCAACCACGCTC\n") - f.write("ACATCGTAGAAATTCAGCTTGTCTTTGCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226789910|gb|GO546137.1|GO546137 Mdas9002P10_e161.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTGACAGACACAAAAATAAAGTTCATTAGCTAATTACATAACTTCGTAGATACATGAGAATGTACAACCG\n") - f.write("AATGTCGAATAATAGAGACAAAAGTGATTTGATGTGCAAATAATAATATAACATCGGATAGTGCCAATTC\n") - f.write("GAACATCAATTTGCAAACACTCCTCGTACAGCCAGCTGCCAATTATATATGCTTTATAATACACACATGA\n") - f.write("GCATACACAACTAAATCAGAGATTAAACGAGGAATTATATTGCGATTAGCTTAAAAAGAAGATTAGCAAG\n") - f.write("TGAAGAAAAAAGCAACGAGTAGCGTTGCAATTTGCTTTGATTGGAGTGGATTATCATGTTTAACCCAACA\n") - f.write("AAATGTATTTACAAGTTCTTCTTCGAACCTTGAAATTCAAGACCTTATTACATAATTAAGCCTAAAACCA\n") - f.write("GCTGCTAATCTAACTACCAAACGACGTCACAGCGTTTGGGTTTTGCCGAGCTGGACGTGGTTTCACCAAC\n") - f.write("TATTCTACTGCTCAATCATCCCATAATCTAACGACGTTACCGTT\n") - f.write("\n") - f.write(">gi|226789909|gb|GO546136.1|GO546136 Mdas9010B16_e723.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB10038.1| dihydropyrimidinase [Arabidopsis thaliana] gb|AAO33381.1|AF465755_1 dihydropyrimidine amidohydrolase [Arabidopsis thaliana], mRNA sequence\n") - f.write("TGCAAACTGCAGTGAAAATCTTATTGATTGACCTTAAAGCGAATTCATATACATGACATACAATGAAAAT\n") - f.write("ACAAAAAACTTTGATCTTATTATTCAAACACGATGCGATATATACAGGAGCATCTTCTCCATTTCTAATC\n") - f.write("AAGTTTAAAAAAATAATACAAAAAAAGGAAAATAGTCAAAGTACCTGCAATTTTTAAACAGTTGCTCTAA\n") - f.write("AACGCTTTACAGGGGCTTTCATAAAAAATAGGTACTTAACATCTGCCTTGTCAATTCCATTAAAAAGATA\n") - f.write("TCCGAAAGGCGGCATTTCTATGTACTTTCCAAAACTAGGAACAACCTTCAATTCATCATTTTCCCAAACA\n") - f.write("ACCCTTCCACCAGAAATGGTCA\n") - f.write("\n") - f.write(">gi|226789908|gb|GO546135.1|GO546135 Mdas9002B23_e97.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAD29671.1|AF126402_1 major allergen Mal d 1 [Malus x domestica] emb|CAD10375.1| allergen Mal d 1 [Malus x domestica], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTGATTAAAAAGTAATTTCATTATATTTATAGAAGATAATACACTCCGT\n") - f.write("TCAGTCTGCAACTTTTTTCCAAACAAAGACATCAATAGCAACAAGAAGATCATCACAACCATAACACTTA\n") - f.write("TTTTTCAAGCCCAAACTGCCCAAACCATGGTTATTACTTTTGGCTGACGTGAAAAAAACATACAAAGAAA\n") - f.write("AGCCACACAACCTTCGACTGACCATATAGTAACGGTAACACCCAAAACACCATAGATACTTATGATTAAT\n") - f.write("TTAGTTGTATGCGTCGGGGTGGTCCTTAAGGTAGCTCTCAATAAGTTTGAACAAACCATGGGCCTTCTCT\n") - f.write("TTTCCAGCCTTGACGTGCTCTTCCTTGATTTCAATGTTTCCCTTGGTGTGGTAATGACTGATGCTCTTGA\n") - f.write("TGGTGGAACCACTTCCACATGCCACCAA\n") - f.write("\n") - f.write(">gi|226789907|gb|GO546134.1|GO546134 Mdas9002L06_e143.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTCTCTGAAAACTGAATTCTTGAATTGAGATTTATATATCATAGAGTT\n") - f.write("CTAGGGCAATATATTACAAGCAGAATATTACGCAATTCTTCTTAAATAAACATAAATAGCAAAGCACAAG\n") - f.write("ACACAGAAATTGAAATAGCACAGATATAATTATATTTGAGGATGACGATAACAGCCTTTGTTGTACGTGC\n") - f.write("CGCAGTTTTCAAGTCTTACATCTGGTCTGGTTGTAGCGCAGGGGGGCAGCCTTGTCCGACCACATTGCGG\n") - f.write("CGTTAGCGT\n") - f.write("\n") - f.write(">gi|226789906|gb|GO546133.1|GO546133 Mdas9002G02_e119.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAB77025.1| putative Rho GDP dissociation inhibitor [Nicotiana tabacum], mRNA sequence\n") - f.write("TTTTTTGACAATTCAATTTTACATTTGTATCGATCACCCCTACAAGGAAAAGCTTATACAACAAAGATGT\n") - f.write("GTGGTTCATGGAGGAAGAAATAAATCTAAGGATCCCGGATCTTCCGAAAAAAATCAGCTATCTGCCCTTT\n") - f.write("TTGATCTCGAAGGAGTACTGAAGTTCCATATGGCATCTCCTGTCATCGTCTTCGAACTTAAGCTTTGCTG\n") - f.write("AATAAATGCCCCTTGCAAGCAACCCAGATGGAGTGGTCTCCTCTTCCAAAGTGTGCACGTATAGTTCTTT\n") - f.write("GTTAGGAGCAAACGTACCCAACATTCCTTTGCTCTGATCGACTTGGAGTCC\n") - f.write("\n") - f.write(">gi|226789905|gb|GO546132.1|GO546132 Mdas9002C11_e100.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_193037.1| oxidoreductase, zinc-binding dehydrogenase family [Arabidopsis thaliana] pir|T10203 hypothetical protein F25G13.100 - Arabidopsis thaliana emb|CAB45500.1| putative protein [Arabidopsis thaliana] emb|CAB78343.1| putative protein [, mRNA sequence\n") - f.write("CCGGGAGGGAGGAGCTTCAAGTTTCTGCGGCTCTTCGAAACGTTAGTTGGACTTACAACTGAGAGACTAT\n") - f.write("GGCCAATGAGACCATGCATGCGGTTCAGTACGACAACTATGGGGGCGGAACTTCTGGTTTAAAGCATGTT\n") - f.write("GAAGTTCCAATTCCAAATCCGAAAAATGATGAGGTGCTGCTGAAATTGGAGGCAACTAGTCTAAACGCAA\n") - f.write("TTGATTGGAAAGCTCAGAAAGGCATGCTCTGGCCTTTGTTGCCTCGCAGGTTTCCGCACATACCTGGTAT\n") - f.write("TGATGTGGCAGGAAAGGTTGTAAAGGTAGGACCTGGAGTAAAAAATTCAAACCTGGTGACAAAGTTGTTG\n") - f.write("GAAAGGTTAACACTCTTACTGGAGGTGGACTAGCTGAATTTGCCGTGACAATGGAGAGTTTAACTGTTGC\n") - f.write("AAGGCCATCGGAAGTTTCAGCAGCCAACGCTGTAGGATTACCCGTTGCTGGTCTCACAGCTCACCAGGCT\n") - f.write("CTTACACAAACTGCAGGGATCAAGCTTGATGGAAGTGGTCAGCAAGCAAACATCCTGATCACAGCTGCTT\n") - f.write("CAGGTGGTGTAGGTCTCTA\n") - f.write("\n") - f.write(">gi|226789641|gb|GO546131.1|GO546131 Mdas9002A16_e91.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n") - f.write("TTTTTTTTGAAAAACAGGAAGGCGCTCAATATATAAATGGTTTCACCTCGCACATTGTCTCTCGTGGCAA\n") - f.write("TATAATCTGATGAGTACAGAAGCCCTACTTTACCTCCCAAAAAAGGAAGCATAAATACAATTCATCAGAC\n") - f.write("ACAACTGAATTAGTTAACGGTAACTTTACCGACATGCCAGCTCCCTGGTGAGGAGAGCAGTAGAAAGAGT\n") - f.write("ATGAACCTTTTTCGGTCAAGGTGACGGCGTAGGTCTCCCCGGGGGCATTCAGGAGGTCCTCCTCGCTCAT\n") - f.write("CGATATCTTTCCGGCATCCACACCGCTGGGAACCTCGTCCTCGTCGAAGACAATGTTGTGTGGGAATCCA\n") - f.write("GCATTGTTCTTGAACACAATCTTCTCGCCGGGGGCGACGGAGAAGCTGTTGGGGACGAAGGCCAAGCCCC\n") - f.write("CGTCATCGCTGCCGAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCGCTGGCTGCGGTGGC\n") - f.write("GGCGACGGCCACACCGACATCCTTGAGGGATGACTTGACGACGCACATCTGCCTTGAGGAGGCTGAGACC\n") - f.write("TTAACGGCAGCGCTAACCTTGGCTGCGCCAGAGGACTTGAGT\n") - f.write("\n") - f.write(">gi|226789640|gb|GO546130.1|GO546130 Mdas9002A15_e90.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P52706|MDL1_PRUSE (R)-mandelonitrile lyase isoform 1 precursor (Hydroxynitrile lyase 1) ((R)-oxynitrilase 1) pir|S32156 mandelonitrile lyase (EC 4.1.2.10) - black cherry emb|CAA51194.1| mandelonitrile lyase [Prunus serotina] gb|AAB38536.1| (R), mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTAAATCTCAAGAGATCTAATTTTATTAGATAACCTCAACATTAAA\n") - f.write("AGAGAAATATGTTAAACATGAAATAAAGAGGTACAGATAGCCCGGTGCATAGAAAGAACACGTCCCTTTC\n") - f.write("GAGCAGCCAACCATAATCCCCAATAACTAATGGGTTTATTATTAAGGCATTGAAAAGTAAAGGATAGTGC\n") - f.write("ATAATTAAGGAAAATATCGGTTTGAATGTTGAATCACGCGGATGATATACCAATCCAAGGTGATCTCTCT\n") - f.write("TGCAGAATTTGAAGACCCATATACCTGCCTAACATCAGATAGAAGCCCATAGGGTGGCTCGCCGGTGTGA\n") - f.write("CAGGGAATGTGGAAGAATCAACAACGCGTAATGCATCGATCCCACTAACACGCAAACCACCGTCAACCAC\n") - f.write("CTTTCCAACAATGCATCCACCGTGGTAATGCCAATATGAGGCCAGTGAATCATGACAAAATGTTTCGAGT\n") - f.write("GCATCATCTGTTTGGTTATTTGGAAAAGGAACTCCTAAAAAGGTGAAGCCTTCTACACCTGGCAAATCTT\n") - f.write("CGGTTTTATATGGTTTAAATGCATCGGTCCTTAATAAATCACTGA\n") - f.write("\n") - f.write(">gi|226789639|gb|GO546129.1|GO546129 Mdas9002E22_e113.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ATCCAAAAATTGCATATAAATCAAAAGGCCCTGAACATGGCCCTTACATGACACCATCCCAAAAACCCCA\n") - f.write("ACATATGAATGACATGTTTTCACAAAACTACAACATGTCCCTCCACAAACTCCAATACTATAAACCAACC\n") - f.write("AAAAAAAAAACCCCAAAATTATTTTTTCCCCCAAACACTTTTCATTAATTAAAGGGCCATAATCCCCTAA\n") - f.write("TTAAAAAGACACTTTTATTAATCCCATCCTAATTTGGTTCCCCGGGCTTACTGACCACAGGGGCAATTCA\n") - f.write("CACATGGGCAGGTTGTGCCACACTTGCACTTTCCCTCCTTCTCCGCTGCA\n") - f.write("\n") - f.write(">gi|226789638|gb|GO546128.1|GO546128 Mdas9002E11_e112.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_817268.1| ORF46c [Pinus koraiensis] gb|AAO74136.1| ORF46c [Pinus koraiensis], mRNA sequence\n") - f.write("TTAGGGGCCTTAGCTGGTGATCCGGGCTGTTTCCCTCTCGACGATGAAGCTTATCCCCCATCGTCTCACT\n") - f.write("GGCCGACCTTGACCCCTGTTATTTTGAGGTCATATCTAGTATTCAGAGTTTGCCTCGATTTGGTACCGCT\n") - f.write("CTCGCGGCCCGCACCGAAACAGTGCTTTACCCCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTC\n") - f.write("GGGGAGAACCAGCTAGCTCTGGGTTCGAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTC\n") - f.write("AACATCAGTCGGTTCGGACCTCCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAG\n") - f.write("GTTCGGGTCCATAAGCAGTGACAATTGCCCTATGAAGACTCGCTTTCGCTACGGCTCCGGTGGGTTCCCT\n") - f.write("TAACCAAGCCACTGCCTATGAGTCGCCGGCTCATTCTTCAACAGGCACGCGGTCAGAGCCCTGGGCTCCT\n") - f.write("CCCTCGTGCCGAAA\n") - f.write("\n") - f.write(">gi|226789637|gb|GO546127.1|GO546127 Mdas9002L19_e144.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CCCTTGAAATCCTATTTGAAAGGTTTCATTAATAACATCTCATACAGTGCAGGATTAATATGAAGCCAGT\n") - f.write("AGTTTATAGCACAAACATATAACAGATACATGTTTCTCCACATCCATCCTTAAAATATACACTATCGTTT\n") - f.write("GCATTCTTCCGCATTGTACGCTCGCAAGACACTGCCTGGATTTTTCCTTCCGTATGAGTTACTCTGTTTG\n") - f.write("CACCAGGAAGGCCCTGAATGTAATCATTTGCATTGATGCTCACAGCCTTGAAACTGGTAAACCTAAGGCC\n") - f.write("TTTGAGTTGACAATGCTAGGACTGGCAGCAGGTGGCGGAGCATTCTCGTTGAGAAATGGTT\n") - f.write("\n") - f.write(">gi|226789636|gb|GO546126.1|GO546126 Mdas9002P14_e164.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTGTCTTTTTTCTATGCAAAATATAGGGAATTTTTTTACACAAAAAATACCTCTAAAGGTAGGCATG\n") - f.write("CTAAAATTACAACTAGGGAGTAAACCTCCTAATTTAAGTTAAAATAAAGGAGAGGGGAGGCAACCAAAAT\n") - f.write("GTCAGGACGAAATACCTAGAAGACAGGTTACCTCCACTTCTCTTTTAGTTCTTTCTTCTCCGACCAGACC\n") - f.write("CATGTTACATAGATTGCT\n") - f.write("\n") - f.write(">gi|226789635|gb|GO546125.1|GO546125 Mdas9002J20_e138.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179402.1| elongation factor beta-1 -related [Arabidopsis thaliana] sp|Q9SI20|EF1C_ARATH Probable elongation factor 1-beta (EF-1-beta) pir|D84560 probable elongation factor 1-beta [imported] - Arabidopsis thaliana gb|AAD31355.1| putative el, mRNA sequence\n") - f.write("GCAATCCATTCACTCTTATTAAAAGACTTTTCTAACAAGTTCTTTGAAAAAGATCAAAAGGATTGACAAG\n") - f.write("CACTGAATTCTTGTGAAAAATAAAAGGATCAACATCGAAGTCAAAAAACAAGCTACCAAAAACCACCATA\n") - f.write("ACAAAACTGAAATTATGTTTTCAACAGTAACTGAAACCATACCAAACAAGCAAACAGCCTCGGAAACTAT\n") - f.write("TCATCAAGGGAATACTAATACATCAAAACCAAATATAATGTCTCAAATCATACCGCCAGAAACAAAATAC\n") - f.write("ACATCCGCAAGCTCCAATCATATCTTGTTGAAGGCTACGATGTCGCAACTCTGGACATACTCGTTAATTG\n") - f.write("GTTCAACAGTAAGTTGCTCCTCAATGAAAGTATCAACAGAGACCAGGTCATCAACAATTGTCATCATTAT\n") - f.write("T\n") - f.write("\n") - f.write(">gi|226789634|gb|GO545875.1|GO545875 Mdas9005N07_e385.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CTGACATGTGTGCGAGTCAACGGGCGATCAAACCCGTAAGGCGCAAGGAAGCTGACTGGCGGGATCCCCC\n") - f.write("TGGGGGTTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGCGAGCATGCCTGTCGGGACC\n") - f.write("CGAAAGATGGTGAACTATGCCTGAGCGGGGCGAAGCCAGAGGAAACTCTGGTGGAGGCCCGCAGCGATAC\n") - f.write("TGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCGTCTAGTAGCTGGTT\n") - f.write("CCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGTGAACGAGTTCTATCGGGTAAAGCCAATGATTAGA\n") - f.write("GGCATCGGGGGCGCAACGCCCTCGACCTATTCTCAAACTTTAATAAGGTAGGGACGGCGCGGCTGCTTCG\n") - f.write("TTGAGCCGCGCCACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGAT\n") - f.write("GAACCGGAAGCCGGGTTACGGTGC\n") - f.write("\n") - f.write(">gi|226789633|gb|GO545874.1|GO545874 Mdas9004K09_e300.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q02980|RBS_MALSP Ribulose bisphosphate carboxylase small chain, chloroplast precursor (RuBisCO small subunit) pir|JQ2241 ribulose-bisphosphate carboxylase (EC 4.1.1.39) small chain precursor - apple tree emb|CAA46475.1| ribulose bisphosphate ca, mRNA sequence\n") - f.write("TTAAAAATAATATAAGGATATAATTTATTTCATGAATTTCTCAATAAACATCATCCTGAATCCGTTAAAA\n") - f.write("CACCAAATTCGAAAACAAAAGAGATTGCCTCGAAAAGGGAAAGAAAATTAAAGAAACAAATTGACAAAGG\n") - f.write("TCTTGAAACCCTAATCAAGGACAAACTTAAACAAACCACCGAAACCCTTGGCTAAGAGCCACAATGGTAC\n") - f.write("GTACAACAACAATATTAATTACGACGAAGAAACATGATGAAACATGAATAACAACAACAACAACAACTTA\n") - f.write("GTAGCCTGCAGGCTTGTAGGCGATGAAACTGATGCACTGCACTTGGCGGACGTTGTCGAATCCGATGATA\n") - f.write("CGGATGAAGGCGTTGGGATAGGCCTTCTTGGCCTCCTCCAGCTCCTTCAACACCTGAGAAGAGTCGGTGC\n") - f.write("ATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCGTAGTATCCTGGGGATTTGTGGTTCTC\n") - f.write("ACGGTACACAAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGGAAT\n") - f.write("\n") - f.write(">gi|226789632|gb|GO545873.1|GO545873 Mdas9005K05_e375.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_186921.1| protease-related [Arabidopsis thaliana] gb|AAF26988.1|AC018363_33 unknown protein [Arabidopsis thaliana] gb|AAN41347.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTACATGGAAATACGGCATACATAGATCAAAGAAAGAGTACGCCCTC\n") - f.write("GTAGATACAGACATCAACTTAGACATAACATACATGTCGCCTCTCGCTGGTCGAACATAGCATACATCTC\n") - f.write("TTATTATTTCAGAATAATAGTTAAACATAACTCACGCAAGCGGTTGACCTGGTAAATGGAGCTAGAATGA\n") - f.write("TACTTGAACATCAAGCAATGTCATCAACTGAGAAATGAACTCTGGGTGGCCTGGCCACGCTGCTCCAGTA\n") - f.write("ACCAAATTTCCATCCGTGAAGCAACGATCTATTGGATCAGGTTCCAGCCATGTGCCTCCCGAAAGAACCA\n") - f.write("CATTAAGCTTCACCGCAGGGTATGCAGTACATTTCTTTCCCTGCAGAACACCAGCAGCAGCTAAAATCTG\n") - f.write("CTGCCCATGGCAGATGGACGCAACTGGTTTCCTGGCTTCAACAATTTGCTTCACTAATGCAATAACTTTC\n") - f.write("TCATCCAATGCCAAATATTCAGGAGCTCGACCTCCAGGGATTACAAGCGCATCGTAACTTGAGACATCTA\n") - f.write("GAGCTTCAAAATCAGCTGTTAAA\n") - f.write("\n") - f.write(">gi|226789631|gb|GO545872.1|GO545872 Mdas9005N12_e386.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564944.1| bHLH protein family [Arabidopsis thaliana] pir|H96712 probable DNA-binding protein T6L1.1 [imported] - Arabidopsis thaliana gb|AAG51581.1|AC011665_2 putative DNA-binding protein [Arabidopsis thaliana] gb|AAG52041.1|AC011914_11 pu, mRNA sequence\n") - f.write("TTTTTTTTTAGTGAAATAGTACCATATATATGTAGTTCCAACAGTACCACAACTGTTCTGATCAATTCTC\n") - f.write("TTATTAGATAGAGAGTGATCAACAAAACTAGTAGCAAAAAAACAAAAACCCCAACACACAACACAGACAG\n") - f.write("ACTGCAACTTTGAGTTGAAAGCGGATCAAATCAAAGACCATGATGCAGTTTAGTTTCTATCTTTGGATTT\n") - f.write("TATATAAGGTTTCTCTCCTCACGAAAAAGATCCTTCACTGTTTTTTCCCTTCCTAGCAAACCAAAGCCCT\n") - f.write("TCTCTCTCTGCATATCTCTCCATCTCTCTCTCTCACCAATTTTTTGGAGTAATGCAGGTGGTACACAAAC\n") - f.write("CACACCATCATTACCCATTTGTGCACTCACGGAAATACACCACAACAAACACGCTAAACCAACCAAAAGA\n") - f.write("ACAAAAACCACCAAGAGAAATAAAAGAAGTTTAATTAAAACTAGTAAACCCTAGGCATGATATTAATTAG\n") - f.write("TCAGAGGGACCTGTGTTCAAGGATATTGATGTTATTAGTCCTTTGTCTCTTAGCACTCCCTGTGGAAGAT\n") - f.write("TGATCCTGATCGCCGCAGCCGGTTTTCTCCATGACAGCCTTCAGTGCTTCTTGAATCGAGCTTTTACATA\n") - f.write("CTGTTGATGCTGCATTTGTACTTGCTCT\n") - f.write("\n") - f.write(">gi|226789630|gb|GO545871.1|GO545871 Mdas9004L12_e304.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTCTCAACATATTTGAGAAGATGAGTACCACTGGAACTGGCTTTAGCAACCACGCTTTCACCATGCCCGG\n") - f.write("CGGTCTCCAAGTAAATGAGCAAACTAGCAAGAACAACACCCCATGCAACTTCCAGATGCCTCTGCACTAC\n") - f.write("CCAAGGTACCAAAAGAGTGACTATGAGAGCATGCCTGAATGGAAACTGGACTGCCTTATGAAGCAGTACG\n") - f.write("GCCTCCCACTCATTGGGGATGTCAACCAGAAAAAGAAGTTTGCCATGGGAGCCTTCCTTTGGCCTTCACA\n") - f.write("ATACGAATGATAAACCCTATCTAGTAGCTTAATTGCTACGATTTCTAATAATATTCTACATATATATGGT\n") - f.write("ATTACAAAAGACTACTGGCATGCATGTATATAGTGAAATAATATTAATTGCTTTTTAGTAGTATCCCTTA\n") - f.write("TTTAAGTACTGTCTATCTGTATTCAGCAGTGTATTACTGTG\n") - f.write("\n") - f.write(">gi|226789629|gb|GO545870.1|GO545870 Mdas9005F09_e355.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P32980|ATPD_TOBAC ATP synthase delta chain, chloroplast precursor pir|S26198 H+-transporting two-sector ATPase (EC 3.6.3.14) delta chain precursor, chloroplast - common tobacco emb|CAA45153.1| chloroplast ATP synthase (delta subunit) [Nicotiana, mRNA sequence\n") - f.write("TTTTTTTTTTGTGAGCAAAAAGGCCTTCAAAATTGCCTCAAATTCACGTAAAAACTCCCCATACATACAT\n") - f.write("ATATATACTCAAACGTACGGTTTTACACATTACAGTGGTTAAACCATAATCAAAATCAAGAGCAAATTTG\n") - f.write("GAGTTATAAATTGAGCTTAATGTCACCCAAATCAAGCTCCGCCGCAATCTCCTCCAGCTGCTTCTTCACG\n") - f.write("CTCAAGTCAATAAGCTTCGACCCCGACTGCCCGTACCTCACCGTGAACCCCGCCACCAGGCTCGGATCAA\n") - f.write("TCTCCGTCTTGATCCTCACGTTCTGCGCCCCCGTCAGCTTCTGCACCTGCTTCGCTATCTGCGCCAAGTG\n") - f.write("CTGCGACTCCAGCTTCACCACCGAGCTCACGATCGCCAGCTCCGTGTCCGTTATCTTGTTGTACACCACC\n") - f.write("TCGAACTCCTTCACGATGTCCTTTATCAGGTCGATCCGCTTCGCGTCCACCAGGATGTTGAGGAAGTTGA\n") - f.write("TCGTGTGCGGCTGCAGCGCCGACGACTTGGCGATGTCGTCCAGCACCTGCCGCTTCTTCTCCAGGCCGAT\n") - f.write("TGTGGCCTCGTG\n") - f.write("\n") - f.write(">gi|226789628|gb|GO546124.1|GO546124 Mdas9002H19_e127.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_565379.1| Calmodulin-binding protein [Arabidopsis thaliana] pir|A84533 hypothetical protein At2g15760 [imported] - Arabidopsis thaliana gb|AAD41988.1| expressed protein [Arabidopsis thaliana] gb|AAK31147.1|AF345343_1 unknown [Arabidopsis t, mRNA sequence\n") - f.write("TTTTTTTTTTGTGTAAAATTCAAACATCTATATTTCACAACGATGAAATTATAAAAAACAAAATGTATCT\n") - f.write("ACGACCACAGATTGAATTATTATCTGCATCCTCCACCACGTGTCAAAGACACGAATGCTCCTCTGGAAAC\n") - f.write("CTCGTGCAACCCAGTGTTGAATCCCAAGCAACCCAAGAGCCCATGCTTGTAAGGTAAGAAGGTCTTCCTC\n") - f.write("CTCATCTCCTCCGTAACCGCCCGGTTCGCCGTATAATGCAACTCGTGCGGCGAAACCGGTCCTTTCCTCC\n") - f.write("TCGAGCTCACCGACCCCACGCTGTCGGTGGACCGGAAACTCGAGTTCTTCACGTCCTGCGCTAAACTACT\n") - f.write("ACTCTTCATCTTGGGCGACAACATGGCATAGTTCCTCGAATGGTCTTTGCCCGTTGTGGCTCG\n") - f.write("\n") - f.write(">gi|226789627|gb|GO546123.1|GO546123 Mdas9002M24_e152.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P13869|CB12_PETHY Chlorophyll A-B binding protein, chloroplast precursor (LHCI type II CAB) pir|S00442 chlorophyll a/b-binding protein precursor - garden petunia gb|AAA33711.1| chlorophyll binding protein precursor prf|1503272A chlorophyll bi, mRNA sequence\n") - f.write("TTTTTTTTTTTTTACATATTTATAAGTTCCGATTTTGTAGGTCACCAGCTGATTTCATACATATTGGAAT\n") - f.write("GAAGGTTCCAAATAGATTTTTGTACACAAGGCAAGCAGATAAAATTACAAGTTTTTTGTCCTACCAACGT\n") - f.write("TGCCCCTTCTCCTCCCGCACTTGAATCCCAATTAGAGTTCTCCTTCTTTCCTCACTTCGGGGAAAAAGAA\n") - f.write("GCAAAAATGGTGGCATGGCCGGGATCGGCGAGGTGAGCGAAGAGGTTGTCAATGGGGCCAGTCCCAGTGT\n") - f.write("AAATGTGTTGGAACCAAGCTCCCATCACAGCCAACATAGCCAGCCTTCCGTTCTTGATCTCCTTTGTCCT\n") - f.write("CAACTCCTTGATCTTCTCAGGCGAGCCGCTTCCCCATCCAAGTGGGTCGAACCAGAGCCCTCCCGGGTAC\n") - f.write("CCAACATCTGTCCCGGTGAGCTTGTTGT\n") - f.write("\n") - f.write(">gi|226789626|gb|GO546122.1|GO546122 Mdas9002M07_e147.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAF61440.1|AF138264_1 papain-like cysteine proteinase isoform I [Ipomoea batatas], mRNA sequence\n") - f.write("TTTTTTTTTAACAAGACATAAAAATGGACATTTAAGCTGTTCGGGCAAACACCGAGAATTATAAGATACA\n") - f.write("TGGGGTGTTATGTTTGTTTGGTCATTTGTTTAGCAAGCCCGACAGAAGACAGCAAACAACTGGAGTTTGC\n") - f.write("CCGATAAATATCACCACAACTGTATATACATTAAACAGAACTGCTATTGTAAGTTAGGGTTGAACCCTAC\n") - f.write("TACTCTGAGTTGGTCTTAACCGAAGCTGCAGCAACAGTCGAGACCATGGAGTCCACGCCACAGATGTTTC\n") - f.write("GGCCCCTGCAGATTTTGTAGAATCCACTCTCTCCCCAGTTCTCTCCCCATGAGTTCTTAATAATCCAGTA\n") - f.write("TGGCTTCTCCTTCAATCTGATGGGAGAATACCCAGCTGCACCATAACCTACGAGTAACACTCCGTGATCC\n") - f.write("AACCGCTTTGAGCATATGTAGGGGCATGACACTCCACCAACATA\n") - f.write("\n") - f.write(">gi|226789625|gb|GO546121.1|GO546121 Mdas9010A14_e717.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CATTATTTTATAGATTGGCATCTGCTTAAGTAGGACTACATAAATTACGTTACATTTCTCCATAAAATTA\n") - f.write("TGAAGTAGCTACAAACATTTAGAAATAAACTGTATATGCATAATTGCCAAAAAACTCATCATCACTCAGC\n") - f.write("TTCGATGAGTCCAATTCCGGCATGAAAATCAAAGCCTATGTGGTATAAAAGTACC\n") - f.write("\n") - f.write(">gi|226789624|gb|GO546120.1|GO546120 Mdas9002D05_e105.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTGCGTTTCAAGAACAGAGAGAGGCTTGAGTTTTAAGATGGTATAAAAGTTTAAATTTTGGATAAT\n") - f.write("TTTGTCTTTACATGTCCATATGGATTTGGTTTTCTTTTTACTAGTTGAACAGGATTTTTTTTATTTTTTT\n") - f.write("ATAGGAAAACAAACGAAAAATAAACTTGGAATTTGTATAAAAGTCAGAATTTATAAATTGACATATACCA\n") - f.write("ATTCCTTTGTTTGGATTCATAAACATACAAATTTAGAATTTTAGCGTGGAAAAAAACTTGGAATTTGGGA\n") - f.write("TCTCCAATTCTCAAGTTTAAATTCCATGTGAATAGGTGTCATTTCCCAATTTCTATGATTGAGAGTTTAA\n") - f.write("AAATAACAAATTCCATATTCATTTAGGTTAACCAAACAAAAAAATTCACAAATTCTAGAAAAATAAAATC\n") - f.write("CTATCAATTTCATCACCGTCATTTTTAAAATTTCTTAGTAATCTTAAATTTCTTCATCCAAACATAATGT\n") - f.write("AAAAGTGAACAGTACTAGGAGTGTTTCGTTAAAACTCCATTTTTT\n") - f.write("\n") - f.write(">gi|226789623|gb|GO546119.1|GO546119 Mdas9002P24_e169.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTAATTTTCCTTCCCGAAAAAAAACACCCATGCATGCAACAATGCTTTCACAAATAAAAACAAATGGTGT\n") - f.write("GTACAATATCCCATCCCAATTAACATCATCTCCATACCCTTAATAATCAAAAAAAAAAAATATTGGGGGG\n") - f.write("AAAATTAAACCAATGG\n") - f.write("\n") - f.write(">gi|226789622|gb|GO545869.1|GO545869 Mdas9004N13_e314.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTAGCCAGAAAAAACTAATGGTACTAATCAATAGGGCTAGTAACAATAATAATTATAAAATTCAGA\n") - f.write("AAAAAATTGCAACACTGAAAATTACAAATAAACATCTATTAGAATTCTTCAGGGATGCTCTTCAGGACTG\n") - f.write("GACCTACAGCACATAAAGTGCTAGCTGGAGATGACTCAATAGTAATACGACCTGTTGGAATTTGCGTAAG\n") - f.write("CTCACGAGCTACATCCTTGAAATCAAGAATGCCTCCATTTTTGCACTTTGAAAGCATTCGTGCCGCTTCT\n") - f.write("TGCTTTGTCATCTTGACTTTCACTCTAATCGCCCCTCTTTTCACATCTTCTATTTCCTCCTTGATCAGTG\n") - f.write("GTTCCGAATTTTCATGGTAAGTGCAACTGCTATTAACTTTTTGCTTCCTCGACAAGGGCTTGTTACTAAT\n") - f.write("TAACTCATCTATGTATACAACATTCTTTACGTAGGGTTTCCTAAGTTCTAGCATGTCATCTATTGGTTTG\n") - f.write("ATCCTACTGAAGAAAGAAAGCAAAGAATTCAACATTGTTGAGAGAGAGAGAGAGAGAGAGAGAGATTTAA\n") - f.write("ATCACAATAATTTCATACCAGAAAAGATCTTAACATTATTGAAACTACATTAGTTTTGATACAATCCACA\n") - f.write("AAAAATATCGGAAAGATGAGTCAACTGATGCCTCAAGGTCATGAAATGTCACTG\n") - f.write("\n") - f.write(">gi|226789621|gb|GO545868.1|GO545868 Mdas9005E13_e348.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P42896|ENO_RICCO Enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) pir|S39203 phosphopyruvate hydratase (EC 4.2.1.11) - castor bean emb|CAA82232.1| enolase [Ricinus communis], mRNA sequence\n") - f.write("AATTAGGCAGCTTCAAACACTTAAAAAAACAACTCAAAACAGAGTACATAGTCAAACATGCTTACTCGAA\n") - f.write("AATTTCCAGTGTACTGTTTTCAAGCTCTCAGAACAAAACTTATCTGAAAATTATTGGAAAAAGGGTTTCA\n") - f.write("AGTTCCACATAACTATTCCCTATGTTGTGAAACTCCGATTTCTCACATCCCGCAAAAGCTTTGGAAGCAC\n") - f.write("TTCATAATCTAATAGGGCTCCACGGGCACACGGAACTTGGCTCCAGCATACACTGCCTCTGAACCGAGCT\n") - f.write("CCTCCTCAATTCGCAAGAGCTGGTTGTACTTGGCAAGACGCTCTGACCTACAGGGAGCTCCTGTCTTGAT\n") - f.write("TTGTCCCGTGGCCAAACCCACGGAGAGATCAGCAATGAAGGTATCCTCGGTTTCTCCACTGCGGTGGCTG\n") - f.write("GCCATCACACCCCATCCAGCTTTCTTGGACATTCTTACAGCCTCAATGCTCTCAGTTACGGATCCAATTT\n") - f.write("GATTCACCTTGAGAAGAAGAGCATTGCAAGATTTCTCCTTGATTGCCTTCTCAACCCTCTTGGGGTTGGT\n") - f.write("GACCAACAGATCATCTCCCACAATTTGTACTTTTTCTCCAACTTCAGCTGTCATCT\n") - f.write("\n") - f.write(">gi|226789620|gb|GO545867.1|GO545867 Mdas9005D23_e344.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("CAATCAACCCCACTCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAAAGTGCCTCGAAAAAGGG\n") - f.write("ACAGAAAATTAAAGAAACAAATAGACCGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAAACCA\n") - f.write("CCGGGACCCTTGGCTAAAAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAAAACAA\n") - f.write("CTTAAACCCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGCCAAATCCAAT\n") - f.write("GATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCACCTCTTTCAACACCTGGGAAGAGTCG\n") - f.write("GTGCATCCGAAAATGGGCAGCTTCCACATTGTCCAGAACCTTCCATCAGAATATCCTGGGGATCTGT\n") - f.write("\n") - f.write(">gi|226789619|gb|GO545866.1|GO545866 Mdas9005K14_e377.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAAC\n") - f.write("ACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGG\n") - f.write("TCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTA\n") - f.write("CATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAA\n") - f.write("ACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTC\n") - f.write("TTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTG\n") - f.write("TCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTC\n") - f.write("AAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAA\n") - f.write("AGGGGAGGAAGGTAAGAGAGGGTCTCGAACTTCTTCAGTCCAAGTGGAGGCCACACCTGCATGCATTGCA\n") - f.write("CTCTTCCTCCATTGCTTGCAATAGAGGTAATGTCA\n") - f.write("\n") - f.write(">gi|226789618|gb|GO545865.1|GO545865 Mdas9005L22_e380.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CACAATAACGGGGTATTATTTTTTAGGGTAAATTACATAGTTACCCCTCAAGTTTAAAGTCTATTACAAC\n") - f.write("TCTATACAACATCTTTAAAACATTTCACTTTCATACCCCACCTACTATTTTATTTCAAAATAGTACCTCC\n") - f.write("ATTACAACATTTACCCAGTAAAATACTTGACAATTTGAACATGGTACATAATTTACACTAATTCGGGAAA\n") - f.write("ATTCAATTGGATGAACGTAATTAAATCAAATATTCAAAGCTTATGACTAATTTGATCTGCTAATTAACCC\n") - f.write("AACAATCATTATGATCCCTTCTCTGAGGCTGCAGGCTCAGCAACCTTCTCCTTGGAAAATTCCTCCACAT\n") - f.write("CAGCCTTACCTTCATCCTTCACAGCCAGCAAGATCAAAACCAGCAGCACCGGATAACTCACGGGGTTGAG\n") - f.write("CGCGAAATTGGTAACCAATTGGGAAAGGAAGGATGCCTTGAGCGTATCCACTTGCCAA\n") - f.write("\n") - f.write(">gi|226789617|gb|GO545864.1|GO545864 Mdas9005I15_e369.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD41136.1| OSJNBa0084K20.16 [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTGGAAACAAAGAAACTATATCTCTATATCTATCTGTCAATATATA\n") - f.write("GATACACACATGTTCATACATAATCAATTTCCCCAATTCCTAGATATCAGAAACCTATATCCAGTTGGAA\n") - f.write("AAATAAAATTTACATGGGCATTAATAATATCGAAGTTATGACTGGGACAGGCAAATAATGAACAATGACC\n") - f.write("ACAACATTGGTTTTAAGGGTAACATAATCATACAGCTGCAGCCCTGAAAAACAAAAAGTCTGAAATCTTG\n") - f.write("TTCGCGTACAAAATCTGGTTGTATGGAGTTGTCAGGACTCTGAAGCCCTGGTAAGGTGGTGACGCCCGAC\n") - f.write("AGAACAAGAATAGTTTTGCAACCACCATTTTGTCCAAACACAATATCCATATCTAATCTGTCCCCAACCA\n") - f.write("TGCAAATCTGCGACTTCAGAGATG\n") - f.write("\n") - f.write(">gi|226789616|gb|GO545863.1|GO545863 Mdas9005J04_e372.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_849999.1| tyrosine decarboxylase -related [Arabidopsis thaliana] gb|AAL69507.1| putative tyrosine decarboxylase [Arabidopsis thaliana] gb|AAM20115.1| putative tyrosine decarboxylase [Arabidopsis thaliana], mRNA sequence\n") - f.write("CAGGACAAGGCGGTGGAGTGATACAAGGCACAGCGAGTGAAGCAGTTCTGGTTGTACTATTGGCTGCTCG\n") - f.write("TGATAGGATTTTGAGGGCGGAAGGAAAAAAAGCCCTCGAGAAGCTTGTTGTCTATGCATCTGATCAAACA\n") - f.write("CATTCAGCTTTACAAAAGGCTTGTCAGATAGGGGGAATCCATCCTGAGAATTGCAGGGTGCTGAGTACCG\n") - f.write("ATTCCTCTACTAACTATGCCCTTTCTCCCAATGTACTTAATGAGGCGATTTCAAATGACATCGCGAGTGG\n") - f.write("TTTAGTACCATTTTTCTTATGTGCAACGGTTGGTACTACTTCATCAACAGCGGTTGATCCTTTGCTGGAA\n") - f.write("CTGGGAAAGATTACTAAGAGCAATGGAATGTGGTTCCATGTGGATGCTGCATACGCTGGTAGCGCTTGTA\n") - f.write("TATGTCCAGAATACCGACACCACATTGATGGTGTTGAAGAAGCGGACTCATTTAACATGAATGCACATAA\n") - f.write("ATGGTTTCTTACGAACTTTGATTGTTCGTTGCTCTGGATCAAGGATAGAAACGCTTTGGTCCAGGCGCTG\n") - f.write("TCTACAAATCCTGAGTTCCTTAAAAACAAGGCCTCTCAAGCAAACCTGGTTGTGGATTACAAAGATTGGC\n") - f.write("AAATTCCACTTGGACGTCGGTTTAGATCATTAAA\n") - f.write("\n") - f.write(">gi|226789615|gb|GO546118.1|GO546118 Mdas9002G24_e124.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P13869|CB12_PETHY Chlorophyll A-B binding protein, chloroplast precursor (LHCI type II CAB) pir|S00442 chlorophyll a/b-binding protein precursor - garden petunia gb|AAA33711.1| chlorophyll binding protein precursor prf|1503272A chlorophyll bi, mRNA sequence\n") - f.write("TGATTTCTACATATTGGAATGAAGGTTCCAAATAGATTTTTGTACACAAGGCAAGCAGATAAAATTACAA\n") - f.write("GTTTTTTGTCCTACCAACGTTGCCCCTTCTCCTCCCGCACTTGAATCCCAATTAGAATTCTCCTTCTTTC\n") - f.write("CTCACTTCGGGGAAAAAGAAGCAAAAATGGTGGCATGGCCGGGATCGGCGAGGTGAGCGAAGAGGTTGTC\n") - f.write("AATGGGGCCAGTCCCAGTGTAAATGTGTTGGAACCAAGCTCCCATCACAGCCAACATAGCCAGCCTTCCG\n") - f.write("TTCTTGATCTCCTTTGTCCTCAACTCCTTGATCTTCTCAGGCGAGCCGCTTCCCCATCCAAGTGGGTCGA\n") - f.write("ACCAGAGCCCTCCCGGGTACCCAACATCTGTCCCGGTGAGCTTGTTGTTGGGGAAGATTGGGTCTGTGTT\n") - f.write("AACAGACCCGGGCTTGAGGATGTCCGCCCATCTCCTTCCCTCGGCCCACCCGATCAAAACAAGCTCAACG\n") - f.write("ACGAAGAGAGTGGTGGTGTCTGTGAAGTACTCTTGCTCTCCGGC\n") - f.write("\n") - f.write(">gi|226789614|gb|GO546117.1|GO546117 Mdas9002D04_e104.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTCGTAAGTACCAAGTTTGCAATCTTTAAGTTGAGTACAAGGATACAAGTACCAACAG\n") - f.write("TGGACCGAGAACATATGCCATCCATGCAGATGTCCTCCGTTTCCGGTTGGAGCCACCAGTCCGACGTTGC\n") - f.write("CATTGCACTTGCAAAAGTCCATCTTGAAGTGAGAAATTATCTCCTCTTCACCCTTGTCTGCTTAATAGAC\n") - f.write("AAACAATAAAGATAAACCTAATAAGATACAGGACACATTTTTCTACATGGATAATGTTACATACAATATA\n") - f.write("TACACATCAACACTTCTACTGCAGTACATGCGTAAACACATTGATTACATGTTGCAGAAAGCAGTCGCGT\n") - f.write("TAAGAACTACTAGATTTTCCCCATGACCTAAAGAACCTAATCACGGGGTCATGGAGGTCTTCTTTGGCCC\n") - f.write("TCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226789613|gb|GO546116.1|GO546116 Mdas9002P23_e168.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to prf|0512262B plastocyanin, mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTAGCATGAAGGCGCTCAATATATAAATGCTTTCACCTCGCACTTTGTCTCTCTCGC\n") - f.write("ACATTGTCTCTCATGGCAATCTGATCATTACAGAAGTCCTACTTTGCCTCCAAAAAAGGAAGCATAAATA\n") - f.write("TTATTAATCAGACAACTGAATTAGTTAACGGTAACTTTGCCGACCATGCCAGCTCCCTGGTGAGGAGAGC\n") - f.write("AGTAGAAAGAGTATGAACCTTTTTCGGTCAAGGTGATGGCGTAGGTTTCCCCGGGGGCATTCAGGAGGTC\n") - f.write("CTCCTCGCTCATCGAGATTTTTCCAGCATCCACACCGCTGGGAACCTCGTCCTCGTCAAACAAAACGTTG\n") - f.write("TGTGGGAATCCAGCATTGTTCTTGAACACAATCTTCTCACCGGGGGCGATGGAGAAGCTGTTGGGGACAA\n") - f.write("AGGCTAAGCCACCGTCATCGCTGCCTAGCAAGACCTCAATGGCCATGGCATTACTGGCGAGGATAGCACT\n") - f.write("GGCGGCAGTGGCGGCAACGGCCACACCAACATCCTTGAGGGATGACTTGACAATGCACA\n") - f.write("\n") - f.write(">gi|226789612|gb|GO546115.1|GO546115 Mdas9002K24_e142.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S31865 chlorophyll a/b-binding protein Lhcb5 - Scotch pine emb|CAA78900.1| Lhcb5 protein [Pinus sylvestris] prf|2104448A Lhcb5 gene, mRNA sequence\n") - f.write("GTGAAAAGATAGAGCAATTCCATTTAAGGATCAAGGTTAAAAGCCTTTAAAAGGACTCAATTTGATATAC\n") - f.write("AATGCTTTTAATTTTGATTGGAGGAGAATAAGGAGGAAACTTAAAATTACAGGGTTGGAGCTCTTTCGAT\n") - f.write("AGATCCACCAATGACAGTAAGCAAGTTGTTGCCGAAGGGATCGCTCAGATGCTTTGATAGGTTTTCGACA\n") - f.write("GGACCTTCTCCGGTGACATACGCTTGGAGGAAGAAACCGAGCATGGAAAACATGGCAAGTCTTCCGTTCT\n") - f.write("TAATCTCCTTCACCTTTAGCAATGCAGCCTGGTCTGGATCCTTAGCCAGCCCCAGTGGGTCAAAAGGACC\n") - f.write("ACCTGAGTGAAGCTTGTCC\n") - f.write("\n") - f.write(">gi|226789611|gb|GO546114.1|GO546114 Mdas9010C03_e727.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTGACTAAAGATTGTATTCCTTGAACAATGAATGAATTACAGAGAGGTGTTTGTTAT\n") - f.write("TTATACAAGTTTCTCCAGAGCTCTTCTCAGAAGACTTCTTCCACAACCACTTGCGCTCCATCTACGGTTC\n") - f.write("GATTCTCCAACTCCCCAACTAGCACATCACAATGTGTTCATCTACAACACACAACTACAATTTTACAGAG\n") - f.write("TCATCAAAAACCCACCTCAAATCCTCTTCAAAGTTGCACGAAACAGAAGATGAAAGCCTTAAATAGTTAG\n") - f.write("CCAACAACGAAATCCTTAGAGATTGTTGCTGCACAACTATAACTCCAACTAATACAGCAAAGCCTTTCAA\n") - f.write("ATTTAGGAAGCAAATTCTTTCCACCAAATCTAAAGCATTTAAGCAAAAAAGGAAAGACTTCGCTTATCGC\n") - f.write("ATTCTCTCACCTTTGCTTCAAATCCATTATCACACTATATAAGAATCAAAACAAAATGGATCTGCAG\n") - f.write("\n") - f.write(">gi|226789610|gb|GO546113.1|GO546113 Mdas9002C19_e102.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S16294 chlorophyll a/b-binding protein type I precursor - tomato, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAACGGACGTGAAAAGATAGAGCAATTCCATTTAAGGATCAAGGTTAA\n") - f.write("AAGCCTTTAAAAGGACTCAATTTGATATACAATGCTTTTAATTTTGATTGGAGGAGAATAAGGAGGAAAC\n") - f.write("TTAAAATTACAGGGTTGGAGCTCTTTCGATAGATCCACCAATGACAGTAAGCAAGTTGTTGCCGAAGGGA\n") - f.write("TCGCTCAGATGCTTTGATAGGTTTTCGACAGGACCTTCTCCGGTGACATACGCTTGGAGGAAGAAACCGA\n") - f.write("GCATGGAAAACATGGCAAGTCTTCCGTTCTTAATCTCCTTCACATTTAGCAATGCAGCCTGGTCTGGATC\n") - f.write("CTTAGCCAGCCCCAGTGGGTCAAAAGGACCACCTGGGTGAAGCTTGTCCTCCAATTCCAAACCGTTAGTG\n") - f.write("ATTCTGTAGTATTCAGCTCCACCAAGAAGAACAACCTCAGCAACAACAGCGAAAATAAGATTAATCGGTA\n") - f.write("TGTTCTTCCCAAAGTAATTCAGTGT\n") - f.write("\n") - f.write(">gi|226789609|gb|GO546112.1|GO546112 Mdas9002G13_e120.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_176347.1| light-harvesting chlorophyll a/b binding protein [Arabidopsis thaliana] pir|E96640 PSI type III chlorophyll a/b-binding protein [imported] - Arabidopsis thaliana gb|AAD25555.1|AC005850_12 PSI type III chlorophyll a/b-binding prote, mRNA sequence\n") - f.write("TTTTAACATGTTTTTTCTCACAGAGTCACAGACAACCATAACAAACAACAAACAAAGGCCAAATTATATT\n") - f.write("AATTGTACAAACGTTACTTAATGGAACTTGAGGCTGGTCAAGATGTTGTTGTGAACTGGGTCAGCCAAAT\n") - f.write("GATCCAGAAGGTTCTGGTAAGGCCCCACACCAGTCACAAGACCCTGAATAAAATAACCCAATATTGCCAG\n") - f.write("CATGGCAAGCCTCCCATTCTTCACTTCCTTGAGCTTTAACTCGTTCAACGACTTTTCATCTTTCCCAAAC\n") - f.write("CCTAGCGGGTTGAACAAGGGCCCACCAGGGTAAGCCGGGTTCCCGGACCCACCCAAGTACTTCTCAAACC\n") - f.write("CCAAGAAGTATTGCTTGCCCATGGACCCGGGGTTGTACCAGTCCTGGAACCTCCGGTGCTCGGCGAAACC\n") - f.write("CCATTATGGCA\n") - f.write("\n") - f.write(">gi|226789608|gb|GO545862.1|GO545862 Mdas9004N10_e312.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB92996.1| chalcone synthase [Malus x domestica], mRNA sequence\n") - f.write("GTCAATCCATATTTTACTCATCATTACATTGCCCAATCAGGGCCCTTTTTTCATCAATATTGCAGTAAAC\n") - f.write("AACATGAAAGTAAGGGTCCTTCCTTGCACCAAGTTAACCCCATGACGCCCACACACAATATCCCAAAAGC\n") - f.write("CAAATTCTAACCAGAAAAGGCGGAAACAATACATAAACGAAGCAGATAGATAAATGAACACCGATTTTCA\n") - f.write("TGTCATCAAGCACCCACACTGTGAAGCACAACGGTCTCAACAGTGAGGCCAGGCCCAAATCCGAAGAGTA\n") - f.write("CGCCCCACTCCAGTCCTTCTCCAGTTGTTTTGAGTCCTTTCTCAGCAGACTTCCTCCTCACTTCGTCCAA\n") - f.write("AATAAACAAGACACACGCACTCGACATGTTGCCGTAATCAGACAGCACTTGTCTTGTAGCTTCTAGTTTC\n") - f.write("TCCGGCTTAAGGGCCAACTTGGACTCTACTTGGTCCAGAATAGCAGGGCCACCTGGGTGTGCAATCCAGA\n") - f.write("AGAGCGAGTTCCAGTCTGAAATGCCTATAGGCTTGAAGGCCTCGTTAAGGCTCTTTTCGATATTCTTGGA\n") - f.write("AATAAGCCCGGGAACGTCCTTGAGAAGGTGATATGTAAGCCCTACTTCACGGAGATGGCCGTCAATAGCC\n") - f.write("CCATCACTGTCGGGAAGAATGGTTTGTGCTGCTGACA\n") - f.write("\n") - f.write(">gi|226789607|gb|GO545861.1|GO545861 Mdas9005N01_e384.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("ATACGGATCTCATTGAATCATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAACACCAAATTCAA\n") - f.write("AAACAAACGAAAGTGCCTCGAAAAAGGGACAGAAAATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCC\n") - f.write("CTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAAAGCCACAATGGTACATACAACAAC\n") - f.write("AACATTATTTATGAAAATTGTAAAACAACTTAAACGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACT\n") - f.write("GCACTTGACGGACATTGTCAAATCCAATGATACGGATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTC\n") - f.write("CAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTT\n") - f.write("CCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTCAAATTCCAAGC\n") - f.write("AGGGAACCCAGTTTTTGCG\n") - f.write("\n") - f.write(">gi|226789606|gb|GO545860.1|GO545860 Mdas9005B23_e333.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAC34983.1| light harvesting chlorophyll A/B binding protein [Prunus persica], mRNA sequence\n") - f.write("TTCAAACAGAATAAAAGCAGCAAGCAATGGCAACCTCTGCAATCCAACAATCAGCATTTGCTGGCCAGAC\n") - f.write("TGCTTTGAAGCAGTCCAATGAGCTCGTCCGAAAGATCGGCGGCCTTGGCGGCGGCCGCTTCTCCATGCGG\n") - f.write("CGCACCGTCAAAAGTGCCCCCCAGAGCATATGGTACGGCCCAGACCGCCCCAAGTACTTGGGACCATTCT\n") - f.write("CCGAGCAAACTCCGTCATACTTGACCGGTGAATTCCCCGGAGACTACGGATGGGACACTGCTGGACTATC\n") - f.write("TGCAGACCCCGAGACATTTGCCAAGAACCGTGAGCTTGAGGTGATCCACTCCAGATGGGCCATGCTTGGT\n") - f.write("GCACTGGGATGCGTCTTCCCAGAAATCTTGTCAAGGAATGGCGTCAAGTTCGGCGAGGCTGTCTGGTTCA\n") - f.write("AGGCTGGATCGCAAATCTTCTCTGAGGGCGGCCTTGACTACCTTGGCAACCCAAACCTTATCCATGCTCA\n") - f.write("GAGCATCTTGGCAATCTGGGCTGTCCAGGTCGTGCTCATGGGATTCATTGAGGGATACAGAGTTGGAGGA\n") - f.write("GGACCACTCGGTGAAGGACTAGACCCACTTTACCCAGGAGGGGCCTTTGACCCCCTTGGACTTGCTGATG\n") - f.write("ATCCCGAAG\n") - f.write("\n") - f.write(">gi|226789605|gb|GO545859.1|GO545859 Mdas9005L02_e379.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P28475|S6PD_MALDO NADP-dependent D-sorbitol-6-phosphate dehydrogenase (Aldose-6-phosphate reductase [NADPH]) (NADP-S6PDH) pir|T17013 D-sorbitol-6-phosphate dehydrogenase, NADP-dependent - apple tree dbj|BAA01853.1| NADP-dependent D-sorbitol-6-p, mRNA sequence\n") - f.write("TTTTGACTGTGCTGCTCATTACAAAAGTGAAGCAGACGTTGGAGAAGCACTTGCAGAAGCATTTAAGACT\n") - f.write("GGACTTGTTAAGAGGGAAGAACTTTTCATTACCACCAAGATTTGGAATTCAGACCATGGGCATGTGGTGG\n") - f.write("AGGCCTGTAAGAACAGCCTCGAGAAGCTTCAGATAGATTATCTGGATCTCTACCTGGTTCACTACCCAAT\n") - f.write("GCCCACAAAGCACAATGCAATTGGTAAAACTGCCAGTCTTTTGGGCGAGGATAAGGTGTTGGACATCGAT\n") - f.write("GTAACAATTTCCCTTCAACAAACCTGGGAGGGCATGGAAAAGACCGTCTCTTTGGGCTTAGTTCGCAGCA\n") - f.write("TTGGTCTCAGCAACTATGAGCTCTTTCTAACTAGAGATTGCTTGGCTTACTCCAAAATAAAGCCTGCTGT\n") - f.write("GAGCCAATTTGAAACCCACCCCTATTTCCAGCGCGACTCTCTCGTCAAATTCTGTATGAAACACGGCGTT\n") - f.write("CTTCCCACAGCTCACACCCCTCTCGGAGGTGCTGCTGCCCACAAGGATATGTTTGGTTCTGTT\n") - f.write("\n") - f.write(">gi|226789604|gb|GO545858.1|GO545858 Mdas9004M07_e309.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTAGAAATACACAGCCATAGGCATAGGGTAGGTAACCATTAAGTTGCATATAA\n") - f.write("TATGTAACACAGTCAACTCCAGCTCTGCTACCAACGGGTATTAGCACACAGAATAGTAGAATACTACTAC\n") - f.write("TTTTAGCACTACAGCACATAAATAGGCAGCCTCCGCTGCAGCACGCCTCTACATTATTTATCTATAATAT\n") - f.write("ATATAGTTCATATGTTGCCTCGGAGTTAGGGAAGGTGAGGCTTCTCCAAGTCCTCGATGCTGGTAGGGCG\n") - f.write("AAACCACGCCTCCTGCTCCATCACCGAGGATCCCTCCCCACCATCGCCCGTGGAGGAGCCGTCCTCCCTG\n") - f.write("CCTGCGGAAGATGTGTGTTCAGCTTCAGGCCCGAACACCCCCGGGTGGGGATGTGGAGCCCAGTACTTGT\n") - f.write("CCGGTTGGGGTGGGATCACATCATCTGGAACAAAGCTGGGTCGAGTTTGTTCCTCTGGGTTCTTGTCATA\n") - f.write("GGTCGAGGTGTGAGCAGCCCTCCTGAGAGTGAGAGCGGAGAGCTGAGCTGAATCGCGCGCTCGGATCTCG\n") - f.write("TTGATAAGTCGCTTCCCCAAGCTCGCGATACCTCGACTGCTCGAATTGGCGGCCATACAGTAAAA\n") - f.write("\n") - f.write(">gi|226789603|gb|GO545857.1|GO545857 Mdas9005D10_e341.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_181415.1| histone H2A, putative [Arabidopsis thaliana] ref|NP_850298.1| histone H2A, putative [Arabidopsis thaliana] ref|NP_850299.1| histone H2A, putative [Arabidopsis thaliana] pir|F84809 histone H2A [imported] - Arabidopsis thaliana gb, mRNA sequence\n") - f.write("TCGAGGATTGAGGCCAAGTACACAGCAGCAGTGGCGCCAACACGCCCATGAGCAGCAATTCGCTGTTTCA\n") - f.write("GCTGCCGATGAATTCGACCCACCGGAAACTGGATACCAGCGCGAGATGAACGAGAAACAGGCCTCTTCTT\n") - f.write("GTCCTTGTCCTTGTCCTTGTTAGCTGCTGTGGTTTTCGCTGCTATAAGCCCCTTCCCGCCCTTGCCCGCC\n") - f.write("ATTTCTACCTGAAGAGTTCTTGGGAAGCTTGAAGACCGAAGGGAACCGTAGAGAGAGAGAGGGGAAAGCT\n") - f.write("AAACCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226789602|gb|GO546111.1|GO546111 Mdas9002M09_e149.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P93768|PSD3_TOBAC Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Nuclear antigen 21D7) pir|T02207 protein 21D7 - common tobacco dbj|BAA19252.1| 21D7 [Nicotiana tabacum], mRNA sequence\n") - f.write("ACCTGATAAACATGTTCAATGTCTGGTGAAAAATGTCAAATATTCAATGTTCGTATCATATATAACGGAA\n") - f.write("TGAAACAAGCAACCTCAAAATATGATTGAAACAGGTCGCTTAGGCTCAACACAACAAATCTTTAACATAA\n") - f.write("ACGGAAACAGGCACCATCCCGGGTCAATCAAACAAGGAACCAAAATGTTCTTGATAAACATTTTCAAAGA\n") - f.write("AACGCGGATAGCTTTTTGAAAGCATTGCACAGAGCGTAAATGTAACTGCTTCAAAACTCATCATCGTCCT\n") - f.write("CCTCAGCTATGTGCTTTGCAAGCTCTTGCTCCTGTTGTTGCCTCTCCCTCCTCTTCTCAGCACTTTCTTT\n") - f.write("CTCCTTGTGGGAATTTGGCGGGAATCGAAGCGCTCGCACTGCATCATTGTGCAAATTAAGGCAAAATGCA\n") - f.write("ATTCTCGTGTCAAATGCTGCTT\n") - f.write("\n") - f.write(">gi|226789601|gb|GO546110.1|GO546110 Mdas9002D02_e103.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTCATTATCTGTAGTTGGACTTCTATGAAACAGATAAATGCATCAGGAGGAAACGGAAGTGCGGAAATC\n") - f.write("ATTTTCCACGACAAACGCTCCAAAGATGCCAGAGGAAATAAAGGATCAACCCATTTAACTCTACTCATCA\n") - f.write("TCTAAAGACTCTCAGTGAGTGATTCACACA\n") - f.write("\n") - f.write(">gi|226789600|gb|GO546109.1|GO546109 Mdas9002D06_e106.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q41048|PSQ1_MAIZE Oxygen-evolving enhancer protein 3-1, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving system of photosystem II) (OEC 16 kDa subunit) pir|T01747 photosystem II oxygen-evolving complex protein 3 precursor - maize, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTATGATGCTTAAATATCACTAGATTTCCTCCAAATAGCATCCAAACA\n") - f.write("TTTTGATCTCATAAACAGGCAAACAAAGCTCTTAAAAAGCCTTATACATCAAATACATTAATCCCTTTTA\n") - f.write("GGGTTTTAGCCAAGCTTTGCAAGAACATCGTTGAGGGAAGATACGGTTGCGGTGTAGTACTTCTCTGCTT\n") - f.write("CCGGGGTGCTCTTGATCTTTGCTGCATAGTCCAAGCCGTCAATGTCTTTGAAGAGCTTTCCGGTGAGTTC\n") - f.write("CTTGAGGGGCTCCTTCTCGGCTTTAGATTTGGCAGAAATGACGGTCTTGAGGTCATAACGGAGATATGAG\n") - f.write("GCTCTGAGACGAAGATCGTTCTGGACGTAAGGCCATGCCTTTTTGTCAATGTACTCCTTGACAGCTAAAA\n") - f.write("TCTCCTTGGCTGACTCCTTCGCCCTCGCGGCTGCCTGAGCCGGAGTGAGTGGTTGGATGAAGAACCTCTC\n") - f.write("CTTCAATGGCAGGTCAAGGTCTCTTGCCTCATCCGAGTTTAGGGTTCCAGCCAATCC\n") - f.write("\n") - f.write(">gi|226789599|gb|GO546108.1|GO546108 Mdas9002P16_e165.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA03104.1| light-harvesting chlorophyll a/b-binding protein (LHCP) precursor [Lactuca sativa], mRNA sequence\n") - f.write("TTTTTTTTTTTTTAATAAAAACTCGTATTTGCTCTCTTCTCGTAATTCAGAACAGATTAAAGATTGTCCG\n") - f.write("AAAAAATATTGATATATTGAAAAAAATAGAAATTTACTCCAACATCAACAAATTTTCCACGCTCAAATCC\n") - f.write("ACACTCAAACAAAAGGGACTCACAACAAGTCTTCAATTCTTCTCATACTCTCACTCACTTTCCGGGAACA\n") - f.write("AAGTTTGTGGCATAGTTCCAGGCATTGTTGGCGACTGGGTCCGCAAGGTGGTCGGCAAGGTTCTCCAATG\n") - f.write("GTCCCTTACCGGTGACAATGGCCTGCACAAAGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTT\n") - f.write("GAGCTCCTTCACCTTGAGCTCAGCAAAGGCTTCTGGGTCGTCAGCAAGACCCAATGGGTCGAAGCTTCCG\n") - f.write("CCGGGGTAAAGTGGGTCGGTCACCTCTCCGAGGGGGCCGCCGGCAATTCTGTATCCCTCAACTGCGCCC\n") - f.write("\n") - f.write(">gi|226789598|gb|GO546107.1|GO546107 Mdas9002A06_e89.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_564664.1| expressed protein [Arabidopsis thaliana] gb|AAN13084.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TCGAGGATCCTCCTCCAATTAGATGCCTGCCATTCCAGTCAGACCGAAATCTATGAAAGGGATGAACAAC\n") - f.write("AGGTAGCAAATCCTTCCGCCTCATTTCAACCTCTTGACCAGGAACCTTCTCTATTTCCATCTCTCCGCGG\n") - f.write("GTAAGATCTTTACCAAAATTTAGCTCACCAGCAGCACATGGACTCATTGTATAGAAATATATCTTCGACT\n") - f.write("TTTGCCAGATTGGAATCCTTCCGGAATTGATCTGAACCTCAGCATTGGAGAGATACACATGAGATCGTTC\n") - f.write("AAGGGGTTTTGCCAACTCCTTATCCCCAACATCACTATCATCACAGTCAGAACTATCAATTGTGTCAATA\n") - f.write("TCTTCTTGTTTCCCAAGTATAACCCCAGAAAATGCATTCCTCTCTTTCAGGCCAATCATTTCTTCGGCAA\n") - f.write("ACATCCAAAAAATGAAGAGATTCAACTTTCACTCGCAAATCTTCATCCTGTATCTGTACTGAAGAACCTG\n") - f.write("GCCCTGCTCTCGAAGCAGCGTCGCCTGGCTCTCCTCCCAAT\n") - f.write("\n") - f.write(">gi|226789597|gb|GO546106.1|GO546106 Mdas9010B12_e721.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S20925 polyubiquitin - maize gb|AAB21993.1| polyubiquitin [Zea mays] gb|AAB21994.1| polyubiquitin [Zea mays], mRNA sequence\n") - f.write("CCGGAACCGAATTTATTTATAGAAACATAATATAAGATAACACAAACTTGCCCAGATGCCTCATCTTAGG\n") - f.write("AGGCAAAAACAGTACCATTAAACTTAAAAACATAAAATATAAACCATAAACTTCTTCCAACGGGAACAAA\n") - f.write("TAGCAGACGGTCACCGGCCACACCAGCACTTAGAAACCACCACGGAGACGGAGGACAAGGTGAAGGGTGG\n") - f.write("ACTCCTTCTGGATGTTGTAATCAGCCAGGGTCCTTCCATCCTACAACTGCTTACCAGCGAAGATCAACCT\n") - f.write("CTGCTGGTCCGGAGGAATACCCTCCTTGTCCTGGATCTTTGCCTTCACATTGTCGATGGTGTCCGAGCTC\n") - f.write("TCCACCTCCAAGGTGATGGTCTTCCCTGTCAAGGTCTTCACAAAGATCTGCATACCACCCCTCAGACGTA\n") - f.write("GCACCAAGTGAAGGGTCGACTCCTTCTGGATGTTGTAGTCCGCCAAAGTGCGGCCATCCTCGAGCTGCTT\n") - f.write("CCCGGCAAAGATCAGCCTCTGCTGGTCCGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTAACATTG\n") - f.write("TCGATGGTGTCGGAGCTCTCAACCTCCAAAGTGATGGTCTTGCCAGTCAGGGTCTTCACAAAAATCTGCA\n") - f.write("TGCCACCACGGAGACGAAGCACCAAATGGAGAG\n") - f.write("\n") - f.write(">gi|226789596|gb|GO545856.1|GO545856 Mdas9005C15_e336.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAC69854.1| putative thioredoxin m2 [Pisum sativum], mRNA sequence\n") - f.write("TAAGTCACTAACATTCTCGTAAAGTAAAAAAAATAGTTACAACTTCATCCAGATAACTAACTATACAGGA\n") - f.write("GCAGACGTGAGTTTATTTTGGGAGAGAAGCCTCCGAAATCTGAGAGATCATAATCTAGAAAGAGAAGAAA\n") - f.write("CAGATACAAGGCACAGCTTAGGTCCAACAAGGGGAATAATACTTACCACACTCTACAAGAACTTCTCTAT\n") - f.write("GCTGGGGGTCAATGTAGATTTTGGAACAGCACCAATAACGGCATCTTTCTTCTCGCCACCTTTGAATATG\n") - f.write("ATGACAGTTGGGATGCTTCGAATCCCATATCGGGTTGCAATTGAAGCACTCTCATCAGTGTTAACTTTGT\n") - f.write("AGCATTTGAGCTTCCCAGCATATTGCTTTGCCAGTTCATCAATTATGGGGTGGATCATACGGCAAGGCCC\n") - f.write("ACACCACGGAGCCCAGAATTCAACCAAAACAGGGTATTCAGAATCTAGGACAAGTGACTGCCATGTTGCA\n") - f.write("TCACTAACAGCAGGCACTTCGACGGCAGTGTCCTGAGCCTCGCAGACGACGAGCCCGCCACGGCGGCTCG\n") - f.write("CTTGTCCGGAAGCGGGACCGTAACTCA\n") - f.write("\n") - f.write(">gi|226789595|gb|GO545855.1|GO545855 Mdas9005E17_e351.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CGAAGACTATCATATAGAATTTTATATGTCTGAACCAATCTCCAAAATAGAAGTGCAAAAACATGAAATA\n") - f.write("TAAATTATACTCGGCCACTCAAACACCATAGAAACAAACCCTAACAAAAAATAAGGACAAAAAAACACCA\n") - f.write("TTTCGAGTGAAGGGACTAGATTTAGATATTTTCACTTGAAGCACTTGGCATCCAAAAGAGCCTCTCCCT\n") - f.write("\n") - f.write(">gi|226789594|gb|GO545854.1|GO545854 Mdas9006P05_e481.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAATTCATATTCACACATGTAACCACTAATCCACCATTAACTTCCGACACTGATTTAATTGTTCATGAA\n") - f.write("ATATTACTGCAACGTAAAAGGATCCAGGTTACAATTCCTCGCACGAAAAAAGTAACTACATGAAAAAGTT\n") - f.write("TCACCTATAAAACCATATTGCGGTCTTCACCATCATCACTTGGATCAACATCGTAATCAAAGTCATGGCC\n") - f.write("GTCATTGTTTTCATCATACATATCATCTTCAAGAAAGTCATTTTCTTCTAAATCCTCGGGTTCTGATGAT\n") - f.write("TTGTCGCTGGAACTCTCCTTCTCTTCTGATTCATCATCGGAATCTTCGTTCTCTGATTCCTCTTCTTCCT\n") - f.write("CTTCAGAAATCTCATCCGGATAATCATTAAGCGGGTTGTTTTCAGCATTTGAATCATCAGATTCATATTC\n") - f.write("GGATTCATCAGGCCCATCATAAAAATCCTCGTCATCAACTTGGACCAAGGGGAATGGATTTGAAGATAAT\n") - f.write("TCGCGGACGCGTGGGT\n") - f.write("\n") - f.write(">gi|226789593|gb|GO545853.1|GO545853 Mdas9006N11_e469.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAATTCATATTCACACCTGTAACCACTAATCCACCATTAACTTCCGAAACTGATTTAATTGTTCATGAA\n") - f.write("AAATTACTGCCACGTAAAAGGATCCAGGTTACAATTCCTCCCACGAAGAAAGTATCTAAATGAAAAAGTT\n") - f.write("TCACCTAAAAAAACATATTGCGGGCCTCACCA\n") - f.write("\n") - f.write(">gi|226789592|gb|GO545852.1|GO545852 Mdas9005N24_e391.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("ATTTTAAAATATCTGTTTGACGAAACAACAGAAACGATACATTCAATGTACATCCTAGAGCTCAAATCCA\n") - f.write("ACACAGCAATTACCCCAAAAAAGCAACTCAAAAAAGAAGCAACTCTAAAAATTTATGCTTCTTGTACCCT\n") - f.write("TGCATAGGATGCTGATTGAAACATAACCAATGCAGGTGCTTTTCTCTAACTTGGTGGAC\n") - f.write("\n") - f.write(">gi|226789591|gb|GO545851.1|GO545851 Mdas9006M12_e463.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTTTTTACGGCATCTCTTGCTCTTAAATCTCTTTATTTTCTTTTGAAGCACTC\n") - f.write("ATTACATCACATTCCTATTAAAGTACATCAACATCCACTAGTGTTTTCAAATTCCTTGAAACATTAGGTA\n") - f.write("GTCTCCATTTTTCCTTAAATTAAATTTAGAAACATACTTGAATCCCTCTGGTGCGATTGGCCATAAGTTA\n") - f.write("GGCTTTCTGTACCGGACGCGTGGGT\n") - f.write("\n") - f.write(">gi|226789590|gb|GO545850.1|GO545850 Mdas9006J24_e457.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCCTAATCCTTGAATTAAGGTAAAAAGCCAAGGGAAAATGATATTAAATCCAAAAAGAAAAAAGGGTGTT\n") - f.write("ACTCATACATTCCTAGTTAGCCACTGTGGCCATCCTAAAAAATACATCTCGTCCTCTTATTAAGGACTTG\n") - f.write("AAAAAAAGACACAGGGAAGTCAAAACACGGAAAAACGGACGCGTGGGT\n") - f.write("\n") - f.write(">gi|226789589|gb|GO545849.1|GO545849 Mdas9006G18_e438.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_742507.1| glutamate-ammonia-ligase adenylyltransferase [Pseudomonas putida KT2440] gb|AAN65971.1|AE016225_4 glutamate-ammonia-ligase adenylyltransferase [Pseudomonas putida KT2440], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTCTTTTTTATTTTTTCTACTTCTCTATTGCCTCCCGATCCCTTCTTGATGTTCT\n") - f.write("CGGCCATTGCCCTGCTCCTCACTTCCTGCTGGATCATCTGCTTCATGGTGCGCATCGCTTCTATGGCGGA\n") - f.write("TAAGTCCAGGTAACGCCGGTAGACAAACGGTCGCAGCATGTCGAGCAGTTGTGCGCCAGCCACCTGGTCA\n") - f.write("CCCGCCACCACCCGCGCCTTGATCATGGCGTAACGTTCCCAGTCGCGGCCCTGATCCTGGTAGTACTGCT\n") - f.write("CCAGCGCGTTGAAGCTGAGCACTAGCGCCCCGGCTGAACCGTAGGGCCGCACGCGCATGT\n") - f.write("\n") - f.write(">gi|226789588|gb|GO546105.1|GO546105 Mdas9002H15_e126.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("CAACTGCATTTTTTCGTTATAACGCGAAAAAAAAAGGTGCATGATTCCGCGAATTTCTTCTGAAAAAAAA\n") - f.write("ATTGAAGAACCATAGCATTTCGCGATTCATTGGTAAATCTACTTTGATTCTCTATCAACCAATAATGTAA\n") - f.write("ACCATTAACAGGGTTAAAGCTAAACCGTTTGAAGTTCAGATGCAGCATGGTATTCTTTCTACTACTATGT\n") - f.write("TAGTTAATAAGTTAAGACAGAAATGGTTTCAAAACAAATAGTTGGAATTTTTTTTCGATATAAAACACTC\n") - f.write("ATGTCGATAAAATGATTTGAATCCGTTATTTGATTGGAAAAAATGGGTATTTCATCCCACGTTTTATCTT\n") - f.write("TTTTATCCAATGCTGAATCGATGACCTATGTATTATGTATTAAAGTAAGAAGAATTCTTTGAAAAAAACC\n") - f.write("TCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226789587|gb|GO546104.1|GO546104 Mdas9002J05_e136.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTAAGAAACATGACTGCACTTGCTATTTCCTTTCATAACTTAAAGTTTGACACTCATATCACACTATTGC\n") - f.write("TTGCTTGCTTGTAAGACTCTGGACAAAAGAAAACCCACAAAATCATTCATATCCCTGTAAACCCAAATGC\n") - f.write("ATGCAGAGAGATAAAAAAAAAAGACTCACACTGATGGGAGGAGGAAGATTGACACACAAATGGTAGTTAG\n") - f.write("AATACCAAGGGATCAAACAGACCGAGACCACAAGGACAACGAAGAAAAATAAATGAACAACGCTTCTGTA\n") - f.write("CCTGCTCCTAAAAATGGCATTGTATTTTCACTTGAAGCAGACCGAGGTTGACCAATAACAGAAGGACAAT\n") - f.write("CTGGGGAGGGAGGG\n") - f.write("\n") - f.write(">gi|226789586|gb|GO546103.1|GO546103 Mdas9002E03_e110.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P16059|PSBP_PEA Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving system of photosystem II) (OEC 23 kDa subunit) (23 kDa thylakoid membrane protein) pir|JS0771 photosystem II oxygen-evolving comp, mRNA sequence\n") - f.write("TTCATAACGATAGAAACAATAGAACGAACATAGGAACTCTGACGCTCGAGGGTAAACGCTCTTAACCACT\n") - f.write("CGAGTAAGAGGCCCGTAATTTCTTTGACTTACACAAGCAGAAGAGAACTGGTCCTTCTCTTAATACCATG\n") - f.write("AAACAACTATATATGCTCAACCATTTCCTCAGTTATAGCCAACTCTTAAACACTTGAGAGGAGAAAAGAA\n") - f.write("GAAGAAAAACTAGAGAGCTCAAAGACAATTCACAATCTTAAGGTAATTTACATTACACAAACCCTCTCAA\n") - f.write("ATAAATTCTTATGCAACACTGAAAGAACTTGCAGTGCTCTCTACAAACTTCCTTGCTCCTTTGAACCACC\n") - f.write("TCTTGTCTCCGGCTTGTGCCTTTAGAATGTAGAGCTTGCCGTCTTTCACGGTGGCTGTGATAAGCTGGTG\n") - f.write("CTTGCCTCCTTCATCTCCGTCGGCTGTCCTTGTCAACACAGATACGTAGTAGTACTGCTTTCCGTCAATC\n") - f.write("ACTCGACTAGAACTCTCCAATATGTTGGCTGTGGCCACGGCACCCGGGTCGAAACCACCCTCGG\n") - f.write("\n") - f.write(">gi|226789585|gb|GO546102.1|GO546102 Mdas9002M03_e145.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK25798.1|AF338237_1 rubisco activase [Zantedeschia aethiopica], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTGAGTATCAATAGCTTGTTTAATAATTAAAACAAAATAATTGCAAGA\n") - f.write("ATTTCCATAGAAATACAAGCGCAAATTACAAAGAAAATATCAATAACCCAGCAAACAGAATATTTATTTT\n") - f.write("CTTCAGCTCCAATTACTCGTACTGACAGCTACCGTCGTCACTCCTTGCTGCTGGGTTGAAGTTTGCAGCT\n") - f.write("GTTCGATCAGTGCAGCCTTCTGGGACTGGTACATTAACTTGTTGGGCTGCCTTTCCATAGAATTCTCCTC\n") - f.write("GGTTAATGGAGTCCTGGTTTGCATCTCCAAGGGCTGCATCGGCCAAGTACTTGTCAGCCAGTTGGACTCT\n") - f.write("CTTCACATTGTCCTGCTCCTGAACAAGCATTTGTCCGTAGTGAAGGAGCTTCTCCAGAGTCATCTTAGGT\n") - f.write("TGATCGAAAGTCGGGGGACCTTCTTTTGAGTTCACAAGCTTCTTCCCAATCCCG\n") - f.write("\n") - f.write(">gi|226789584|gb|GO546101.1|GO546101 Mdas9002M08_e148.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAAAAATAAAATACGGATCTCATTGAATCATGAATTTCTCAATC\n") - f.write("AACACCATCTTGAATCCGATAAAACACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAG\n") - f.write("AATTAAAGAAACAAATAGACAGAGGTCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGA\n") - f.write("CCCTTGGCTAAGAGCCACAATGGTACATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGA\n") - f.write("CGCCTGGAGGCTTGTAAGCGATGAAACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACG\n") - f.write("GATGAAGGATTGGGGGTAGGCCTTCTTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCAT\n") - f.write("CCGAACATGGGCAGCTTCCACATTGTCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCAC\n") - f.write("GGTACACGAATCCATGCTCCAACTCAAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAAC\n") - f.write("TTCCTTGGCCAAGGACTCGGTAGAAAGGGGAGGAAGGTAAGAGAGGGTCTCGAACT\n") - f.write("\n") - f.write(">gi|226789583|gb|GO546100.1|GO546100 Mdas9002D09_e107.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTTAAGATGACAAACATCCCTCCATCCGCTTTATTAACAAAACTC\n") - f.write("ACATAAGTCCCAAACCGCATCAAATATCCACTATAACCATCACT\n") - f.write("\n") - f.write(">gi|226789582|gb|GO546099.1|GO546099 Mdas9002M17_e150.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P34105|MAOX_POPTR NADP-DEPENDENT MALIC ENZYME (NADP-ME) emb|CAA39690.1| malic enzyme [Populus balsamifera subsp. trichocarpa], mRNA sequence\n") - f.write("TTGATCTGCAGGAACAAATACAATTAGCATATTTATTCGAATTTTACAAACCCTTGTGATTTACACGCAT\n") - f.write("CATCTTTCACGAATTTTACAAGCACTGATACAGCACATCTTCAGAAACACACATTCTTGATAACTAGCCT\n") - f.write("CGAAGCGAAGCATAACACACAACAAACAACGGAGCCAGACACTGTTTAGCGGTAGTTTCTGTAGACGGGA\n") - f.write("CTGTACATGCAACTCTCGGCATGCTTCACAAGATTCTCAGGACGAGGGAGACGCGTAGCCACGCCTAGGT\n") - f.write("CATATGCCTTGGCAGCTACATTAGCAGCTACTTGGGCAGAAATCTTTCTGATGTTTGACAATGGTGGATA\n") - f.write("GATCAGCCCCTGTGCAAAATTCTCCTCGGAAACTTGCCCCGCCAAGGCTTCCGAGGCTGCCAGAAGCATG\n") - f.write("TCATCGTGAACACGGATTGCTCCAGAGATAACCAAACCCAGACCAAATCCAGGAAAAATGTATGCATTGT\n") - f.write("TGGACTGGCCAGGAACAAAAACTTTGCCCTTGTACTCAAAAGGATCAAATGGACTTCCGCTGGGCAAAAT\n") - f.write("TGCACGACCCTCACTGTAAGTATA\n") - f.write("\n") - f.write(">gi|226789581|gb|GO545848.1|GO545848 Mdas9006P17_e484.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTTCTGGCGTTTCGGTTGTGTGGATTATACAACGAAACACTTACAAGGGTTTAT\n") - f.write("ATTACAACAAATGGGAACAATTAATGAAGGAAACAAATAAAATTGCAATCCGAAAAACCAAGCTAAGCTC\n") - f.write("GACAGAGACACCTAATTTCAAAGGAGGCCAAAAAAGATTGACAGAAACGATACTTTCTCTACCTTAAGCT\n") - f.write("TTCAAAAAACACCCTCAGGAATCGATTATTTACTCTTAAACAATAAATTCATCGATAGCCCTATCGAGGA\n") - f.write("AGGCTTGAACGCCTGGATGAACTTCCAAGGTGGAGCCATCAAGGGGTCTTCTCTATTTGTTTTCTTC\n") - f.write("\n") - f.write(">gi|226789580|gb|GO545847.1|GO545847 Mdas9005P08_e396.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAATTCATATTCACACATGTAACCACTAATCCACCATTAACTTCCGAAACTGATTTAATTGTTCATGAA\n") - f.write("ATATTACTGCAACGTAAAAGGATCCAGGTTACAATTCCTCGCACGAAAAAAGTAACTACATGAAAAAGTT\n") - f.write("TCACCTATAAAACCATATTGCGGTCTTCACCATCATCACTTGGATCAACCTCGTAATCCAAGTCATGGCC\n") - f.write("GTCATTGTTTTCATCATACTTATCATCTTCAAGAAAGTCATTTTCTTCTAAATCCTCGG\n") - f.write("\n") - f.write(">gi|226789579|gb|GO545846.1|GO545846 Mdas9006A17_e402.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAAAAGAAACCGTCAGTACAGTACGTCTAGCTCAAATCAAATATATGGACCTAGCAACCAAGTTGGGAA\n") - f.write("CAAATTTATGCACTATCAAATGAGACTAGCTGCAAATGTCTCATGGCTATTGCAAGTCCGATCACCCCAC\n") - f.write("AAGCTCAAAGGGTCCCCGATACAATAAAAATC\n") - f.write("\n") - f.write(">gi|226789578|gb|GO545845.1|GO545845 Mdas9006P08_e482.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("AAAATTCATATTCACACATGTAACCCCTAATCCACCATTAACTTCCGACACTGATTTAATTGTTCATGAA\n") - f.write("ATATTACTGCAACGTAAAAAGATCCAAGTTAGAATTCCTCGCCCGAACAAAGTAGCTACATGAAAAAGGG\n") - f.write("TGACCTATAAAACCCTATTGCGGTCTTCACCATCATCACTTGGATCAACATCGTAACCCTTTTCATGGGC\n") - f.write("GTCATTGTTTTCATCATAC\n") - f.write("\n") - f.write(">gi|226789577|gb|GO545844.1|GO545844 Mdas9006N01_e465.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTCTGATGTGTATGTTACACAATGATATTTGGAGGGAACGTTGATGGATTTTACAATCTTGATGAAT\n") - f.write("CTGACAGCGTTTCTTACCAAAGGCAAAACTCCGGTGACCACTTAAACACTCAAAACCTCGTGAAGAATTT\n") - f.write("ACATTGAGGACCAACAAGCCAAGGAATCATAGAGTCGGAGGAAAACTTCCCATTGTCTTACATTTATGGT\n") - f.write("CACGTGCTATTCACATGGATCAAATGTTCGACACTCGTCCCATGGTGCATGAAAGTCAAGGGCTACAGGT\n") - f.write("AGAGATAGGACAAGAGGATAAATAAAGCTGCTGAGGCAGTGAGTGAGTGTAGAGTGGGGAGAGGTACTGC\n") - f.write("CCTAGGTGAGTCTCCCATGGCCAAACCGGCTAACCATGACCCATCTGCCAGCATTGCTTCACCAGCCCCC\n") - f.write("GTGCCGGAACCTGCCCCAGTACCCGTACCCGCACCCGTACCAGAACCAGACACTGCACCGCCTAAGCCGG\n") - f.write("CACCGGAATTCCAATAAGTAAACCCGGGATCCGACCCGGCGGTAG\n") - f.write("\n") - f.write(">gi|226789576|gb|GO545843.1|GO545843 Mdas9003I17_e213.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T45666 hypothetical protein F14P22.50 - Arabidopsis thaliana emb|CAB68184.1| putative protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTTTTGTAAACCATATCAGTGCTTTCATTTAAACAAGATGTTAGTGTGTGCAGTCAT\n") - f.write("ATCCCATATCCAGAATCTTTTGTCACCGAATCAAATATTCACCGCAAACAATATACAATATGCAGACATG\n") - f.write("AAACTTTACATAAACGCGATACCATATCTTTGGGAAGTCAGAGTTCGTTTGCTTGCTTGCATTTAGCCCT\n") - f.write("GTTGGCTCAGAATCTCCACTGCCACATTAAGATCCCCATCTGCAGCTGCTAGGGCAACTTCTACCTGTGT\n") - f.write("CCTCTCAAAACCCATTGATACAAGCTTTTGGATTTCTTCTTCAGATGCAACATAATCCTGATGGTGTACA\n") - f.write("GGAATTTCTGCCGCTGCATTATTTAGTGTTGCCTGCCTTCCATCAGATAAATTCTGTCCTGTACCAATAA\n") - f.write("CTGCCACATCTGATGGACGTTCTGAGTTGCTATTGTCCAAGAGTCTAGCCTGTAAGTTTGATTCTGAATC\n") - f.write("AGCATCAGAAATAGTACCTCGACCAGATCCAAGTGTTCTTCCTCTCCCAGGAAACATGTGACCATCTTGT\n") - f.write("GCTGACTGTACAG\n") - f.write("\n") - f.write(">gi|226789575|gb|GO545842.1|GO545842 Mdas9004H21_e286.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTAATATTAAACCATAATATACATAATATATTTCATTAATTACACAAAATGAAGAAATCAAATTA\n") - f.write("GTTAACCCAAAGTATTAACTAATCGTAAATTCCTCCGAAAAAACTAATTAAAATTACTAATACAAAAAAA\n") - f.write("TTCAAAACTTAAGAGAAATTAATTAATTTTCAATTACTTGATCGCTCAAAATGGATGCAAATTCCTGCTA\n") - f.write("ATCCCATTCACATTAGAGAAAAACCCCACAAAGTCCTGCCTGTACGGCAGGAACGACCGTCGTTTATCCC\n") - f.write("CTGCCTCCTCGGCCTTGCTCCTCACGACAAAACGCTCTCTATTCTCCGACACGCCGCCGCCGCCGCCGCC\n") - f.write("GTTGTCGACTCTTTTCCTCGTGACGTCATCTCCCTTGTTGTTGTTAGCTCTCTTGGTCGACGAGGGAGCT\n") - f.write("AAAAAGACGATGCCGTCGCTGCTGCTCCGGTGAAGAAGGTTCCAAAATTTCCACCGCTTCGACGACGAGC\n") - f.write("CTGCGGAGCTGCTCTTATTGCAGCGGCGCTGTCCAGGCGACGATTTCGGAGGGGCCCACTCGCAGTACGT\n") - f.write("GCCAGGTGGCAGGTTCTCGAGGTCGTCGGCCTCGGAGGACGA\n") - f.write("\n") - f.write(">gi|226789574|gb|GO545841.1|GO545841 Mdas9003G07_e202.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P46486|PSAF_FLATR Photosystem I reaction centre subunit III, chloroplast precursor (Light-harvesting complex I 17 kDa protein) (PSI-F) pir|S31165 photosystem I chain III precursor - Flaveria trinervia gb|AAA33344.1| photosystem I subunit III g, mRNA sequence\n") - f.write("TTTTTTTTCTTGTTTAACACATGCATTTGGTACCTTAATTCCTAGTAATTTTACAAATTATACGATGAAT\n") - f.write("TTAAAAACATATAATAAAAAGAAGCTCAAACGTCCTTGGCAACAAGTTCACCATTCACTATCTCTCTGTA\n") - f.write("AGCAGCCTTAGGCCAGCTGAAGCCTCTGAAAACCTAGCTAGTAGCCAAAGGCACATCAATGATGATCTCC\n") - f.write("TTCTGTGTCGGCTTCTTATCATCCCTAGTGGCAATCAAGTAGCTCCTCCCAACCCGCCCGATCCACCCAG\n") - f.write("CAATGTACAGGAACTAAATACCACGCGTGATAAACTCTCCCCATTGCCTCTGGTCACCGCTGACAATCCT\n") - f.write("ATGGGGGAGCCCATCCGACCCACAAAGTAAACCCTGCTTGCCATAGTTGGAAAACCTCCTCTGAGTCTTC\n") - f.write("TCTATGGTGGCCTTGATGGCTATCGCGGGTGCACTGTCGGGTGGATAGAGCTTCAGTGAGGACTCGAGTT\n") - f.write("TTTTTTTCTGCTGCTT\n") - f.write("\n") - f.write(">gi|226789573|gb|GO546098.1|GO546098 Mdas9002F02_e115.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAB03604.1| putative glycoprotein [Oryza sativa (japonica cultivar-group)] dbj|BAB44013.1| putative glycoprotein [Oryza sativa (japonica cultivar-group)], mRNA sequence\n") - f.write("AAAAAGGAGAAATTTCATAGTCAACTAGTGCAAATTACAACACAGTTCAAACAAGAAGAACAAGATGACC\n") - f.write("TATCTTATATAGATCGACAGCGAATCCTAAGTAGTTCAAATGAACAGAATCTAAACGGAATGCTACGATA\n") - f.write("ATTCATGAGATAAATATGAGATTTTAACTCCCTCAAGCCCGCATGGGTGGAATGGAATCCAGGAGCCAAT\n") - f.write("CGCTTCTACAGGAATGGAGGTAGGATCACCCATCGGCGCGGATACTTGGGTCTTCCGTCTTTCCCATCAA\n") - f.write("ATATCTTCTTAAGACGTCGGTGCTTTGTAAGCGCCCAATTGGTCATGATGGAAGCAGCAACTATGAGAAA\n") - f.write("GATAAAACCAGCGACTGTCTGCGTTGCTATATTGAAGCCCAACCATTGATAG\n") - f.write("\n") - f.write(">gi|226789572|gb|GO546097.1|GO546097 Mdas9002G16_e121.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P29063|PR4B_TOBAC Pathogenesis-related protein PR-4B precursor emb|CAA42821.1| PR-4b protein [Nicotiana tabacum], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTTTTTAGCTAATGGTGCAGTTATACATTTATCATAAGATTGAAGTGCT\n") - f.write("TATACAATCTATATAATATAATACTTCTTGTTATAATTCAAGAAGCAATTCCACTTCAATTTATTCCATG\n") - f.write("GTGAAGCTTATTTATTAGTAATACATAGTTAAGTTCCCTACCAATACTGGAAGTAAAGAACTATATAGCT\n") - f.write("ATTGAAAAAATTAAGGTTTATAGGCTTTAGTCGCCGCAGTCGACAAAGTCGTAATTGACGATAAGGTGGC\n") - f.write("CTTGTTGGTAACCAATGCCGTCGGTGTCAATTTGGTTAAAAACATTCACGTCCAAGTCCAATCCTCCGTT\n") - f.write("GCTGCACTGATCAACAATTCTCACCGTTGCTTGAGCTCCAGTCCGAGTGTTTGTCACCAAGAGGCACCTT\n") - f.write("CCGCATGCGGCTTGCCCAGTAGGGCCAGCAGGTCCGCAAAAGGCAGTCCATCCATATTTGCTGCGCCATT\n") - f.write("CGAGGGATTTATCGGCATCCCATGTTGCGCAGTAGGCACTTACTGCCCGCAAGTCGTAATTGTTTTGCTG\n") - f.write("TGGATTGTAGA\n") - f.write("\n") - f.write(">gi|226789571|gb|GO546096.1|GO546096 Mdas9002M04_e146.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|F86214 protein T6D22.2 [imported] - Arabidopsis thaliana gb|AAF79822.1|AC026875_2 T6D22.2 [Arabidopsis thaliana], mRNA sequence\n") - f.write("CTGAAGTCGGTCGCGAGATCTTCTTACGCTCCTCCATTTTCTTGAGATAATTTGCTGAAATTCCATCATG\n") - f.write("GGTAAGGAAAAATTTCACATCAACATTGTGGTCATTGGACATGTCGACTCTGGGAAGTCGACCACCACTG\n") - f.write("GTCACTTGATCTACAAGCTTGGAGGAATTGACAAGCGTGTCATCGAGAGGTTCGAGAAGGAAGCTGCCGA\n") - f.write("GATGAACAAGAGGTCATTCAAGTATGCCTGGGTGTTGGACAAGCTCAAGGCTGAGCGTGAGCGTGGTATT\n") - f.write("ACCATTGATATTGCCTTGTGTAAGTTTGAGACCACCAAGTACTACTGCACTGTTATTGATGCTCCCGGAC\n") - f.write("ATCGTGATTTCATTAAGAACATGATTACTGGTACCTCCCAGGCTGATTGTGCTGTCCTCATTATTGACTC\n") - f.write("CACCACTGGTGGTTTTGAAGCCGGTATTTCCAAGGATGGTCAGACTCGTGAGCATGCTTTGCTTGCTTTC\n") - f.write("ACTCTTGGTGTCAAGCAGATGATTTGCTGCTGCAACAAAATGGATGCCACCACTCCCAAGTACTCAAAAG\n") - f.write("CAAGGGAAGATGAA\n") - f.write("\n") - f.write(">gi|226789570|gb|GO546095.1|GO546095 Mdas9001P20_e87.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA86284.1| geranylgeranyl pyrophosphate synthase [Croton sublyratus], mRNA sequence\n") - f.write("ATTTGACCCATCTCTGTGTCGACTCTTATCCAGTTCTCCAACACAAACATGCGGATCAGACATTCTAAAT\n") - f.write("TCCCACGAACAAACATTAAATTCTACGGTACAACAAAAGGGTGTCTTTAGTTTTGCCTGTAAGCAATGTA\n") - f.write("GTTCGCCAGAGCAATCAAAGGGGCAGCCTTTTCGGGATCGAAACCGGCGAGCTGTTCCTTGGCGTCTTTG\n") - f.write("TTCAGTTTCTCTGCAAACTCTCTCGACTTCTCGATCCCCAACAGCTTCGGATAAGTCACCTTATCCGCCA\n") - f.write("CCAAGTCCTTCCCTGCCGTTTTCCCCAATTCCTGGGAAGATTTGGTCACGTCGAGGATGTCATCGACGAC\n") - f.write("CTGAAACAACAATCCAATGTACCGAGCGAAAGTCCTCAGCTTTTCGATTTCGGAATCCGACCCACCTCCC\n") - f.write("AGAACCGACCCCAGAACCACCGAGCACTCCAGCAGCGCC\n") - f.write("\n") - f.write(">gi|226789569|gb|GO546094.1|GO546094 Mdas9002I21_e133.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTATCATTCAACAATTTTATTAAAAAGAAAAATAAAAAGAAACAAAAACAATTTTTT\n") - f.write("AAGCTGACAATACTTAGCTGCCAATCAAACTATTGGCTTTTAACATACAAACTTATGGAGGCCAGCATGT\n") - f.write("TCTGTTTTACAAGTTACAACTGGCATCTAGCAACATCTCAACTTAACCATGTGACCGGCTTGAATTACGT\n") - f.write("CCATCAGTGACCGTTGGCAACCACACCGTTGGCATTGGT\n") - f.write("\n") - f.write(">gi|226789568|gb|GO546093.1|GO546093 Mdas9002K12_e141.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S00443 chlorophyll a/b-binding protein type I precursor (cab-6A) - tomato gb|AAA34140.1| chlorophyll a/b-binding protein prf|1402358A photosystem I protein CAB, mRNA sequence\n") - f.write("TTTTTTTTTGATAAGAAGTTCGGATTCATCGAAGATGGTTACATGGAATTCTAAACTTTACAGTGGGTGT\n") - f.write("GAAATCAATACTGCATGAATTAATCAAGGCAAAATCCCTTTGGGGATGATGACATCCCCAATGTTGTTGT\n") - f.write("GCCATGGATCAGCCAAGTGAGTAGCCAAGTTCTCCAACGGTCCGGTGCCAGGGTACGCCGATTGTTGAAC\n") - f.write("AACAAACCCGACGAAAGCCAACAACGCAAGCCGGCCATTTTTGACCTCTTTGACTTTGTATTCCTCGAAC\n") - f.write("TTCTTGGGGTCCTTGGAGTAGCCCAAGGGGTCAAAAGCGCCACCAGGGTACTTCTTCTTCTCAGGGTCCT\n") - f.write("TCTCCATGCTGCGTTGGTGTTCTACAAAGGCAATGGAAAGGAATTCGATGACCAAAATTGTAGGCAAAGT\n") - f.write("GCCCCATGGAACT\n") - f.write("\n") - f.write(">gi|226789567|gb|GO546092.1|GO546092 Mdas9002J23_e139.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAD36199.1| NLS-TIR-NBS disease resistance protein [Populus tremula], mRNA sequence\n") - f.write("AAAAAGTGTACTTGAATATATTTCTATGTTTCCATCCAAAATGCACTAGTAATTAACTATACTGATGACA\n") - f.write("TTATTCCAGGAAACTAATTATATAAATACACCGTAAGGGGAAGAAATGTACGTACTCTCCTTCGTTGACA\n") - f.write("GGATGTCCTGACAAATTTGCTGCTTCTCTAAGAGCACTCCTCCATGCGAGGATCTTCTCCTTATTGTCCT\n") - f.write("CGAATTTGCACTCAAGTTTTTTGAACTCGTCACCGAAACTACTCGTTTGACTTCGTACATGGGACGGATC\n") - f.write("CACCTTGTAAAAAACTGGCAAAACTATTTGTTGCTTTGATTGTCTACATTGAAGAATCTTGACGAGCTCG\n") - f.write("TCCAAGCACCACCTTGAAGCTCCATAGGTTTTAGAGAATATGACGAGAGAAATTCTTGACTCTTCAATTG\n") - f.write("CTTGGAGGAGCGCTGGTGATATTTCTTCTCCTCTTACAAGTTGGCGATCAATGAAGGTGTGGATTCCCTT\n") - f.write("GTCGACCAAGGCCTTGTATAAATGATCTGTAAAAGTGGTGCGTGTATCC\n") - f.write("\n") - f.write(">gi|226789566|gb|GO545840.1|GO545840 Mdas9004B03_e255.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTATAGCAGCAAAAATGACATTACCTATTTAGTACATATGGAAAGATTACATTGTTCA\n") - f.write("CAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGC\n") - f.write("CAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGC\n") - f.write("CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACG\n") - f.write("AGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCC\n") - f.write("AAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGCGAGCGGGCCTTGGTTCCAAAAAGAGGGG\n") - f.write("CGATGCCCCGCCTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCAATTTCGCCGC\n") - f.write("GAGGCTCCCACTTATACTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGGT\n") - f.write("CTTCTTTCCCCGCTGATTCTGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACA\n") - f.write("GTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAGATGACGAGG\n") - f.write("\n") - f.write(">gi|226789565|gb|GO545839.1|GO545839 Mdas9003K15_e218.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("CCATTGATGCAGTTTTTAAAGCTTGAGTTTACATACAAGCAGGTAGCTTAAAGATCATCTATTGTACACA\n") - f.write("CTGATTAGGTTTCCTCACTTCCCGGGCACGAAGTTGGTGGCATAAGCCCAGGCATTGTTGGTAACAGGAT\n") - f.write("CAGCCAGATGATCGGCAAGGTTCTCGATAGGGCCCTTTCCAGTGACAATGGCCTGCACAAAGAAGCCGAA\n") - f.write("CATTGAGAACATGGCAAGTCTTCCATTCTTGAGTTCTTTGACCTTAAGCTCTGCAAATGCCTCTGGGTCA\n") - f.write("TCTGCAAGTCCCAAAGGATCAAAGCTGCCTCCGGGGTACAGTGGGTCAGTGATCTCACCAAGGGGTCCTC\n") - f.write("CGGCAATGCGGTAACCCTCAACAGCACCCATGAGGACCACCTGGGTTGCCCAGATTGCTAGAATGCTCTG\n") - f.write("TGCATGAACCAGGCTTGGGTTTCCAAGGTAGTCAAGGCCACCTTCGCTGAAGATTTGAGCTCCGGCTTTG\n") - f.write("AACCACACTGCTTCACCAAACTTGACTCCGTTCCTGGAGAGGAGCTCCGGGAAAACACAGCCCAAAGCAC\n") - f.write("CAAGCATTGCCCATCTTGAGTGAATGACTTCAAGTTCACGGTTCTTGGCAAAGGTTTCGGGGTCTGCTGA\n") - f.write("TAGCCCAGCAGTGTCCCACCCGTAG\n") - f.write("\n") - f.write(">gi|226789564|gb|GO545838.1|GO545838 Mdas9003M10_e229.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|P36491|PSBA_POPDE Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) pir|S42492 photosystem II protein D1 precursor - cottonwood emb|CAA55040.1| D1 protein [Populus deltoides], mRNA sequence\n") - f.write("TGCAGCTATAGGTTTGCACTTTTACCCTATATGGGAAGCGGCTTCCGTTGATGAATGGTTATACAATGGT\n") - f.write("GGTCCTTATGAGCTAATTGTTCTACACTTCTTACTTGGTGTAGCTTGCTACATGGGTCGTGAGTGGGAAC\n") - f.write("TTAGTTTCCGTCTGGGTATGCGCCCTTGGATTGCTGTTGCATATTCAGCTCCTGTTGCAGCTGCTACTGC\n") - f.write("TGTTTTCTTGATATATCCAATTGGTCAAGGAAGCTTTTCTGACGGTATGCCTCTAGGAATCTCCGGTACT\n") - f.write("TTCAATTTCATGATTGTATTCCAAGCTGAGCACAACATCCTTATGCACCCATTTCACATGTTAGGCGTAG\n") - f.write("CTGGTGTATTCGGTGGCTCCCTATTCAGTGCTATGCATGGGTCTTTGGTAACCTCTAGTTTGATCAGGGA\n") - f.write("AACCACAGAAAATGAATCTGCTAATGAAGGTTACAGATTCGGTCAAGAGGAAGAAACCTACAATATCGTA\n") - f.write("GCCGCTCATGGTTATTTTGGCCGATTGATCTTCCAATATGCTAGTTTCAACAATTCTCGTTCTTTACACT\n") - f.write("TCTTCCTAGCTGCTTGGCCTGTAGAAGGTATCTGGTTCACCGCTTTACGTATCAGCACTATG\n") - f.write("\n") - f.write(">gi|226789563|gb|GO545837.1|GO545837 Mdas9004I08_e288.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_563649.1| expressed protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTTTCTTTTTGCAAAGTCATGCTAGATATTACATAAAAAAAAGGCAATGCTTTAGCGAAACTATGA\n") - f.write("GTTTTCGCCACATAAACTGCAATGGATGCCGTATTTTAATTAGTACATTACCTAATGAGTGCACAAGCTA\n") - f.write("CTCGACTCCTTTTTATTACCTAAATTTTCCATCTTGGCATTTTATCTCCTCATGACGCGGTGACGCTCTC\n") - f.write("GTTTGCGGAAGCGCTCGAGCATGAACTGATCTGTTGCAGCTTGCCTCTGCCCTGCTGCTTCTGTGCCAGT\n") - f.write("ATCATTTTGTCTGGAAACACCACCATCATCCTGTGAACTTTTGTCCTTGTACAGCTCGGGATGTTCTCGT\n") - f.write("CTAAGCTTCTCAACATAATCCCTGCCACGCTGGAAATAGTCAGCACTGTAACTTGAAGGGATGCTAAATT\n") - f.write("CTGATTTTGTCCGCCCAGTGAGCCGCTTCTCCTGCAAAAACTTCTTGGCAGCCTCAGTTTCCTCAATATT\n") - f.write("TCTCAGCTTATATTCAATGGGAAGCTGAACCTCGGCAATCCCAGTAGTCCATTGAGTGGAGCTTTCTTCT\n") - f.write("GAGTTCCGCCTTTTCACTTTAAGATGGTCAGGTATTTTGTACAACTCATCTTCAGCACGCTTTAAATCAT\n") - f.write("TTTCAACTTGATCTGAAGTATCAATTTTTTTGCCCCTCT\n") - f.write("\n") - f.write(">gi|226789562|gb|GO545836.1|GO545836 Mdas9004A20_e253.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAL26889.1|AF317062_1 abscisic stress ripening-like protein [Prunus persica], mRNA sequence\n") - f.write("CACCGAGTAAACAGTATTATTATGAACAATAACAATGACATACATACATACATACATACATAGATGGCAT\n") - f.write("GCTAAAAAAAAACCAAATAGCACCCATTAATTGAAAAGGACATTTAACCACTCAACTATTGTAGCGATAT\n") - f.write("TGTTGAAATTAAGCATCACACTCTCACTGATCACACCACATGATAACTAGTAAAAACACAACATTGCATA\n") - f.write("TGTAGTCAAAAAATGATGTTCCACAATCCACATAAATCTAAAAGTGGTGGTGCTTCTTCTTTCCATAAGC\n") - f.write("CTCTTCCTCTTCTTCCTTTGTCTCTTTCTTCTCATGATGCTCATGGAAGGCAAATCCACCCGAACCAACT\n") - f.write("GCAGCTGCTGCAGCAATCTCCTCTTCTATCTTGTGCCTGTGGGCATGCTCTGGGTCTTTCTTTTCATTGT\n") - f.write("GCTTCTCATGCAAGGCAAAAGCGCCGGCAGCAGCT\n") - f.write("\n") - f.write(">gi|226789561|gb|GO545835.1|GO545835 Mdas9003P12_e244.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to emb|CAC38395.1| ferredoxin I [Solanum tuberosum], mRNA sequence\n") - f.write("GCCAAGGCTTTCACTCCCACTCTCTTTAGCCACAACACAAAAAAGCCTTGCAACCAAAGCAAACCAACAA\n") - f.write("ACATGGCAGCCACAGCTCTCTCAGGCACCATGGTCAGCACCTCCTTCATCCGCGGCCAGCCGATGACCAG\n") - f.write("CCTGCGGTTATCCCCCAACGTCGGTCAGGCCCTTTTCGGGCTCAAGGCCAACCGCGGAGGGCGTGTGGCG\n") - f.write("ATGGCTGCCTACAAGGTGAAGCTGCTCACACCACAAGGGCCACAAGAGTTTGAGTGCCCCGACGACGTGT\n") - f.write("ACATTCTCGACGCGGCGGAGGAGGCCGGGATTGACCTTCCCTACTCATGCAGGGCAGGGTCTTGCTCCTC\n") - f.write("GTGCGCCGGCAAAGTTGTGAGTGGGGGTGTGGATCAGTCGGACCAGAGCTTTTTGGATGATGAGCAGGAT\n") - f.write("GGACGGTGGATTTGTGCTCACTTGTGTGGCTTATCCGTCGTCTGACGTCACACTTGAGACCCACAAGGAA\n") - f.write("GAGGAGCTTACTGGTTAAGTGCTTTTGAGCTTTCTCATGATGACGTCATGTTTTGATGGCTGCTGGCTGG\n") - f.write("TTGGATCTGCCTTAAGTTTGTTTCAGGATAATGTTGTCTTGTTTCTAATTATATGAGTTGCTTAATGTTT\n") - f.write("GTGTACTCTCATTTGTGGTATGGAGATCATTGTATCTTGTAAACTCGCCCTTGTATGAATCT\n") - f.write("\n") - f.write(">gi|226789560|gb|GO545834.1|GO545834 Mdas9004I02_e287.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pdb|1CBG| Cyanogenic Beta-Glucosidase Mol_id: 1; Molecule: Cyanogenic Beta-Glucosidase; Chain: Null; Ec: 3.2.1.21, mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTATATAGTTGGCATATTTATTTCACGAAAAAGGAAGAACATTCATAAA\n") - f.write("GGAATACAATTATGAAAATAGGGAAATGATATGCTTGGCATATTTATTTCACGAACAACAACCGCAGCAG\n") - f.write("GATATCTTCACCATTATCCAAGGAAACATTTGAACCAGCTTGCTGAGAGTTTTGGGTGCCTCTTAAGTCC\n") - f.write("ATCATTGTAATCTATATAGACAAAACCAAATCGTAAGGTGTATCCAGAAGCCCATTCAAAATTGTCCAGC\n") - f.write("AATGACCATGCAAAGTATCCCTTCACATTTACACCATCATTGATTGCTTTTCGAAGATAGTCGAGGTGGT\n") - f.write("GGTAGTGGTAATCAATTCTGTGGGTATCATTGAGGGATTGCGGAAGTGACAATGTGGGATCATCGAACTC\n") - f.write("GTCAAGGCCGTTCTCAGCTAGGTCCAATGGCTTTTGCTGAGAAGATGGTACTGGCTTTGTTTTCGATGCT\n") - f.write("GATTGTTTTGTGGATGACAAGAAGCATAACGGAGGATATTCCGGGCTGGGGAGTCCTCTTCAACGGGCGT\n") - f.write("GCCGGAGATGGAACTGTCAGTGTTATGGTTGCAACATTTTTGTTCATATTTCCAAGCAAAAAGGAAAAGG\n") - f.write("GTGAGAAGTTGATGGACTGGGAAAAATGCAAGAAGCTACCCTGGA\n") - f.write("\n") - f.write(">gi|226789559|gb|GO546091.1|GO546091 Mdas9002H01_e125.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_179106.1| expressed protein [Arabidopsis thaliana] pir|A84524 hypothetical protein At2g15020 [imported] - Arabidopsis thaliana gb|AAD03359.1| hypothetical protein [Arabidopsis thaliana] gb|AAL91197.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("CAAAAAGACTATCTGGGTTTCTGACATGTGTTCACTCTCCTCGGACAAACCCTACCTCGCTCTCTTACTC\n") - f.write("CAACTTCTCCAAGAAATTATAGCCCGTTCGCCCACCGCGCACGGTAGCGGCACCTGCCCGCGCTCCCAGC\n") - f.write("TTCAGGCCCTCAAACCCGACCCATTTTCTTGGATCATGGACTCCCACTCCCCCGAGTCCTTCTCCACGTT\n") - f.write("CTTCGACCTGGTTTTCATCACGCGCCTCTTCTGGCTCTGCGCGTGCGACTCTCCATCCGAAGTCGGCTCT\n") - f.write("CTGTACTTCAAGTCGCTGCTGGCTCCTAACCTCGAGGCGTTGTTGTGCAAGCACGCGCCGGCCCTGCGGA\n") - f.write("CGTTTCTGATCACCGCGGGTGTGGATGCGGAGCTGTGCTTCATGCGCACCCTCGGGTACATGTTAGCCAA\n") - f.write("ATGGTGCATTTTGAGAGATGTGGGCGTAGGTCTACAGACGCTGACGTCATCTCCCTCTCAGAACTTGGGT\n") - f.write("TTCTCTTACGC\n") - f.write("\n") - f.write(">gi|226789558|gb|GO546090.1|GO546090 Mdas9002E04_e111.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T06431 ribosomal protein L27-5 - garden pea gb|AAA86952.1| ribosomal protein L27 homolog, mRNA sequence\n") - f.write("TTTTTTTTTAAAATCGCAGGAAAATAAAGCAAAATCCAGAAATACCCAAAATAATACAAAATCTAATCAT\n") - f.write("TTTAGCTAAACATTAGTCCACTAAATCCATAAAACCGTCTCATTTCATTTCAAAATTCAATGAAACTCGA\n") - f.write("AAAAACATAAACCCAAAATCAGACAGACCCATTTACGATGCGACGCCGTATGGAAAGGTCCTCAGAACCT\n") - f.write("GAGCTTGGTGAAGAACCACCTGTTCTTCCCGGTTTTGAACCGCTCCTCGAACCGCTTCTTGACCTCCTTC\n") - f.write("AATGCAGTGACCTTCTTGTCCTTTGTCTGCAAGCACTCGACGTTGACGACGTCCTTGAGATCCACATCCA\n") - f.write("GGGTGTAGCGCGTGGGCATCAGGTGCTGGTAGTTCACGAGCTTGATGAAGGCCTTCACTCTGGATTTCTT\n") - f.write("CGCCGTCTTCTTGGCGGAGTCCTTGCGGATGACCTTGCCTGGGTACTTCTTAATCCCCGCAACCAAACAG\n") - f.write("TGGCCATAGG\n") - f.write("\n") - f.write(">gi|226789557|gb|GO546089.1|GO546089 Mdas9002F22_e117.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566435.1| membrane protein common family [Arabidopsis thaliana] dbj|BAB02418.1| gb|AAD25612.1 gene_id:MBK21.12 strong similarity to unknown protein [Arabidopsis thaliana] gb|AAK76578.1| unknown protein [Arabidopsis thaliana] gb|AAK95295.1|A, mRNA sequence\n") - f.write("TTTTGACATAACTTTAGATGTATTCAATACTACTTCTGGAATTATACATGGACACGTTCATTCAGTCATT\n") - f.write("CTCTCGAAAGAGATTGCGAAAAAAATTAAAGAAAACTCCAAATGACAAAATTATTTTCAAAGTTATATGT\n") - f.write("ACTGCTCACACTGAAAACACTAATATACATATAATTAAAATCGGTCGTTGGGAAACGCTTAAGCCAGTCC\n") - f.write("GTCGACATCAGCAGTTCTACTCGCCTTAGTGACCTCCCGGATTTCTGTTCCACGACAAATACGATGGGTC\n") - f.write("TCCAAGTTGCCTTGGCTTAACAAGATACACAACAGTGAAAGCCATGGCCAGAAAGAAGCACAACCCTCCA\n") - f.write("ACAGTGAGATAAGCAATGCCAAGGAAGTCATTCCTGCCACCAATCCAACTGGTGGTCGAGAGCACAAGCT\n") - f.write("TCTTTTTTCCATTAAAACTGTATGTGTTGTAATTGTTCTCCAGTGTCACTTCTATCGTATCATTTTCTTT\n") - f.write("CAGATCTACCTCTATCTTCCCGTACAGCTTTCTAAATGTCGGTAGTGCAGCAGTTCTCATCCAAACAATA\n") - f.write("AGGTCCTCTTGCTCACTTAATGGTTTAGAGGTATCCAGAGACTTGCCACCTTTAAGAGTTCCATTCTGAA\n") - f.write("AGTTCTTTGGAAAGACATTTTTGCCAAATTTGTGCTCCCTATCA\n") - f.write("\n") - f.write(">gi|226789556|gb|GO546088.1|GO546088 Mdas9010A19_e718.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|S28827 chlorophyll a/b-binding protein type I - common tobacco emb|CAA45523.1| photosystem I light-harvesting chlorophyll a/b-binding protein [Nicotiana tabacum], mRNA sequence\n") - f.write("CAAACCCTTAATCTTGCAGGCACTAAATTTGCCAATGGCTTCCAACACTTTGATGAGCTGTGGCATCGCC\n") - f.write("ACTACTGCCTTCCCTTCAGTCCTCTCATCCTCCAAGTCTAAATTTGCGACCAGCGCAGTCCAGCTCCCAA\n") - f.write("GTATTGGTGCCAATGCCTCCTCCAGGTTCTCCATGTCCGCCGAGTGGATGCCCGGCGAGCCCCGCCCTCC\n") - f.write("TTACCTCGACGGCTCTGCCCCCGGTGACTTTGGATTTGACCCACTTCGGCTAGGAGAAGTGCCAGAGAAC\n") - f.write("TTAGAGAGGTTCAAGGAGTCCGAGCTCATTCACTGCAGATGGGCAATGCTTGCTGTTCCAGGGATTCTAG\n") - f.write("TACCAGAGGCTTTGGGATTGGGCAACTGGGTAAAAGCACAGGAGTGGGCTGCCGTTCCAGGAGGCCAAGC\n") - f.write("CACCTACTTAGGCAACCCAGTTCCATGGGGCACTTTGCCTACAATTTTGGTCATCGAATTCCTTTCCATT\n") - f.write("GCCTTTGTAGAACACCAACGCAGCATGGAGAA\n") - f.write("\n") - f.write(">gi|226789555|gb|GO546087.1|GO546087 Mdas9002P21_e167.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_172076.1| glycosyl hydrolase family 19 (chitinase) [Arabidopsis thaliana] pir|C86193 hypothetical protein [imported] - Arabidopsis thaliana gb|AAF29391.1|AC009999_11 Contains similarity to a basic endochitinase from Arabidopis thaliana gb|A, mRNA sequence\n") - f.write("TCAAATTGCATAAATGCAAATAATATTCAAAACTTGTAAACCACAAATCACAAAATTTGCACCAAATAAT\n") - f.write("AAAATGCAGGGCTTACTGCAACATCACACAAAGATAAACTTGAAACAAATCGAATAAAAACCTTAAAAAA\n") - f.write("ACAAAAAAAATGATGAAGGTTGAAAAGCCTTCTGCTCAGCGCAACTGAACACATCATGAGGGCCAGCGTC\n") - f.write("TTCACGGCCGACGCCGACTTTGTCAACGTAATACAGGTAATGGGAAATGATGTTGTTCATGGAGTCAACG\n") - f.write("TCACCTTGGCCACAGACTTGGTCCCCGTAAAGCACATTCATGGTGGTGCCAAAGCCAGGAACCCTTTTGG\n") - f.write("ACAAAGTGTCGTTCTTGGTTGGCTTCCA\n") - f.write("\n") - f.write(">gi|226789554|gb|GO545833.1|GO545833 Mdas9004H03_e280.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAA24493.1| chlorophyll a/b-binding protein [Fagus crenata], mRNA sequence\n") - f.write("TTTTTTAGTTCAAATTATTGTTGTCCAATACTTGGTACCAAATTTACATCACCGACAACAATACAAACGA\n") - f.write("AAGTACAAGACAACTCCTGAGCTCTCACTTTCCGGGAACAAAGTTTGTGGCGTAGTTCCAGGCATTGTTG\n") - f.write("GCGACTGGGTCAGCGAGGTGGTCGGCAAGGTTCTCCAATGGTCCCTTTCCGGTGACGATGGCCTGGACAA\n") - f.write("AGAATCCGAACATGGAGAACATGGCCAACCTTCCATTCTTGAGCTCCTTCACCTTGAGCTCGGCAAAGGC\n") - f.write("TTCTGGGTCGTCAGCAAGGCCCAAGGGGTCGAAGCTTCCGCCGGGGTAAAGGGGGTCGGTCACCTCTCCG\n") - f.write("AGGGGTCCGCCGGCAATTCTGTATCCCTCAACTGCTCCCATCAACACAACTTGGGTAGCCCAGATGGCCA\n") - f.write("AGATGCTCTGTGCATGGACCAAGCTAGGGTTTCCCAGGTAGTCGAGACCGCCCTCGCTGAAGGTCTGGGC\n") - f.write("TCCGGCCTTGAACCACACAGCCTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCGGGGAAAACGCAT\n") - f.write("CCAAGAGCTCCGAGCATGGCCCATCTGGAGTGGATCACTTCGAGCTCACGGTTCTTGGCGAAGGTCTCTG\n") - f.write("GGTCGGCTGAGAGTCCAGCGG\n") - f.write("\n") - f.write(">gi|226789553|gb|GO545832.1|GO545832 Mdas9004B13_e258.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAA33866.1| ribulose 1,5-bisphosphate carboxylase small subunit, mRNA sequence\n") - f.write("TTTAAAATAAAATACGGATCTCATTGAATTATGAATTTCTCAATCAACACCATCTTGAATCCGATAAAAC\n") - f.write("ACCAAATTCGAAAACAAACGAGAGTGCCTCGAAAAAGGGACAGAGAATTAAAGAAACAAATAGACAGAGG\n") - f.write("TCTTGAAAGCCCTAATCAAATACAAACTTAAACAGACCACCGGGACCCTTGGCTAAGAGCCACAATGGTA\n") - f.write("CATACAACAACAACATTATTTATGAAAATTGTAGAACAACTTAGACGCCTGGAGGCTTGTAAGCGATGAA\n") - f.write("ACTGATGCACTGCACTTGACGGACATTGTCGAATCCGATGATACGGATGAAGGATTGGGGGTAGGCCTTC\n") - f.write("TTGGCCTCTTCCAGCTCTTTCAACACCTGGGAAGAGTCGGTGCATCCGAACATGGGCAGCTTCCACATTG\n") - f.write("TCCAGTACCTTCCATCATAGTATCCTGGGGATCTGTGGTTCTCACGGTACACGAATCCATGCTCCAACTC\n") - f.write("AAATTCCAAGCAGGGAACCCAGTTTTTGCGGAGGAGGTAGTCAACTTCCTTGGCCAAGGACTCGGTAGAA\n") - f.write("AGGGGAGGAAGGTAAGAGAGG\n") - f.write("\n") - f.write(">gi|226789552|gb|GO545831.1|GO545831 Mdas9004A03_e250.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to dbj|BAC53656.1| 1-aminocyclopropene-1-carboxylate oxidase [Malus x domestica], mRNA sequence\n") - f.write("AATCTTGAAGTCATATTATATATAATAAAGTAGTGATCACATTGGTTACTTTCTACAACGATTTCCACAT\n") - f.write("TAATAGTAAATAAAACCTTGAAATCTAGTTCAAGGAAAAATTTCGTTCACACACCCATAATTACTTTTAA\n") - f.write("GCAAACAACCCTTTTTTCCAACAGCTTCTAGTAAAAGTATTTAATCACTCTCAAGCAGTACTTATAACTG\n") - f.write("GACCCAAACCAAAACTGGCCTTAATTTTCCACCGGCTTTCATGGCTTCAAATCTTGGTTCCTCGGCCTCG\n") - f.write("AACTTGACCCCAGCATAGAGCTTCATGTAGTCTTCGAACACGAATTTCGGGTACACTTGATTCTTCTCCT\n") - f.write("CTGCTTCTTTCTCCACTAGGGTTGGTGCTGGGTAGATCACCGCATCACTGCCTGGGTTGTAGAATGAAGC\n") - f.write("TATTGACATTCTGGTGCCATCTGTTTGGGCAATCACCCTGTGTTCCACACTCT\n") - f.write("\n") - f.write(">gi|226789551|gb|GO545830.1|GO545830 Mdas9003M05_e226.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTGAATACAAAAACTCTCATTTTATTTCAGATATAATTGAACCAAACTTGAGCATGT\n") - f.write("TCGCATGTCAAAATACACAAGACAGACCATAAAGTCTGAAGAATATATTAAATAGAAAGCCTAAAACGAC\n") - f.write("AGATTACAAAATAAATAACGGTCTTGAAACAACACAAATATATACTCCTGCAAGTGTAAGGGGTCTTTAG\n") - f.write("ATCCTAGATGGCCCCGACTGTTCCTGAAACTTTCGCTTCGGGAGAGAAGAAGCATAATCAAACCACAACC\n") - f.write("GGGTGACAAGCTAACAAATGAGAAGCGAAAATACAAAGCGCTACAAGATCTCCAAACGTCCTCATTGAAA\n") - f.write("GAATTCTGGACTAGTCGAGAACTTTTAGGGACTCGAACAGACCGCAACCTTTATTATGTATGCCGGTAAA\n") - f.write("GAAGAGATGCAACCTAGGCAGGCAGAGAATCAATAAACGAATTGCAGAGCTCATTGATGGCTAAATAGGC\n") - f.write("TGAAGAACTTCGACAAACAAGGATCTATGAACTCCTCAATTTAGCGGTGTCTCTGC\n") - f.write("\n") - f.write(">gi|226789550|gb|GO545829.1|GO545829 Mdas9003L20_e222.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TCGAGAAACAAATATTTTTCCAATTTGGAGATCATAAAGACGATGCCATTTTTGCCTATAAAGGTATCCA\n") - f.write("AGGAATATGCATTGGGAGGCACATGCATCAAATTTGGTGAGTCGTTTATCATCTGTGGAGCTTATGGTGG\n") - f.write("ATGGTGAACGGGTATGTTTAGCTAAAGGGCAAACTGAACAATAATTAATTTCAGAAAACTGAATGTCTTT\n") - f.write("TACATATGCTTGCATTAATCGGAAATGTTTATCGGAAAGGTGCCCAAGGCGTTCATGCCAAAGGCAGGAA\n") - f.write("ATAGCGGACTTGCTGACAAAATTGCAGATAGCCTCCATAGTAACAATGTTGAGATAGTAGAGTCATCCCC\n") - f.write("TTTCAGTTCTCGTCCCAATCATCATCCCCAAGCATTGGTCCTGTAACACAAATAGGTTTTTAGCAAAAAA\n") - f.write("GGCAATGTAGTCCGAGTGTTGGACAAGTTTAGCGACGGATATTAGATTCAATTGGAATGAAGGAACACAT\n") - f.write("AAGACATTACGAATGGTCAAATTGAGAGAGAATTTGACACTCCCTACGTGTGTAACAGTAGCACTCATGC\n") - f.write("CATTTGGTAATTGTATGGTTCGATTATGTATTAATGAGCACGTAATAAGTATGGCAGGAGAGTACACTAT\n") - f.write("ATGATCAGTTGCTCCTGTGTCAAGATCCCAGCTACGTCTTTCA\n") - f.write("\n") - f.write(">gi|226789549|gb|GO545828.1|GO545828 Mdas9003I08_e212.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to gb|AAK60319.1|AF385728_1 AT3g47831/T23J7 [Arabidopsis thaliana] gb|AAL77725.1| AT3g47831/T23J7 [Arabidopsis thaliana] dbj|BAC43208.1| unknown protein [Arabidopsis thaliana], mRNA sequence\n") - f.write("GAAAAGTTTATTTAGTAAATATTGAAAAACAATTACATATTCGAGCTATCGAAATCACGTAGAAATAAAA\n") - f.write("TGCGTCATCCGAAACACAAATATGTCCATAGCATTTGGAAGTAAAGCCAACTGATGGCTCTACTGGTTCA\n") - f.write("AAATCTAATTCGATTACTTAAAACGCGAAGGACAAAGACCAACACTGTAATTTTCATAGAGGAATAAGGT\n") - f.write("TACCGACTCACCTGATTGCCGTGAAAACTCAAAATTAAGGGGCTTGCTCAGCAGAAGCACCCTCTTTCTC\n") - f.write("GATTTTCGATTGAGCTTTGTGCCAGGCGAGGCCTTTGTAGACATTGGCGGAGAAAGTGGCGGTGAGGTAT\n") - f.write("AAAGTGGTGACGCCGAGCCCCGCTGTGAACGCCTTGAATGCCCAATCCCCTGCCTTGCTCACTATCCCCA\n") - f.write("TCTCTATCTCAATCTCTCTCTCTCTCTCTGCGAGTTTTTTTGGTATCGTCCCTCGTGCCGAA\n") - f.write("\n") - f.write(">gi|226789548|gb|GO545827.1|GO545827 Mdas9003H03_e207.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|O24059|MT3_MALDO Metallothionein-like protein type 3 pir|T17015 metallothionein-like protein AMT2 - apple tree gb|AAC23698.1| metallothionein-like protein [Malus x domestica], mRNA sequence\n") - f.write("AAGCGAAAACCCTAATTTAAACACATCTTCAGCTCCAAGTTCTTAAGTTTATCTTCAACATGTCGGGCAA\n") - f.write("GTGCGGCAACTGCGATTGTGCTGACAGCTCCCAGTGCGTGAAGAAGGGAAACGGCTACGACTTGGTGATC\n") - f.write("GTGGAGACTGAGAACCGCTCCATGGACACCGTCGTCGTGGACGCTCCTGCAGCCGAGAACGACGGAAAGT\n") - f.write("GCAAGTGTGGCACAACCTGCCCATGTGTGAACTGCACCTGTGGTCAGTAAGCCCAGATAACCAAATTAAA\n") - f.write("GATGTGATTAATAAAAGTGTCATATTAATTAAGGGATTATAGACCCTTAATTAATGAAAAGTGTTTGTGG\n") - f.write("GATAAAATAACGTTGTGGCTTTGTCTCTTGTTTGCTTATAGTATTTGAGTCTGTCGAGTGACATGTTGTA\n") - f.write("CGTCTGTGAAAACATGTCACTCATATGTTTGTGTTTCTGTGATTGTGTCATGTAATGGCCATGTTCATGG\n") - f.write("CCCTTTGATTTATATGCAAATATTAGAATAAAAAAAAAAAAAAAAAA\n") - f.write("\n") - f.write(">gi|226789547|gb|GO546086.1|GO546086 Mdas9002B15_e96.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q40163|PSBR_LYCES Photosystem II 10 kDa polypeptide, chloroplast precursor emb|CAA65231.1| PSII polypeptide [Lycopersicon esculentum], mRNA sequence\n") - f.write("TTTTTTTTTGACAGTGGAAGGGCAACTTGCCCATTATTTAATTATTTGAGTGGACATTCACTGTTCTACA\n") - f.write("ACACATCACAATATATACAGGCATCAAACTGGATCCATGCCAAAACATTACAATTAAGGTTTGCACAGAG\n") - f.write("TATTTCTTTAATGTTCTTGTTTAGGGCAGCTAGTTGGGACAGGCTATAGTTATTAACAACACATAAATTA\n") - f.write("CAACCAAAGATGAATAATTAATAATTTTACTGTGACAAAGCACTTGTGTTGTAGACAAGAAGAGCACCCC\n") - f.write("CTGCAAGAATGCCAACTAGGGTAACTGCCCAGATGGACAAGCCAGTAACACCCCCAGCATAGACATCACC\n") - f.write("ACTTGGAGACCAGTCATCTTTGTTGTAGATGGGGCTGTATCCA\n") - f.write("\n") - f.write(">gi|226789546|gb|GO546085.1|GO546085 Mdas9011C13_e821.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_566086.1| expressed protein [Arabidopsis thaliana] pir|T02683 hypothetical protein At2g46820 [imported] - Arabidopsis thaliana gb|AAC33500.1| expressed protein [Arabidopsis thaliana] gb|AAL38332.1| unknown protein [Arabidopsis thaliana] g, mRNA sequence\n") - f.write("TTTTACGTAAGTGTACTTTTATCATTTATTTCTATAATAAAATATCGGAAGCATCGCGATATGAATTACA\n") - f.write("AGGAGCTAACAGGAAAACAAATGACAGTAGTACTAGTTACATGTATCTCGCAGACAAAGTACATACATAA\n") - f.write("CATTAAGTATAACTTTGGTCAGAATATGCTTCTGCAAACAACATGAAGAATGTTCACTTCTTTTGCGGAC\n") - f.write("AATGCTGCGAGATATTTACGTATGTAGATAGAAGCTTCAAAAACCGGCCACGATTTCATCTCATCTCAGC\n") - f.write("AGCAATACTTTTCGGTTTGTTCTAGCTGCTGCCGATTATATCTTTGTATGTGCCCTTAATCTTCTGTGTC\n") - f.write("AAGGCTTCTCTGTCTGGTTTGAAAACAAGGTTCTTGTATGCAAACCACCCAGTGTAACCAATTCCTACAA\n") - f.write("GCTCAAGAACACCAGGGACTAAAGGAAGCCTATCAATTGCCGAGATCATTCCACTGAAGCCCCATACTGC\n") - f.write("AACAGCAACAGCTACTGCAAGTGAAGACACTGCATATTTATCTTCCACTTTCTCCCAAGCCCTCGTGCCG\n") - f.write("AA\n") - f.write("\n") - f.write(">gi|226789545|gb|GO546084.1|GO546084 Mdas9010K20_e773.b1 Apple_EST_Mdas Malus x domestica cDNA 3', mRNA sequence\n") - f.write("TTTTTTTTTTTTTTTAAAAGCGTATCATCCTTCCATTATTATTCTGTTCCCATCATTTCTTACATACGCA\n") - f.write("CTTGTCTTATTTCTGCTTTAAAAAAATGAAAATCAGAACGTTATTTCTCTGCTCGTAAGGGAAGTTGCTG\n") - f.write("GGTACTCTGCGACTTATTTAGGAGTAATGTCGACACCCTTGATAACAAGCCCTTTCTTCCATTTCCCAAC\n") - f.write("AGTTTGACGGAGCATAAAATACATCCGGCCAGATTGCCCAGGCGATGTTGTAAATTCGGCAACTCGGACA\n") - f.write("TAACTCCACCATCTTCCTTTTGTCCTCAGATCAAGTGTAGAGTTTCTCGGGACAATCTGCAGGTTCTGAG\n") - f.write("GGGGAGTGACGCTGAATTCGACTTTATCTTCCCATCCATATTTTGGGTCCTTCATCATGATTATATATGA\n") - f.write("AACTTCATACACAGTTCCGGGTGTCAGGTATGCGGTCTCAAAATCCCCTTTCACTTCTAGCGA\n") - f.write("\n") - f.write(">gi|226789544|gb|GO546083.1|GO546083 Mdas9010J14_e763.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|T07080 shock protein SRC2 - soybean dbj|BAA19769.1| SRC2 [Glycine max], mRNA sequence\n") - f.write("CTAAGTCGAACTATCTTCTTCTTCCAAATTCCAATTTCAACAACTCTCAAGAATCATCGCCATGGATTGC\n") - f.write("AGGCCTCTGGAGGTAATCATCGACTCGGCCAACGACATCAAGGATGTCAACCTCTTCTCCAAGATGGACG\n") - f.write("TCTACGCCGCCGTTTCGGTCGCCGGCGACCCGCGCAACAAGAAGCAGAAGAACAAAACCCCCGTCGTCAA\n") - f.write("GGACGGAGGCACCAACCCCAAGTGGACCAGCTACCCCATCAGGTTCACCGTCGACGAAGCCGCCCTCCTC\n") - f.write("AACAACCGCCTCACCCTCAACATCAAGCTCGTCTCCGAACGCACTTTGGGAGACACCAAGATCGGCAAGG\n") - f.write("TCAAGATCCCGCTCAAGGACCTACTAGACACCATGAGCGGCGGCGATGATCACA\n") - f.write("\n") - f.write(">gi|226789543|gb|GO546082.1|GO546082 Mdas9010H14_e752.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to pir|G86463 hypothetical protein F12G12.18 - Arabidopsis thaliana gb|AAG12539.1|AC015446_20 Unknown protein [Arabidopsis thaliana] gb|AAG12849.1|AC079286_6 photosystem II 22 kDa protein, putative; 13290-12539 [Arabidopsis thaliana] gb|AAK55677.1|A, mRNA sequence\n") - f.write("TTTTTTTATCAACGAGCTCTGGGGAACTTCTTCAATCGTTGAAATCCTGNTAAACATTGTAAGTAAAATA\n") - f.write("CAGCAGCGTATGATAGCCGAGTATTTCTTGCAAATGAAATTTAAACAAATTACTCAACAAAGTTACAAGT\n") - f.write("GAAACAGTGAATGTATCTGCAGTAGCTCCAGAGACAAGAAGGTATTAAGGCTTTCAACATCCCACCGGGC\n") - f.write("CGGTGTATCATTCCAGATCCAGTATTCCGAAATTTGAAAGAAGTATCTTTACTTGATCAACAAAGTCCGA\n") - f.write("GCCAGTTGCATACTCCGTTAGCATTCCAACAGCAAAACCGAACATTGCCCATCTGCCATTGCTAATCTCG\n") - f.write("TTCTTGCCAACAAAGCCAAAGAAAGGACCCTGGTTAGCAGCCTCAAGCTTCTTCTGCTTGAAGTACTCCT\n") - f.write("GAATCTCCTTAGCCTTCTGCCTCTGAAACTCCAAGGTCACCACATTCTTGTCCTCCACCATCGTCAGCCC\n") - f.write("GGAAACCTGGGCCGGATTCGAGGGCTGCTGAGGCGGTGGAGAAGGAGACGGAGGAGAAGGAGGCGTTGGT\n") - f.write("TTGAGAGGGGAAGACGGCTGGGAGGGTTCTCGGAGGGAAGGAGCAGCAGGTCTTCTGATAGGCCCTTCCG\n") - f.write("TCTTGGGAGCTCTTTATGCTAATTTTTA\n") - f.write("\n") - f.write(">gi|226789542|gb|GO545826.1|GO545826 Mdas9003M24_e233.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to sp|Q9M4S8|TPIC_FRAAN Triosephosphate isomerase, chloroplast precursor (TIM) gb|AAF66071.1|AF257322_1 triosephosphate isomerase [Fragaria x ananassa], mRNA sequence\n") - f.write("TCGAGTTTTTTTTTTTTTTTTTTAAGTGACCCATGGAAAATGGATAGAAGATATATTTTACTATCTTTAT\n") - f.write("GGAGGGGGAAACACTTCAAAAACGACCCAGGAAAAAAAATTCCTTATGATAAACTGGCTCATACATTTGT\n") - f.write("TACAATATGCTTCAATCTCAAGGTACCTTCGCATCGGCCCTTTATTTGATCTCGGAACCACCATAATCAA\n") - f.write("GCAGCAACTTTCTTGGCTGTCACAGCGTTGACGATAGTAGCAAATTCAGGGCCCTTTAGGGAAGCACCGC\n") - f.write("CAACAAGAAAACCATCAATATCTTCCTTCTTTGCGAGCTCAACAGAATTGCCTCCATTTACAGATCCTCC\n") - f.write("ATAAATAATTCTTGTTTTAGATGCAACTTCTGCTGACACATTCTGTTTCAGCCAATCACGAACAGCTACA\n") - f.write("TGTACTTCCTGAGCTTGTTCTGGACTGGCTACCTTACCAGTCCCAATGGCCCATACAGGCTCATAAGCAA\n") - f.write("CAACTATCTTATCCCAGCTGGGTACTGCGTCTGCAAAAGCCTTCAGCTGCTGAAAGCAGACGTCAAAAGT\n") - f.write("TTTCCCTGCTTCCCTTTCTTCTAGCTTCTCGCCCAATGCAAGCAATTACTCCGAGACCCTCATTCAACGC\n") - f.write("ATAGG\n") - f.write("\n") - f.write(">gi|226789541|gb|GO545825.1|GO545825 Mdas9003P18_e247.b1 Apple_EST_Mdas Malus x domestica cDNA 3' similar to ref|NP_189513.1| expressed protein [Arabidopsis thaliana] sp|Q9LHA4|V0D2_ARATH Probable vacuolar ATP synthase subunit d 2 (V-ATPase d subunit 2) (Vacuolar proton pump d subunit 2) gb|AAL16278.1|AF428348_1 AT3g28715/MZN14_21 [Arabidopsis thaliana], mRNA sequence\n") - f.write("TTTTTTATAAACTCACTACGAGACTGCTACTATAGTAGCTCTCAAATTGCAATATATATATTCAATTTAT\n") - f.write("CCTCACAACTGTAACATGCTCGATTTCAGAACATGACATATTCCCTCTATGTAAAAACGACCGGAATAAT\n") - f.write("ATATGCAAAAGTGCTTATTAGGAAGGAACACCGGATAGTGCAAACAACGCAACCGCACCCATCTCTACAA\n") - f.write("TTCGTTCGGGGATATGATGGGGAGGAGATTTACAGAAGATTATGCGAAAGAACGAAGGATCATCTGTAAT\n") - f.write("GGTGTGTTCTGAGTCCCAATCCGACTAAAATATGAAGACCACGCTGTCGTGAACTCTGGACTTCTGGTTC\n") - f.write("TGAGCCACACACTCAGATATCCACATCAAATTTCTGATCTCCTGCTCCCTCAACCTCATGTATGCAAAGA\n") - f.write("AAACAGCGTAATGGAACTGTTGCTCAAATGCTAAGCAAAGCCTTTTCACCTCCTCTTCATAAAATGCCTT\n") - f.write("GTCAAGCATCTGGGTTTCGCCATAGGATAGTTTTGAAAAAATAGACTGATAAGGAGGATATTTTTCCATG\n") - f.write("CAACCACGTACCTGATCAATGTCCTCACATACAGCAAGTTCCTCATGGCCATAGGGAATAGAGTAAACCA\n") - f.write("AAGCTAGAGTACAACTTCCTGCGATCATCTCGAGTAAGCTCAGTTCAATACTATTTATGGGT\n") - f.write("\n") - f.close() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/MockOutputForBlat.py --- a/commons/launcher/tests/MockOutputForBlat.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -class MockOutputForBlat(object): - - def write(self, inFileName): - f = open(inFileName, 'w') - f.write('gi|226792305|gb|GO545799.1|GO545799 290 551 Vein_ctg_10639 674 935 1.0e-130 463.0 93.51\n') - f.write('gi|226792305|gb|GO545799.1|GO545799 138 283 Vein_ctg_10639 519 664 1.0e-50 198.0 82.88\n') - f.write('gi|226792305|gb|GO545799.1|GO545799 577 686 Vein_ctg_10639 961 1070 1.4e-46 184.0 90.91\n') - f.write('gi|226792305|gb|GO545799.1|GO545799 566 572 Vein_ctg_10639 944 950 3.1e+05 13.0 100.00\n') - f.write('gi|226792293|gb|GO546055.1|GO546055 107 193 Vein_ctg_10638 87 1 2.2e-42 170.0 100.00\n') - f.write('gi|226792293|gb|GO546055.1|GO546055 34 91 Vein_ctg_10638 161 104 2.5e-22 103.0 94.83\n') - f.write('gi|226792293|gb|GO546055.1|GO546055 521 611 Vein_ctg_10639 1075 985 2.9e-38 156.0 92.31\n') - f.write('gi|226790810|gb|GO546215.1|GO546215 57 520 Vein_ctg_5197 1862 1399 8.7e-128 454.0 72.84\n') - f.write('gi|226790791|gb|GO546209.1|GO546209 135 199 Vein_ctg_5197 1994 1930 7.4e-25 112.0 93.85\n') - f.write('gi|226790791|gb|GO546209.1|GO546209 36 82 Vein_ctg_5197 2126 2080 1.9e-06 50.0 76.60\n') - f.write('gi|226790483|gb|GO545656.1|GO545656 280 541 Vein_ctg_10639 674 935 1.0e-130 463.0 93.51\n') - f.write('gi|226790483|gb|GO545656.1|GO545656 128 273 Vein_ctg_10639 519 664 1.0e-50 198.0 82.88\n') - f.write('gi|226790483|gb|GO545656.1|GO545656 567 640 Vein_ctg_10639 961 1034 1.1e-25 114.0 87.84\n') - f.write('gi|226790483|gb|GO545656.1|GO545656 556 562 Vein_ctg_10639 944 950 3.1e+05 13.0 100.00\n') - f.write('gi|226790458|gb|GO545644.1|GO545644 1 95 Vein_ctg_10638 1369 1275 3.5e-40 163.0 92.63\n') - f.write('gi|226790458|gb|GO545644.1|GO545644 146 185 Vein_ctg_10638 1225 1186 3.7e-07 53.0 82.50\n') - f.write('gi|226790049|gb|GO546186.1|GO546186 177 263 Vein_ctg_10638 87 1 5.6e-39 159.0 96.55\n') - f.write('gi|226790049|gb|GO546186.1|GO546186 106 161 Vein_ctg_10638 159 104 3.8e-21 99.0 94.64\n') - f.write('gi|226790011|gb|GO546174.1|GO546174 138 283 Vein_ctg_10639 519 664 1.0e-50 198.0 82.88\n') - f.write('gi|226789634|gb|GO545875.1|GO545875 135 306 Vein_ctg_10638 1446 1275 7.3e-80 294.0 91.86\n') - f.write('gi|226789634|gb|GO545875.1|GO545875 451 496 Vein_ctg_10638 1132 1087 1.8e-18 90.0 100.00\n') - f.write('gi|226789634|gb|GO545875.1|GO545875 357 393 Vein_ctg_10638 1225 1189 1.8e-05 47.0 81.08\n') - f.write('gi|226789597|gb|GO546106.1|GO546106 432 537 Vein_ctg_2286 1166 1061 5.0e-40 162.0 86.79\n') - f.write('gi|226789597|gb|GO546106.1|GO546106 538 632 Vein_ctg_2286 1008 914 6.0e-33 139.0 85.26\n') - f.write('gi|226789571|gb|GO546096.1|GO546096 353 474 Vein_ctg_5197 2426 2305 4.1e-46 182.0 84.43\n') - f.write('gi|226789566|gb|GO545840.1|GO545840 73 232 Vein_ctg_10639 776 935 2.5e-75 279.0 92.50\n') - f.write('gi|226789566|gb|GO545840.1|GO545840 258 372 Vein_ctg_10639 961 1075 4.2e-50 196.0 92.17\n') - f.write('gi|226789566|gb|GO545840.1|GO545840 247 253 Vein_ctg_10639 944 950 3.1e+05 13.0 100.00\n') - f.close() diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_BlatClusterLauncher.py --- a/commons/launcher/tests/Test_BlatClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -import unittest -from commons.launcher.BlatClusterLauncher import BlatClusterLauncher - - -class Test_BlatClusterLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = BlatClusterLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (format='fasta')" - exp += "\n -p: parameters for 'blat'" - exp += "\n -Z: concatenate output files" - exp += "\n -A: same sequences (all-by-all)" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_BlatClusterLauncher ) ) -if __name__ == "__main__": - unittest.TextTestRunner(verbosity=2).run( test_suite ) diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_BlatProgramLauncher.py --- a/commons/launcher/tests/Test_BlatProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,98 +0,0 @@ -import unittest -from commons.launcher.BlatProgramLauncher import BlatProgramLauncher - - -class Test_BlatProgramLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = BlatProgramLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getHelpAsString( self ): - exp = "" - exp += "usage: BlatProgramLauncher.py [options]" - exp += "\ngeneric options:" - exp += "\n -h: this help" - exp += "\n -i: name of the input file (format='fasta')" - exp += "\n -c: clean" - exp += "\n -v: verbosity level (default=0/1)" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (database, format='fasta')" - exp += "\n -p: parameters for 'blat'" - exp += "\n -A: same sequences (all-by-all)" - exp += "\n -o: name of the output file (format='align', default=inFile+'.align')" - obs = self._i.getHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setAttributesFromCmdLine( self ): - self._i.setAttributesFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - - self._i.setAttributesFromCmdLine( "-o", "dummyOutFile.align" ) - self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() ) - - - def test_setWrapperCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "BlatProgramLauncher.py" - exp += " -i %s" % ( "dummyInFile.fa" ) - exp += " -s %s" % ( "dummySubjectFile.fa" ) - exp += " -o %s.align" % ( "dummyInFile.fa" ) - exp += " -v 0" - self._i.setWrapperCommandLine() - obs = self._i.getWrapperCommandLine() - self.assertEqual( exp, obs ) - - - def test_setProgramCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - self._i.setProgramParameters( "-minIdentity=90" ) - exp = "blat dummySubjectFile.fa dummyInFile.fa -minIdentity=90 -out=blast8 dummyInFile.fa.blast" - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - - def test_setListFilesToKeep( self ): - self._i.setInputFile( "dummyInFile.fa" ) - lExp = [ "dummyInFile.fa.align" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setListFilesToRemove( self ): - self._i.setInputFile( "dummyInFile.fa" ) - lExp = [ "dummyInFile.fa.blast" ] - self._i.setListFilesToRemove() - lObs = self._i.getListFilesToRemove() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setSummary( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "input file: %s" % ( self._i.getInputFile() ) - exp += "\nsubject file: %s" % ( self._i.getSubjectFile() ) - exp += "\nparameters: %s" % ( self._i.getProgramParameters() ) - exp += "\noutput file: %s" % ( "dummyInFile.fa.align" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_BlatProgramLauncher ) ) -if __name__ == "__main__": - unittest.TextTestRunner(verbosity=2).run( test_suite ) diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_BlatProgramLauncher.py --- a/commons/launcher/tests/Test_F_BlatProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,139 +0,0 @@ -import os -import unittest -from commons.core.utils.FileUtils import FileUtils -from devTools.tests.MockFastaSupctg30 import MockFastaSupctg30 -from devTools.tests.MockMiniProtBankSupctg30 import MockMiniProtBankSupctg30 -from commons.launcher.tests.MockDataBankForBlat import MockDataBankForBlat -from commons.launcher.tests.MockESTBankForBlat import MockESTBankForBlat -from commons.launcher.tests.MockOutputForBlat import MockOutputForBlat -from commons.launcher.BlatProgramLauncher import BlatProgramLauncher - -class Test_F_BlatProgramLauncher(unittest.TestCase): - - def test_run_empty_result(self): - queryFileName = "smallProtBank_supctg30.fa" - mock = MockMiniProtBankSupctg30() - mock.write(queryFileName) - subjectFileName = "subjectBank.fa" - mock = MockFastaSupctg30() - mock.write(subjectFileName) - - expOutputFileName = "expBlatOutput.blast.align" - self.writeEmptyExpOutputFile(expOutputFileName) - - obsOutputFileName = "obsBlatOutput.blast.align" - - bpl = BlatProgramLauncher() - bpl.setInputFile(queryFileName) - bpl.setSubjectFile(subjectFileName) - bpl.setOutputFile(obsOutputFileName) - bpl.setProgramParameters("") - bpl.run() - - blastFileName = queryFileName + ".blast" - - self.assertTrue(os.path.exists(obsOutputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) - - os.remove(queryFileName) - os.remove(subjectFileName) - os.remove(blastFileName) - os.remove(expOutputFileName) - os.remove(obsOutputFileName) - - def test_as_script_empty_result(self): - queryFileName = "smallProtBank_supctg30.fa" - mock = MockMiniProtBankSupctg30() - mock.write(queryFileName) - subjectFileName = "subjectBank.fa" - mock = MockFastaSupctg30() - mock.write(subjectFileName) - - expOutputFileName = "expBlatOutput.blast.align" - self.writeEmptyExpOutputFile(expOutputFileName) - - obsOutputFileName = "obsBlatOutput.blast.align" - - cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName - - os.system(cmd2Launch) - - blastFileName = queryFileName + ".blast" - - self.assertTrue(os.path.exists(obsOutputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) - - os.remove(queryFileName) - os.remove(subjectFileName) - os.remove(blastFileName) - os.remove(expOutputFileName) - os.remove(obsOutputFileName) - - def test_run(self): - queryFileName = "smallESTBank.fa" - mock = MockESTBankForBlat() - mock.write(queryFileName) - subjectFileName = "subjectBank.fa" - mock = MockDataBankForBlat() - mock.write(subjectFileName) - - expOutputFileName = "expBlatOutput.blast.align" - mock = MockOutputForBlat() - mock.write(expOutputFileName) - - obsOutputFileName = "obsBlatOutput.blast.align" - - bpl = BlatProgramLauncher() - bpl.setInputFile(queryFileName) - bpl.setSubjectFile(subjectFileName) - bpl.setOutputFile(obsOutputFileName) - bpl.setProgramParameters("") - bpl.run() - - blastFileName = queryFileName + ".blast" - - self.assertTrue(os.path.exists(obsOutputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) - - os.remove(queryFileName) - os.remove(subjectFileName) - os.remove(blastFileName) - os.remove(expOutputFileName) - os.remove(obsOutputFileName) - - def test_as_script(self): - queryFileName = "smallESTBank.fa" - mock = MockESTBankForBlat() - mock.write(queryFileName) - subjectFileName = "subjectBank.fa" - mock = MockDataBankForBlat() - mock.write(subjectFileName) - - expOutputFileName = "expBlatOutput.blast.align" - mock = MockOutputForBlat() - mock.write(expOutputFileName) - - obsOutputFileName = "obsBlatOutput.blast.align" - - cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName - - os.system(cmd2Launch) - - blastFileName = queryFileName + ".blast" - - self.assertTrue(os.path.exists(obsOutputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) - - os.remove(queryFileName) - os.remove(subjectFileName) - os.remove(blastFileName) - os.remove(expOutputFileName) - os.remove(obsOutputFileName) - - def writeEmptyExpOutputFile(self, outputFileName): - f = open(outputFileName, "w") - f.write("") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchBlastclust.py --- a/commons/launcher/tests/Test_F_LaunchBlastclust.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,103 +0,0 @@ -import unittest -import os -from commons.launcher.LaunchBlastclust import LaunchBlastclust -from commons.core.utils.FileUtils import FileUtils - -class Test_F_LaunchBlastclust(unittest.TestCase): - - def setUp(self): - self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa" - os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName) - self._outputFileName = "%s_Blastclust.fa" % self._inputFileName - self._outBlastclustFileName = "%s_blastclust.txt" % self._inputFileName - - def tearDown(self): - if os.path.exists(self._outputFileName): - os.remove(self._outputFileName) - if os.path.exists(self._outBlastclustFileName): - os.remove(self._outBlastclustFileName) - os.remove(self._inputFileName) - - def test_run(self): - iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True) - iLaunchBlastclust.run() - expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"] - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - - def test_run_with_tweaked_params(self): - iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True) - iLaunchBlastclust.setBothSequences("F") - iLaunchBlastclust.setIdentityThreshold(0) - iLaunchBlastclust.setIsBlastToMap() - iLaunchBlastclust.run() - - faExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.fa" % os.environ["REPET_DATA"] - mapExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.map" % os.environ["REPET_DATA"] - - self.assertTrue(FileUtils.are2FilesIdentical(faExpFileName, self._outputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(mapExpFileName, "%s.map" % os.path.splitext(self._outputFileName)[0])) - - os.remove("%s.map" % os.path.splitext(self._outputFileName)[0]) - - def test_run_with_header_options(self): - inFileName = "dummyHeaderForTEdenovo.fa" - expFileName = "expDummyHeaderForTEdenovo.fa" - self._writeInputFile_header_options(inFileName) - self._writeExpFile_header_options(expFileName) - obsFileName = "%s_Blastclust.fa" % inFileName - - iLaunchBlastclust = LaunchBlastclust(inFileName, clean = True) - iLaunchBlastclust.setIsHeaderForTEdenovo(True) - iLaunchBlastclust.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(inFileName) - os.remove(expFileName) - os.remove(obsFileName) - os.remove("%s_blastclust.txt" % inFileName) - - def test_run_as_script(self): - cmd = "LaunchBlastclust.py -i %s" % self._inputFileName - os.system(cmd) - expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"] - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - - def _writeInputFile_header_options(self, inFileName): - f = open(inFileName,"w") - f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n") - f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n") - f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n") - f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n") - f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n") - f.write(">DTX-incomp_DmelChr4-B-R10-Map3_reversed\n") - f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n") - f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n") - f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n") - f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n") - f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n") - f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n") - f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n") - f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n") - f.close() - - def _writeExpFile_header_options(self, expFileName): - f = open(expFileName,"w") - f.write(">DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\n") - f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n") - f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n") - f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n") - f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n") - f.write(">DTX-incomp_Blc1_DmelChr4-B-R10-Map3_reversed\n") - f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n") - f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n") - f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n") - f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n") - f.write(">PotentialHostGene-chim_Blc2_DmelChr4-B-R4-Map5_reversed\n") - f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n") - f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n") - f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchLastZ.py --- a/commons/launcher/tests/Test_F_LaunchLastZ.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchLastZ import LaunchLastZ - -class Test_F_LaunchLastZ(unittest.TestCase): - - def setUp(self): - self._inFastaFileName = "%s/Tools/input_TestFLastZ.fa" % os.environ["REPET_DATA"] - self._expAxtFileName = "%s/Tools/exp_TestFLastZ.axt" % os.environ["REPET_DATA"] - self._obsAxtFileName = "obsLastZ.axt" - - def tearDown(self): - try: - os.remove(self._obsAxtFileName) - except:pass - - def test_run(self): - ilauncher = LaunchLastZ(self._inFastaFileName, self._inFastaFileName, self._obsAxtFileName,verbosity=1) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expAxtFileName, self._obsAxtFileName)) - - def test_run_as_script(self): - #FIXME : change path - cmd = 'python %s/commons/launcher/LaunchLastZ.py -q %s -r %s -o %s' % (os.environ["REPET_PATH"], self._inFastaFileName, self._inFastaFileName, self._obsAxtFileName) - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expAxtFileName, self._obsAxtFileName)) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchMCL.py --- a/commons/launcher/tests/Test_F_LaunchMCL.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import unittest -import os -import shutil -from commons.launcher.LaunchMCL import LaunchMCL - -class Test_F_LaunchMCL(unittest.TestCase): -# TODO: test query coverage filter - - def setUp(self): - self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa" - try: - shutil.rmtree("MCLtmpDirectory") - os.remove(self._inputFileName) - except: - pass - try: - os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName) - except: - pass - self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0] - - def tearDown(self): - try: - os.remove(self._inputFileName) - os.remove(self._outputFileName) - shutil.rmtree("MCLtmpDirectory") - except: - pass - try: - os.remove("DmelChr4_LTRharvest_expected_with_default_params_MCL.map") - except: - pass - - def test_run(self): - iLaunchMCL = LaunchMCL(self._inputFileName, doClean = True, verbosity = 1) - iLaunchMCL.run() - expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"] - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - - def test_run_with_map_file(self): - iLaunchMCL = LaunchMCL(self._inputFileName, isCluster2Map = True, doClean = False, verbosity = 1) -# iLaunchMCL.setCoverageThreshold(0.60) - iLaunchMCL.run() - expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"] - expMapFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.map" % os.environ["REPET_DATA"] - obsMapFileName = "%s.map" % os.path.splitext(self._outputFileName)[0] - - self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName)) - - os.remove(obsMapFileName) - - def test_run_clusterConsensus_headers(self): - os.remove(self._inputFileName) - self._inputFileName = "DmelChr4_LTRharvest_MCL_ClusterConsHeaders_input.fa" - os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName) - iLaunchMCL = LaunchMCL(self._inputFileName, isClusterConsensusHeaders = True, doClean = True, verbosity = 1) - iLaunchMCL.run() - expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_ClusterConsHeaders_expected.fa" % os.environ["REPET_DATA"] - self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0] - - self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName)) - - def test_run_as_script(self): - cmd = "LaunchMCL.py -i %s -j -v 6" % self._inputFileName - os.system(cmd) - expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"] - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory")) - - def test_run_as_script_allParams(self): - cmd = "LaunchMCL.py -i %s -j -I 1.5 -T 0.0 -m -v 6" % self._inputFileName - os.system(cmd) - expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"] - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory")) - - def test_run_as_script_without_join(self): - cmd = "LaunchMCL.py -i %s -v 2" % self._inputFileName - os.system(cmd) - expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"] - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory")) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchMap.py --- a/commons/launcher/tests/Test_F_LaunchMap.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -import unittest -import os -import subprocess -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchMap import LaunchMap - -class Test_F_LaunchMap(unittest.TestCase): - - def setUp(self): - self._fastaFileName = "LaunchMap_seqCluster1.fa" - fastaFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._fastaFileName) - os.symlink(fastaFilePath, self._fastaFileName) - self._obsFileName = "%s.fa_aln" % self._fastaFileName - - def tearDown(self): - os.remove(self._fastaFileName) - try: - os.remove(self._obsFileName) - except: pass - - def test_run_as_script(self): - expFileName = "%s/Tools/expLaunchMap_seqCluster1.fa.fa_aln" % os.environ["REPET_DATA"] - obsFileName = "obs.fa_aln" - cmd = "LaunchMap.py " - cmd += "-i %s " % self._fastaFileName - cmd += "-o %s " % obsFileName - cmd += "-c " - process = subprocess.Popen(cmd, shell = True) - process.communicate() - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - - def test_run(self): - expFileName = "%s/Tools/expLaunchMap_seqCluster1.fa.fa_aln" % os.environ["REPET_DATA"] - iLaunchMap = LaunchMap(self._fastaFileName) - iLaunchMap.setDoClean(True) - iLaunchMap.run() - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._obsFileName)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchMatcher.py --- a/commons/launcher/tests/Test_F_LaunchMatcher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import unittest -import os -import subprocess -from commons.launcher.LaunchMatcher import LaunchMatcher - -class Test_F_LaunchMatcher(unittest.TestCase): - - def setUp(self): - self._inFileName = "DmelChr4.align" - self._fastaFileName = "DmelChr4.fa" - inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName) - inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._fastaFileName) - try: - os.remove(self._inFileName) - except: - pass - os.symlink(inFilePath, self._inFileName) - os.symlink(inFastaPath, self._fastaFileName) - self._iLaunchMatcher = LaunchMatcher(align=self._inFileName, queryFileName=self._fastaFileName, subjectFileName=self._fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True) - self._iLaunchMatcher.setVerbosity(2) - - def tearDown(self): - try: - FileUtils.removeFilesByPattern("%s*" % self._inFileName) - os.remove(self._fastaFileName) - except: - pass - - def test_run_as_class_1_file(self): - expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"] - expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"] - - obsPathFileName = "%s.match.path" % self._inFileName - obsTabFileName = "%s.match.tab" % self._inFileName - - self._iLaunchMatcher.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName)) - - def test_run_as_script(self): - expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"] - expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"] - - cmd = "LaunchMatcher.py " - cmd += "-a %s " % self._inFileName - cmd += "-q %s " % self._fastaFileName - cmd += "-s %s " % self._fastaFileName - cmd += "-o DmelChr4.align " - cmd += "-j " - cmd += "-k " - cmd += "-e 1e-20 " - process = subprocess.Popen(cmd, shell = True) - process.communicate() - obsPathFileName = "%s.match.path" % self._inFileName - obsTabFileName = "%s.match.tab" % self._inFileName - - self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchMummerPlot.py --- a/commons/launcher/tests/Test_F_LaunchMummerPlot.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchMummerPlot import LaunchMummerPlot - -class Test_F_LaunchMummerPlot(unittest.TestCase): - - def setUp(self): - self._queryFastaFileName = "query.fa" - self._refFastaFileName = "ref.fa" - self._writeInputFastaFiles() - - self._inputDeltaFileName = "inputNucmer.delta" - self._writeInputDeltaFileName() - - self._expGpFileName = "expMummerPlot.gp" - self._obsGpFileName = "obsMummerPlot.gp" - self._obsPngFileName = "obsMummerPlot.png" - - def tearDown(self): - try: - os.remove(self._queryFastaFileName) - except:pass - try: - os.remove(self._refFastaFileName) - except:pass - try: - os.remove(self._inputDeltaFileName) - except:pass - try: - os.remove(self._expGpFileName) - except:pass - try: - os.remove(self._obsGpFileName) - except:pass - try: - os.remove(self._obsPngFileName) - except:pass - - - def test_run(self): - self._writeExpGpFile() - ilaunchMummerPlot = LaunchMummerPlot(self._inputDeltaFileName, self._refFastaFileName, self._queryFastaFileName,"obsMummerPlot",fat=True, filter=True, clean=True, verbosity=1) - ilaunchMummerPlot.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expGpFileName, self._obsGpFileName)) - - def test_run_as_script(self): - self._writeExpGpFile() - cmd = 'LaunchMummerPlot.py --input %s --Qfile %s --Rfile %s --prefix %s --fat --filter --clean' % (self._inputDeltaFileName, self._refFastaFileName, self._queryFastaFileName, "obsMummerPlot") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expGpFileName, self._obsGpFileName)) - - def _writeInputFastaFiles(self): - InputFile = open(self._queryFastaFileName, 'w') - InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n') - InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n') - InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n') - InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n') - InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n') - InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n') - InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n') - InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n') - InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n') - InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n') - InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n') - InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n') - InputFile.write('CCAAAAAAAAA\n') - InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n') - InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n') - InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n') - InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n') - InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n') - InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n') - InputFile.write('>SINE_FR2:classI:SINE:?\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>SINEC1B2_CF:classI:SINE:?\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n') - InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n') - InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n') - InputFile.write('AAAAAAA\n') - InputFile.close() - - InputFile = open(self._refFastaFileName, 'w') - InputFile.write('>SINE_FR2:classI:SINE:?\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>SINEC1B2_CF:classI:SINE:?\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') - InputFile.close() - - def _writeExpGpFile(self): - f = open(self._expGpFileName, 'w') - f.write('set terminal png tiny size 800,800\n') - f.write('set output "obsMummerPlot.png"\n') - f.write('set xtics rotate ( \\\n') - f.write(' "SINE_FR2:classI:SINE:?" 1, \\\n') - f.write(' "SINEC1B2_CF:classI:SINE:?" 389, \\\n') - f.write(' "SINE1A_SS:classI:SINE:SINE2/tRNA" 552, \\\n') - f.write(' "SUSINE2:classI:SINE:SINE2/tRNA" 682, \\\n') - f.write(' "Bovc-tA2:classI:SINE:SINE2/tRNA" 891, \\\n') - f.write(' "ALPINE1:classI:SINE:SINE2/tRNA" 1223, \\\n') - f.write(' "SINE2-1_Pca:classI:SINE:SINE2/tRNA" 1349, \\\n') - f.write(' "" 1694 \\\n') - f.write(')\n') - f.write('set ytics ( \\\n') - f.write(' "SINE_FR2:classI:SINE:?" 1, \\\n') - f.write(' "SINEC1B2_CF:classI:SINE:?" 371, \\\n') - f.write(' "" 532 \\\n') - f.write(')\n') - f.write('set size 1,1\n') - f.write('set grid\n') - f.write('unset key\n') - f.write('set border 0\n') - f.write('set tics scale 0\n') - f.write('set xlabel "REF"\n') - f.write('set ylabel "QRY"\n') - f.write('set format "%.0f"\n') - f.write('set mouse format "%.0f"\n') - f.write('set mouse mouseformat "[%.0f, %.0f]"\n') - f.write('set mouse clipboardformat "[%.0f, %.0f]"\n') - f.write('set xrange [1:1694]\n') - f.write('set yrange [1:532]\n') - f.write('set style line 1 lt 1 lw 3 pt 6 ps 1\n') - f.write('set style line 2 lt 3 lw 3 pt 6 ps 1\n') - f.write('set style line 3 lt 2 lw 3 pt 6 ps 1\n') - f.write('plot \\\n') - f.write(' "obsMummerPlot.fplot" title "FWD" w lp ls 1, \\\n') - f.write(' "obsMummerPlot.rplot" title "REV" w lp ls 2\n') - f.write('') - f.close() - - def _writeInputDeltaFileName(self): - f = open(self._inputDeltaFileName, 'w') - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('NUCMER\n') - f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n') - f.write('1 343 1 343 0 0 0\n') - f.write('0\n') - f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n') - f.write('1 161 1 161 0 0 0\n') - f.write('0\n') - f.close() - -if __name__ == "__main__": - unittest.main() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchNucmer.py --- a/commons/launcher/tests/Test_F_LaunchNucmer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,153 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchNucmer import LaunchNucmer - -class Test_F_LaunchNucmer(unittest.TestCase): - - def setUp(self): - self._queryFastaFileName = "query.fa" - self._refFastaFileName = "ref.fa" - self._writeInputFastaFiles() - self._expDeltaFileName = "expNucmer.delta" - self._writeExpDeltaFile() - self._obsDeltaFileName = "obsNucmer.delta" - self._obsCoordFileName= "obsNucmer.coords" - self._expCoordFileName= "expNucmer.coords" - - def tearDown(self): - try: - os.remove(self._queryFastaFileName) - except:pass - try: - os.remove(self._refFastaFileName) - except:pass - try: - os.remove(self._expDeltaFileName) - except:pass - try: - os.remove(self._obsDeltaFileName) - except:pass - - def test_run(self): - ilauncher = LaunchNucmer(self._refFastaFileName, self._queryFastaFileName,"obsNucmer",verbosity=1) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) - - def test_run_as_script(self): - cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) - - def test_run_as_script_gencoords_output(self): - self._writeExpGenCoordsFile() - cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName)) - os.remove(self._obsCoordFileName) - os.remove(self._expCoordFileName) - - def test_run_as_script_with_mincluster(self): - cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) - - def test_run_as_script_showcoords_output(self): - self._writeExpShowCoordsFile() - cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName)) - os.remove(self._obsCoordFileName) - os.remove(self._expCoordFileName) - - def _writeInputFastaFiles(self): - InputFile = open(self._queryFastaFileName, 'w') - InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n') - InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n') - InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n') - InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n') - InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n') - InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n') - InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n') - InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n') - InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n') - InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n') - InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n') - InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n') - InputFile.write('CCAAAAAAAAA\n') - InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n') - InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n') - InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n') - InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n') - InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n') - InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n') - InputFile.write('>SINE_FR2:classI:SINE:?\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>SINEC1B2_CF:classI:SINE:?\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n') - InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n') - InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n') - InputFile.write('AAAAAAA\n') - InputFile.close() - - InputFile = open(self._refFastaFileName, 'w') - InputFile.write('>SINE_FR2:classI:SINE:?\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>SINEC1B2_CF:classI:SINE:?\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') - InputFile.close() - - def _writeExpDeltaFile(self): - f = open(self._expDeltaFileName, 'w') - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('NUCMER\n') - f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n') - f.write('1 343 1 343 0 0 0\n') - f.write('0\n') - f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n') - f.write('1 161 1 161 0 0 0\n') - f.write('0\n') - f.close() - - def _writeExpGenCoordsFile(self): - f = open(self._expCoordFileName, 'w') - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('NUCMER\n\n') - f.write(' [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS]\n') - f.write('=====================================================================================\n') - f.write(' 1 161 | 1 161 | 161 161 | 100.00 | SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 1 343 | 1 343 | 343 343 | 100.00 | SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.close() - - def _writeExpShowCoordsFile(self): - f = open(self._expCoordFileName, 'w') - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('NUCMER\n\n') - f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n') - f.write('1\t161\t1\t161\t161\t161\t100.00\t164\t161\t98.17\t100.00\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('1\t343\t1\t343\t343\t343\t100.00\t389\t371\t88.17\t92.45\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchPhyML.py --- a/commons/launcher/tests/Test_F_LaunchPhyML.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from shutil import rmtree -from commons.launcher.LaunchPhyML import LaunchPhyML - - -class Test_F_LaunchPhyML(unittest.TestCase): - - def setUp(self): - self._curTestDir = os.getcwd() - self._testPrefix = 'test_LRA' - try: - os.makedirs(self._testPrefix) - except:pass - os.chdir(self._testPrefix) - - - self._inputFastaFileName = "%s_input.fa" % self._testPrefix - self._obsOutputFileName = self._inputFastaFileName +'_obs.phylip' - self._expOutputFileName = "%s_exp.phylip" % self._testPrefix - self._writeInputFile() - -# def tearDown(self): -# os.chdir(self._curTestDir) -# try: -# rmtree(self._testPrefix) -# except:pass - - def test_run(self): - #phylip use only same length sequences - self._writeExpFile() - ilauncher = LaunchPhyML(self._inputFastaFileName,verbosity=7) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - - -# def test_run_as_script(self): -# self._writeExpOutputFile_wo_refseq() -# cmd = 'LaunchPhyML.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName) -# os.system(cmd) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - - - def _writeInputFile(self): - InputFile = open(self._inputFastaFileName, 'w') - InputFile.write(""">sequence1 -GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC -GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT -GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAG ->sequence2 -GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA -GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG -GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGG ->sequence3 -ATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTATAGCAATGTCC -TTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGCGTCCAATAGCACAGACTTCA -GCTTGAATGCTGGTGTATCTGCCCATTGATTCGTGGTATTTCAACCTGGG -""") - InputFile.close() - - def _writeExpFile(self): - InputFile = open(self._expOutputFileName, 'w') - InputFile.write(""" 3 170 -sequence1 GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGG -sequence2 GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCG -sequence3 ATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTAT - -CCCCGGGTTCGATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGG -TGATCCTGGAGACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAG -AGCAATGTCCTTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGC - -AGTTTGCATGTTCTCCCTGTGCCTGCGTGGGTTCTCTCCGGGTACTCCGG -CCTGCTTCTCCCTCTGCCTGGGGCGGCACGGTGGTGTGGTGGTTAGCACT -GTCCAATAGCACAGACTTCAGCTTGAATGCTGGTGTATCTGCCCATTGAT - -CTTCCTCCCACAGTCCAAAG -GTTGCCTCACAGCAAGAAGG -TCGTGGTATTTCAACCTGGG""") - InputFile.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchPromer.py --- a/commons/launcher/tests/Test_F_LaunchPromer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,231 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchPromer import LaunchPromer - - -class Test_F_LaunchPromer(unittest.TestCase): - - def setUp(self): - self._queryFastaFileName = "query.fa" - self._refFastaFileName = "ref.fa" - self._writeInputFastaFiles() - self._expDeltaFileName = "expPromer.delta" - self._writeExpDeltaFile() - self._obsDeltaFileName = "obsPromer.delta" - self._obsCoordFileName= "obsPromer.coords" - self._expCoordFileName= "expPromer.coords" - - def tearDown(self): - try: - os.remove(self._queryFastaFileName) - except:pass - try: - os.remove(self._refFastaFileName) - except:pass - try: - os.remove(self._expDeltaFileName) - except:pass - try: - os.remove(self._obsDeltaFileName) - except:pass - - def test_run(self): - ilauncher = LaunchPromer(self._refFastaFileName, self._queryFastaFileName,"obsPromer",verbosity=1) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) - - def test_run_as_script(self): - cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) - - def test_run_as_script_gencoords_output(self): - self._writeExpGenCoordsFile() - cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName)) - os.remove(self._obsCoordFileName) - os.remove(self._expCoordFileName) - - def test_run_as_script_with_mincluster(self): - cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) - - def test_run_as_script_showcoords_output(self): - self._writeExpShowCoordsFile() - cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName)) - os.remove(self._obsCoordFileName) - os.remove(self._expCoordFileName) - - def _writeInputFastaFiles(self): - InputFile = open(self._queryFastaFileName, 'w') - InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n') - InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n') - InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n') - InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n') - InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n') - InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n') - InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n') - InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n') - InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n') - InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n') - InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n') - InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n') - InputFile.write('CCAAAAAAAAA\n') - InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n') - InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n') - InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n') - InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n') - InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n') - InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n') - InputFile.write('>SINE_FR2:classI:SINE:?\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>SINEC1B2_CF:classI:SINE:?\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n') - InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n') - InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n') - InputFile.write('AAAAAAA\n') - InputFile.close() - - InputFile = open(self._refFastaFileName, 'w') - InputFile.write('>SINE_FR2:classI:SINE:?\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>SINEC1B2_CF:classI:SINE:?\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') - InputFile.close() - - def _writeExpDeltaFile(self): - with open(self._expDeltaFileName, 'w') as f: - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('PROMER\n') - f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n') - f.write('1 387 1 369 6 6 10\n') - f.write('115\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('0\n') - f.write('2 388 2 370 6 6 8\n') - f.write('115\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('0\n') - f.write('3 389 3 371 6 6 16\n') - f.write('115\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('0\n') - f.write('388 2 370 2 6 6 6\n') - f.write('10\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('0\n') - f.write('387 1 369 1 6 6 5\n') - f.write('10\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('0\n') - f.write('389 3 371 3 6 6 4\n') - f.write('11\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('1\n') - f.write('0\n') - f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n') - f.write('1 159 1 159 0 0 2\n') - f.write('0\n') - f.write('3 161 3 161 0 0 2\n') - f.write('0\n') - f.write('161 3 161 3 0 0 0\n') - f.write('0\n') - f.write('160 2 160 2 0 0 2\n') - f.write('0\n') - f.write('159 1 159 1 0 0 4\n') - f.write('0\n') - f.write('2 160 2 160 0 0 4\n') - f.write('0\n') - - - - - def _writeExpGenCoordsFile(self): - with open(self._expCoordFileName, 'w') as f: - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('PROMER\n\n') - f.write(' [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] [% SIM] [% STP] | [FRM] [TAGS]\n') - f.write('==============================================================================================================\n') - f.write(' 1 159 | 1 159 | 159 159 | 100.00 100.00 1.89 | 1 1 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 2 160 | 2 160 | 159 159 | 100.00 100.00 3.77 | 2 2 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 3 161 | 3 161 | 159 159 | 100.00 100.00 1.89 | 3 3 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 159 1 | 159 1 | 159 159 | 100.00 100.00 3.77 | -3 -3 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 160 2 | 160 2 | 159 159 | 100.00 100.00 1.89 | -2 -2 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 161 3 | 161 3 | 159 159 | 100.00 100.00 0.00 | -1 -1 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write(' 1 387 | 1 369 | 387 369 | 95.35 95.35 3.88 | 1 1 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write(' 2 388 | 2 370 | 387 369 | 95.35 95.35 3.10 | 2 2 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write(' 3 389 | 3 371 | 387 369 | 95.35 95.35 6.20 | 3 3 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write(' 387 1 | 369 1 | 387 369 | 95.35 95.35 1.94 | -3 -3 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write(' 388 2 | 370 2 | 387 369 | 95.35 95.35 2.33 | -2 -2 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write(' 389 3 | 371 3 | 387 369 | 95.35 95.35 1.55 | -1 -1 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - - - def _writeExpShowCoordsFile(self): - with open(self._expCoordFileName, 'w') as f: - f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) - f.write('PROMER\n\n') - f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[% SIM]\t[% STP]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n') - f.write('1\t159\t1\t159\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('2\t160\t2\t160\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t2\t2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('3\t161\t3\t161\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t3\t3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('159\t1\t159\t1\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t-3\t-3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('160\t2\t160\t2\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t-2\t-2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('161\t3\t161\t3\t159\t159\t100.00\t100.00\t0.00\t164\t161\t96.95\t98.76\t-1\t-1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') - f.write('1\t387\t1\t369\t387\t369\t95.35\t95.35\t3.88\t389\t371\t99.49\t99.46\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write('2\t388\t2\t370\t387\t369\t95.35\t95.35\t3.10\t389\t371\t99.49\t99.46\t2\t2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write('3\t389\t3\t371\t387\t369\t95.35\t95.35\t6.20\t389\t371\t99.49\t99.46\t3\t3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write('387\t1\t369\t1\t387\t369\t95.35\t95.35\t1.94\t389\t371\t99.49\t99.46\t-3\t-3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write('388\t2\t370\t2\t387\t369\t95.35\t95.35\t2.33\t389\t371\t99.49\t99.46\t-2\t-2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - f.write('389\t3\t371\t3\t387\t369\t95.35\t95.35\t1.55\t389\t371\t99.49\t99.46\t-1\t-1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchRefAlign.py --- a/commons/launcher/tests/Test_F_LaunchRefAlign.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchRefAlign import LaunchRefAlign - - -class Test_F_LaunchRefAlign(unittest.TestCase): - - def setUp(self): - self._inputFastaFileName = "input.fa" - self._obsOutputFileName = "obs" - self._expOutputFileName = "exp" - self._writeInputFile() - self._writeExpOutputFile() - -# def tearDown(self): -# try: -# os.remove(self._inputFastaFileName) -# except:pass -# -# try: -# os.remove(self._expOutputFileName) -# except:pass -# try: -# os.remove(self._obsOutputFileName) -# except:pass -# try: -# os.remove("input.fa.2.3.5.80.10.20.15.dat") -# except:pass - - def test_run(self): - ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - -# def test_run_as_script(self): -# cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName) -# os.system(cmd) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName)) - - - def _writeInputFile(self): - InputFile = open(self._inputFastaFileName, 'w') - InputFile.write('>sequence\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>sequence2\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') - InputFile.close() - - def _writeExpOutputFile(self): - with open(self._expOutputFileName,'w') as expOutputFile: - expOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21 -2\t(GGT)5\tsequence\t10\t23 -3\t(GTGTGA)4\tsequence\t222\t242 -4\t(GTCCA)2\tsequence\t282\t292 -5\t(AGTG)4\tsequence\t355\t371 -6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152 -7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151 -8\t(TC)23\tsequence2\t107\t152 -""") - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchRefalign.py --- a/commons/launcher/tests/Test_F_LaunchRefalign.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,104 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchRefAlign import LaunchRefAlign -from shutil import rmtree - - -class Test_F_LaunchRefAlign(unittest.TestCase): - - def setUp(self): - self._curTestDir = os.getcwd() - self._testPrefix = 'test_LRA' - try: - os.makedirs(self._testPrefix) - except:pass - os.chdir(self._testPrefix) - - - self._inputFastaFileName = "%s_input.fa" % self._testPrefix - self._obsOutputFileName = self._inputFastaFileName +'.fa_aln' - self._expOutputFileName = "%s_exp.fa_aln" % self._testPrefix - self._writeInputFile() - - def tearDown(self): - os.chdir(self._curTestDir) - try: - rmtree(self._testPrefix) - except:pass - - def test_run(self): - self._writeExpOutputFile_wo_refseq() - ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - - def test_run_KeepRefSeq(self): - self._writeExpOutputFile_with_refseq() - ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5, keepRefseq=True) - ilauncher.run() - - self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - - def test_run_as_script(self): - self._writeExpOutputFile_wo_refseq() - cmd = 'LaunchRefAlign.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName) - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - - def test_run_as_script_KeepRefSeq(self): - self._writeExpOutputFile_with_refseq() - cmd = 'LaunchRefAlign.py -i %s -r -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName) - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) - - def _writeInputFile(self): - InputFile = open(self._inputFastaFileName, 'w') - InputFile.write('>sequence\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>sequence2\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') - InputFile.close() - - def _writeExpOutputFile_wo_refseq(self): - with open(self._expOutputFileName,'w') as expOutputFile: - expOutputFile.write(""">sequence2 -GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC -GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT -GCCTGTGTCTCTTCTCTC------------------------------------------ ------------------------------------------------------------- -----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------ ------------------------------------------------------------- ------------ -""") - - def _writeExpOutputFile_with_refseq(self): - with open(self._expOutputFileName,'w') as expOutputFile: - expOutputFile.write(""">sequence -GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC -GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT -GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA -TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA -TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC -CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCAAGCGGTAGAAAGTGAG -TGAGTGAGTGA ->sequence2 -GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC -GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT -GCCTGTGTCTCTTCTCTC------------------------------------------ ------------------------------------------------------------- -----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------ ------------------------------------------------------------- ------------ -""") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchRepeatMasker.py --- a/commons/launcher/tests/Test_F_LaunchRepeatMasker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchRepeatMasker import LaunchRepeatMasker - - -class Test_F_RepeatMasker(unittest.TestCase): - - def setUp(self): - self._queryFastaFileName = "query.fa" - self._libFastaFileName = "lib.fa" - self._expMaskedQueryFileName = "expMaskedQuery.fa" - self._obsMaskedQueryFileName = "%s.masked" % self._queryFastaFileName - - self._expCatFileName = "expCat.fa" - self._obsCatFileName = "%s.cat" % self._queryFastaFileName - - self._writeInputFastaFiles() - self._writeExpMaskedQueryFile() - self._writeExpCatFile() - - def tearDown(self): - os.remove(self._queryFastaFileName) - os.remove(self._libFastaFileName) - os.remove(self._expMaskedQueryFileName) - os.remove(self._obsMaskedQueryFileName) - os.remove(self._expCatFileName) - os.remove(self._obsCatFileName) - os.remove("%s.tbl" % self._queryFastaFileName) - os.remove("%s.out" % self._queryFastaFileName) - os.remove("%s.ori.out" % self._queryFastaFileName) - - def test_run(self): - ilauncher = LaunchRepeatMasker(self._queryFastaFileName, self._libFastaFileName,verbosity=1 ) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName)) - - def test_run_as_script(self): - #FIXME : change path to launcher - cmd = 'python %s/commons/launcher/LaunchRepeatMasker.py -q %s -l %s' % (os.environ["REPET_PATH"],self._queryFastaFileName, self._libFastaFileName) - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName)) - - def _writeInputFastaFiles(self): - InputFile = open(self._queryFastaFileName, 'w') - InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n') - InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n') - InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n') - InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n') - InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n') - InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n') - InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTACCTCCTTCCA\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n') - InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n') - InputFile.write('AAAAAAA\n') - InputFile.close() - - InputFile = open(self._libFastaFileName, 'w') - InputFile.write('>RefLib\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.close() - - def _writeExpMaskedQueryFile(self): - f = open(self._expMaskedQueryFileName, 'w') - f.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n') - f.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAG\n') - f.write('ACCCCGGTTCGATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGC\n') - f.write('TACCCACTCCAGTATTCTTGGGCTTCCCTGGTGGCTCAGACGGTAAAGAA\n') - f.write('TCCGCCTGCAATGCGGGAGACCTGGGTTCGATCCCTGGGTTGGGAAGATC\n') - f.write('CCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATC\n') - f.write('CCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n') - f.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTA\n') - f.write('CCTCCTTCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n') - f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n') - f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCTGCGTGGGTTCTCTCCG\n') - f.write('GGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGATTGGGGATTA\n') - f.write('GGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - f.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCC\n') - f.write('AGGGTGTACCCTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCC\n') - f.write('CGCGACCCTCAGTGGAGGAAGGGCAGCCTGGGTGGCTCAGCGGTTTAGCG\n') - f.write('CCTGCCTTTGGCCCAGGGCGTGATCCTGGAGACCCGGGATCGAGTCCCAC\n') - f.write('ATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTGGGGGAGGGTA\n') - f.write('TAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n') - f.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTC\n') - f.write('CCCCACCAAAAAAAAAA\n') - f.close() - - def _writeExpCatFile(self): - f = open(self._expCatFileName, 'w') - f.write('958 0.00 0.00 0.00 Bovc-tA2:classI:SINE:SINE2/tRNA 361 480 (487) RefLib 1 120 (0) 5\n') - f.write('## Total Sequences: 1\n') - f.write('## Total Length: 967\n') - f.write('## Total NonMask ( excluding >20bp runs of N/X bases ): 967\n') - f.write('## Total NonSub ( excluding all non ACGT bases ):967\n') - f.write('RepeatMasker version open-3.2.6 , default mode\n') - f.write('run with blastp version 2.0MP-WashU\n') - f.write('RepBase Update 20080801, RM database version 20080801\n') - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchTRF.py --- a/commons/launcher/tests/Test_F_LaunchTRF.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher.LaunchTRF import LaunchTRF - - -class Test_F_LaunchTRF(unittest.TestCase): - - def setUp(self): - self._inputFastaFileName = "input.fa" - self._obsTRFOutputFileName = "obsTRF.TRF.set" - self._expTRFOutputFileName = "expTRF.TRF.set" - self._writeInputFile() - self._writeExpTRFOutputFile() - - def tearDown(self): - try: - os.remove(self._inputFastaFileName) - except:pass - - try: - os.remove(self._expTRFOutputFileName) - except:pass - try: - os.remove(self._obsTRFOutputFileName) - except:pass - try: - os.remove("input.fa.2.3.5.80.10.20.15.dat") - except:pass - - def test_run(self): - ilauncher = LaunchTRF(self._inputFastaFileName,self._obsTRFOutputFileName,verbosity=5) - ilauncher.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName)) - - def test_run_as_script(self): - cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName) - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName)) - - def test_run_as_scriptNoOutputGiven(self): - cmd = 'LaunchTRF.py -i %s -v 3' % (self._inputFastaFileName) - os.system(cmd) - self._obsTRFOutputFileName = "input.fa.TRF.set" - self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName)) - - def test_run_as_scriptNoOutputGivenDoClean(self): - cmd = 'LaunchTRF.py -i %s -c -v 3' % (self._inputFastaFileName) - os.system(cmd) - self._obsTRFOutputFileName = "input.fa.TRF.set" - datFilePath = os.path.join(os.getcwd(),"%s.2.3.5.80.10.20.15.dat" % self._inputFastaFileName) - self.assertFalse(os.path.exists(datFilePath)) - - def _writeInputFile(self): - InputFile = open(self._inputFastaFileName, 'w') - InputFile.write('>sequence\n') - InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') - InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') - InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') - InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') - InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') - InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') - InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') - InputFile.write('>sequence2\n') - InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') - InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') - InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') - InputFile.close() - - def _writeExpTRFOutputFile(self): - with open(self._expTRFOutputFileName,'w') as expTRFOutputFile: - expTRFOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21 -2\t(GGT)5\tsequence\t10\t23 -3\t(GTGTGA)4\tsequence\t222\t242 -4\t(GTCCA)2\tsequence\t282\t292 -5\t(AGTG)4\tsequence\t355\t371 -6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152 -7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151 -8\t(TC)23\tsequence2\t107\t152 -""") - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_F_LaunchTallymer.py --- a/commons/launcher/tests/Test_F_LaunchTallymer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,151 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -import shutil -from commons.launcher.LaunchTallymer import LaunchTallymer - -class Test_F_LaunchTallymer(unittest.TestCase): - - def setUp(self): - self._inFastaFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"] - - def test_run_output_as_gff_cleaned(self): - iLaunchTallymer = LaunchTallymer(self._inFastaFileName, clean = True, verbosity=2) - iLaunchTallymer.run() - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff" - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - os.remove("DmelChr4.tallymer.stat") - - def test_run_with_remote_dir(self): - os.makedirs("sourceDir") - changedInFastaFileName = os.path.basename(self._inFastaFileName) - changedInFastaFilepath = os.path.join("sourceDir",changedInFastaFileName) - shutil.copy2(self._inFastaFileName, changedInFastaFilepath) - - iLaunchTallymer = LaunchTallymer(changedInFastaFilepath, clean = True, verbosity=2) - iLaunchTallymer.run() - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff" - - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - obsSourceDirFiles = os.listdir("sourceDir") - expSourceDirFiles = [changedInFastaFileName,] - self.assertEquals(expSourceDirFiles, obsSourceDirFiles) - - os.remove(obsFileName) - os.remove("DmelChr4.tallymer.stat") - shutil.rmtree("sourceDir") - - - def test_run_output_as_gff_cleaned_changed_minOccs2(self): - iLaunchTallymer = LaunchTallymer(self._inFastaFileName, minOccs=2, clean = True, verbosity=2) - iLaunchTallymer.run() - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20_minOcc2.gff" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff" - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - os.remove("DmelChr4.tallymer.stat") - - def test_run_output_as_gff_cleaned_relative_input(self): - srcFastaFileName = self._inFastaFileName - dstFastaFileName = os.path.basename(self._inFastaFileName) - shutil.copy2(srcFastaFileName, dstFastaFileName) - iLaunchTallymer = LaunchTallymer(dstFastaFileName, clean = True, verbosity=2) - iLaunchTallymer.run() - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff" - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(obsFileName) - os.remove("DmelChr4.tallymer.stat") - os.remove(dstFastaFileName) - - def test_run_as_script_output_as_gff_cleaned_relative_input_(self): - srcFastaFileName = self._inFastaFileName - dstFastaFileName = os.path.basename(self._inFastaFileName) - shutil.copy2(srcFastaFileName, dstFastaFileName) - - cmd = 'LaunchTallymer.py -i %s -s 20 -c -v 3' % (self._inFastaFileName) - os.system(cmd) - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff" - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(obsFileName) - os.remove("DmelChr4.tallymer.stat") - os.remove(dstFastaFileName) - - def test_run_output_as_wig_cleaned(self): - iLaunchTallymer = LaunchTallymer(self._inFastaFileName, outputFormats="wig", clean=True) - iLaunchTallymer.run() - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.wig" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.wig" - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(obsFileName) - os.remove("DmelChr4.tallymer.stat") - - def test_run_output_as_gff_and_wig_k15_cleaned(self): - iLaunchTallymer = LaunchTallymer(self._inFastaFileName, merSize=15, outputFormats="wig,gff3", clean=True) - iLaunchTallymer.run() - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.wig" - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff3" - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - - os.remove("DmelChr4.tallymer.stat") - - def test_run_as_script_run_output_as_gff_and_wig_k15_cleaned(self): - logFileName = "test.log" - cmd = 'LaunchTallymer.py -i %s -s 15 -f gff,wig,vero -c -v 3 > %s' % (self._inFastaFileName, logFileName) - os.system(cmd) - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.wig" - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - - expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"] - obsFileName = "DmelChr4.tallymer.gff" - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(obsFileName) - - expLogFileName = "exp.log" - with open(expLogFileName, "w") as f: - f.write(" LaunchTallymer - WARNING - Warning: ignoring invalid formats: \n") - f.write(" LaunchTallymer - INFO - Starting to run tallymer search of sequence DmelChr4.fa \n") - f.write(" LaunchTallymer - INFO - Finished running tallymer scan of sequence DmelChr4.fa \n") - f.write(" LaunchTallymer - INFO - Starting to run tallymer search to map conversion\n") - f.write(" LaunchTallymer - INFO - Finished tallymer search to map conversion\n") - f.write(" LaunchTallymer - INFO - Generating wig file\n") - f.write(" LaunchTallymer - INFO - Generating gff file\n") - obsLogFileName = "obs.log" - os.system("cut -d'-' -f4,5,6 %s > %s" % (logFileName, obsLogFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expLogFileName, obsLogFileName)) - - os.remove(logFileName) - os.remove(expLogFileName) - os.remove(obsLogFileName) - os.remove("DmelChr4.tallymer.stat") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_LaunchBlastclust.py --- a/commons/launcher/tests/Test_LaunchBlastclust.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,237 +0,0 @@ -import unittest -import time -import os -from commons.launcher.LaunchBlastclust import LaunchBlastclust -from commons.core.utils.FileUtils import FileUtils - -class Test_LaunchBlastclust( unittest.TestCase ): - - def setUp(self): - self._iLaunchBlastclust = LaunchBlastclust() - self._iLaunchBlastclust.setClean() - self._uniqId = "%s_%s" % (time.strftime("%Y%m%d%H%M%S"), os.getpid()) - - def tearDown(self): - self._iLaunchBlastclust = None - self._uniqId = None - - def test_getClustersFromTxtFile(self): - inFileName = "dummyInFile_%s" % self._uniqId - inF = open(inFileName, "w") - inF.write("seq1 seq3 seq4 \n") - inF.write("seq2 seq5 \n") - inF.close() - dExp = {1:["seq1","seq3","seq4"], 2:["seq2","seq5"]} - self._iLaunchBlastclust.setTmpFileName(inFileName) - dObs = self._iLaunchBlastclust.getClustersFromTxtFile() - self.assertEqual(dObs, dExp) - os.remove(inFileName) - - def test_getClusteringResultsInFasta_without_filtering(self): - inFileName = "dummyInFile_%s" % self._uniqId - inF = open(inFileName, "w") - inF.write(">seq1\n") - inF.write("gaattgtttactta\n") - inF.write(">seq2\n") - inF.write("gaattgtttactta\n") - inF.write(">seq3\n") - inF.write("gaattgtttactta\n") - inF.write(">seq4\n") - inF.write("gaattgtttactta\n") - inF.write(">seq5\n") - inF.write("gaattgtttactta\n") - inF.close() - - tmpFileName = "%s_blastclust.txt" % self._uniqId - inF = open(tmpFileName, "w") - inF.write("seq1 seq3 seq4 \n") - inF.write("seq2 seq5 \n") - inF.close() - self._iLaunchBlastclust.setTmpFileName(tmpFileName) - - fileExp = "getClusteringResultsInFastaExpected.fa" - outF = open(fileExp, "w") - outF.write(">BlastclustCluster1Mb1_seq1\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster1Mb2_seq3\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster1Mb3_seq4\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster2Mb1_seq2\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster2Mb2_seq5\n") - outF.write("gaattgtttactta\n") - outF.close() - - self._iLaunchBlastclust.getClusteringResultsInFasta(inFileName) - fileObs = "%s_Blastclust.fa" % os.path.splitext(inFileName)[0] - - if not FileUtils.are2FilesIdentical(fileObs, fileExp): - print "Files are different" - return - else: - print "Files are identical\n" - - os.remove(inFileName) - os.remove(tmpFileName) - os.remove(fileExp) - os.remove(fileObs) - - def test_getClusteringResultsInFasta_with_filtering(self): - inFileName = "dummyInFile_%s" % self._uniqId - inF = open(inFileName, "w") - inF.write(">seq1\n") - inF.write("gaattgtttactta\n") - inF.write(">seq2\n") - inF.write("gaattgtttactta\n") - inF.write(">seq3\n") - inF.write("gaattgtttactta\n") - inF.write(">seq4\n") - inF.write("gaattgtttactta\n") - inF.write(">seq5\n") - inF.write("gaattgtttactta\n") - inF.close() - - tmpFileName = "%s_blastclust.txt" % self._uniqId - inF = open(tmpFileName, "w") - inF.write("seq1 seq3 seq4 \n") - inF.write("seq2\n") - inF.write("seq5\n") - inF.close() - self._iLaunchBlastclust.setTmpFileName(tmpFileName) - - fileExp = "getClusteringResultsInFastaExpected.fa" - outF = open(fileExp, "w") - outF.write(">BlastclustCluster1Mb1_seq1\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster1Mb2_seq3\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster1Mb3_seq4\n") - outF.write("gaattgtttactta\n") - outF.close() - - self._iLaunchBlastclust.setFilterUnclusteredSequences() - self._iLaunchBlastclust.getClusteringResultsInFasta(inFileName) - fileObs = "%s_Blastclust.fa" % os.path.splitext(inFileName)[0] - - if not FileUtils.are2FilesIdentical(fileObs, fileExp): - print "Files are different" - return - else: - print "Files are identical\n" - - os.remove(inFileName) - os.remove(tmpFileName) - os.remove(fileExp) - os.remove(fileObs) - - def test_getLinkInitNewHeaders(self): - inFileName = "dummyInput_%s.shortHlink" % self._uniqId - inF = open(inFileName, "w") - inF.write("seq1\tHeader1\t1\t5193\n") - inF.write("seq2\tHeader2\t1\t5193\n") - inF.write("seq3\tHeader3\t1\t5193\n") - inF.write("seq4\tHeader4\t1\t5193\n") - inF.close() - - self._iLaunchBlastclust.setInputFileName("dummyInput_%s" % self._uniqId) - dObs = self._iLaunchBlastclust.getLinkInitNewHeaders() - dExp = {"seq1":"Header1", "seq2":"Header2", "seq3":"Header3", "seq4":"Header4"} - - self.assertEqual(dObs, dExp) - os.remove(inFileName) - - def test_retrieveInitHeaders(self): - dIn = {"seq1":"Header1", "seq2":"Header2", "seq3":"Header3", "seq4":"Header4"} - - inFileName = "dummyInFile_%s" % self._uniqId - outFilePrefix = self._uniqId - - tmpFileName = "%s_blastclust.txt" % outFilePrefix - inF = open(tmpFileName, "w") - inF.write("seq1 seq3 seq4\n") - inF.write("seq2\n") - inF.close() - - shortHFile = "%s.shortH_Blastclust.fa" % inFileName - shF = open(shortHFile, "w") - shF.write(">BlastclustCluster1Mb1_seq1\n") - shF.write("gaattgtttactta\n") - shF.write(">BlastclustCluster1Mb2_seq3\n") - shF.write("gaattgtttactta\n") - shF.write(">BlastclustCluster1Mb3_seq4\n") - shF.write("gaattgtttactta\n") - shF.write(">BlastclustCluster2Mb1_seq2\n") - shF.write("gaattgtttactta\n") - shF.close() - - fileExp = "retrieveInitHeadersExpected.fa" - outF = open(fileExp, "w") - outF.write(">BlastclustCluster1Mb1_Header1\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster1Mb2_Header3\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster1Mb3_Header4\n") - outF.write("gaattgtttactta\n") - outF.write(">BlastclustCluster2Mb1_Header2\n") - outF.write("gaattgtttactta\n") - outF.close() - - self._iLaunchBlastclust.setInputFileName(inFileName) - self._iLaunchBlastclust.setTmpFileName(tmpFileName) - self._iLaunchBlastclust.setOutputFilePrefix(outFilePrefix) - self._iLaunchBlastclust.retrieveInitHeaders(dIn) - fileObs = "%s_Blastclust.fa" % outFilePrefix - - if not FileUtils.are2FilesIdentical(fileObs, fileExp): - print "Files are different" - return - else: - print "Files are identical\n" - - os.remove(fileObs) - os.remove(fileExp) - os.remove(tmpFileName) - - def test_filterUnclusteredSequences(self): - dClusterId2SeqHeaders = {1: ["seq1","seq2"], 2: ["seq3"]} - dExp = {1: ["seq1","seq2"]} - dObs = self._iLaunchBlastclust.filterUnclusteredSequences(dClusterId2SeqHeaders) - self.assertEqual(dObs, dExp) - - def test_blastclustToMap(self): - inFileName = "dummyBlastclustOut_%s.fa" % self._uniqId - inF = open(inFileName, "w") - inF.write(">BlastclustCluster1Mb1_chunk1 (dbseq-nr 1) [1,14]\n") - inF.write("gaattgtttactta\n") - inF.write(">BlastclustCluster1Mb2_chunk1 (dbseq-nr 1) [30,44]\n") - inF.write("gaattgtttactta\n") - inF.write(">BlastclustCluster2Mb1_chunk2 (dbseq-nr 1) [100,114]\n") - inF.write("gaattgtttactta\n") - inF.write(">BlastclustCluster3Mb1_chunk5 (dbseq-nr 8) [1000,1014]\n") - inF.write("gaattgtttactta") - inF.close() - - fileExp = "blastclustToMapExpected.map" - outF = open(fileExp, "w") - outF.write("BlastclustCluster1Mb1\tchunk1\t1\t14\n") - outF.write("BlastclustCluster1Mb2\tchunk1\t30\t44\n") - outF.write("BlastclustCluster2Mb1\tchunk2\t100\t114\n") - outF.write("BlastclustCluster3Mb1\tchunk5\t1000\t1014\n") - outF.close() - - self._iLaunchBlastclust.blastclustToMap(inFileName) - fileObs = "%s.map" % os.path.splitext(inFileName)[0] - - if not FileUtils.are2FilesIdentical(fileObs, fileExp): - print "Files are different" - return - else: - print "Files are identical\n" - - os.remove(inFileName) - os.remove(fileObs) - os.remove(fileExp) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_LaunchTallymer.py --- a/commons/launcher/tests/Test_LaunchTallymer.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import os -import unittest -from commons.launcher.LaunchTallymer import ConvertUtils - -class Test_ConvertUtils(unittest.TestCase): - - def test_convertTallymerFormatIntoMapFormatAndGenerateData(self): - inputFastaFileName = "input.fa" - inputTallymerSearchFileName = "input.tallymer" - expMapFileName = "exp.map" - obsMapFileName = "obs.map" - self._writeInputFasta(inputFastaFileName) - self._writeInputTallymerSearch(inputTallymerSearchFileName) - self._writeExpMap(expMapFileName) - - expOccNb = 4 - expDKmer2Occ = {"caagatgcgtaacggccata":1, - "aagatgcgtaacggccatac":1, - "agatgcgtaacggccataca":1, - "gatgcgtaacggccatacat":1} - expPlotData = {4379: 17, - 4380: 17, - 4381: 16, - 4382: 16} - - obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName) - - self.assertEquals(expOccNb, obsOccNb) - self.assertEquals(expDKmer2Occ, obsDKmer2Occ) - self.assertEquals(expPlotData, obsPlotData) - self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName)) - - os.remove(inputFastaFileName) - os.remove(inputTallymerSearchFileName) - os.remove(expMapFileName) - os.remove(obsMapFileName) - - def test_convertTallymerFormatIntoMapFormatAndGenerateDataMultiFasta(self): - inputFastaFileName = "input.fa" - inputTallymerSearchFileName = "input.tallymer" - expMapFileName = "exp.map" - obsMapFileName = "obs.map" - self._writeInputMultiFasta(inputFastaFileName) - self._writeInputTallymerSearchMultiFasta(inputTallymerSearchFileName) - self._writeExpMapMultiFasta(expMapFileName) - - expOccNb = 6 - expDKmer2Occ = {"caagatgcgtaacggccata":1, - "aagatgcgtaacggccatac":1, - "agatgcgtaacggccataca":1, - "gatgcgtaacggccatacat":1, - "agatgcgtaacggccataca":2, - "gatgcgtaacggccatacat":2} - expPlotData = {4379: 17, 4380: 17, 4381: 16, 4382: 35} - - obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName) - - self.assertEquals(expOccNb, obsOccNb) - self.assertEquals(expDKmer2Occ, obsDKmer2Occ) - self.assertEquals(expPlotData, obsPlotData) - self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName)) - - os.remove(inputFastaFileName) - os.remove(inputTallymerSearchFileName) - os.remove(expMapFileName) - os.remove(obsMapFileName) - - def _writeInputTallymerSearch(self, tallymerFormatFileName): - with open(tallymerFormatFileName, 'w') as f: - f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n") - f.write("0\t+4379\t17\taagatgcgtaacggccatac\n") - f.write("0\t+4380\t16\tagatgcgtaacggccataca\n") - f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n") - - def _writeInputFasta(self, fastaFileName): - with open(fastaFileName, 'w') as f: - f.write(">Seq1\n") - f.write("caagatgcgtaacggccata\n") - f.write("aagatgcgtaacggccatac\n") - f.write("agatgcgtaacggccataca\n") - f.write("gatgcgtaacggccatacat\n") - - def _writeExpMap(self, mapFileName): - with open(mapFileName, 'w') as f: - f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n") - f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n") - f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n") - f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n") - - def _writeInputTallymerSearchMultiFasta(self, tallymerFormatFileName): - with open(tallymerFormatFileName, 'w') as f: - f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n") - f.write("0\t+4379\t17\taagatgcgtaacggccatac\n") - f.write("0\t+4380\t16\tagatgcgtaacggccataca\n") - f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n") - f.write("1\t+4380\t16\tagatgcgtaacggccataca\n") - f.write("1\t+4381\t35\tgatgcgtaacggccatacat\n") - - def _writeInputMultiFasta(self, fastaFileName): - with open(fastaFileName, 'w') as f: - f.write(">Seq1\n") - f.write("caagatgcgtaacggccata\n") - f.write("aagatgcgtaacggccatac\n") - f.write("agatgcgtaacggccataca\n") - f.write("gatgcgtaacggccatacat\n") - f.write(">Seq2\n") - f.write("agatgcgtaacggccataca\n") - f.write("gatgcgtaacggccatacat\n") - - def _writeExpMapMultiFasta(self, mapFileName): - with open(mapFileName, 'w') as f: - f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n") - f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n") - f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n") - f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n") - f.write("agatgcgtaacggccataca_16\tSeq2\t4381\t4401\t16\n") - f.write("gatgcgtaacggccatacat_35\tSeq2\t4382\t4402\t35\n") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_MafftClusterLauncher.py --- a/commons/launcher/tests/Test_MafftClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -import unittest -from commons.launcher.MafftClusterLauncher import MafftClusterLauncher - - -class Test_MafftClusterLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = MafftClusterLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -p: parameters for 'mafft' (default='--auto')" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-p", "dummyPrgParam" ) - self.assertEqual( "dummyPrgParam", self._i.getProgramParameters() ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_MafftProgramLauncher.py --- a/commons/launcher/tests/Test_MafftProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -import unittest -from commons.launcher.MafftProgramLauncher import MafftProgramLauncher - -class Test_MafftProgramLauncher( unittest.TestCase ): - - - def setUp( self ): - self._i = MafftProgramLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -p: parameters for '%s' (default='--auto')" % ( "mafft" ) - exp += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-p", "'--auto --maxiterate 500'" ) - self.assertEqual( "'--auto --maxiterate 500'", self._i.getProgramParameters() ) - - self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" ) - self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() ) - - - def test_setWrapperCommandLine( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - exp = "MafftProgramLauncher.py" - exp += " -i %s" % ( inFile ) - exp += " -p '%s'" % ( "--auto" ) - exp += " -o %s.fa_aln" % ( inFile ) - exp += " -v 0" - self._i.setWrapperCommandLine() - obs = self._i.getWrapperCommandLine() - self.assertEqual( exp, obs ) - - - def test_setProgramCommandLine( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - exp = self._i.getProgramName() - exp += " %s" % ( "--auto" ) - exp += " --quiet" - exp += " %s.shortH" % ( inFile ) - exp += " > %s.shortH.fa_aln" % ( inFile ) - exp += " 2> /dev/null" - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - - def test_setListFilesToKeep( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - self._i.setListFilesToKeep() - lExp = [ "dummyInFile.fa.fa_aln" ] - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - self._i._lFilesToKeep = [] - - outFile = "dummyOutFile.fa_aln" - self._i.setOutputFile( outFile ) - self._i.setListFilesToKeep() - lExp = [ outFile ] - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setListFilesToRemove( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - self._i.setListFilesToRemove() - lExp = [ "dummyInFile.fa.shortH", \ - "dummyInFile.fa.shortH.fa_aln", \ - "dummyInFile.fa.shortHlink" ] - lObs = self._i.getListFilesToRemove() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setSummary( self ): - self._i.setInputFile( "dummyInFile.fa" ) - exp = "input file: %s" % ( "dummyInFile.fa" ) - exp += "\nparameters: %s" % ( "--auto" ) - exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_MapClusterLauncher.py --- a/commons/launcher/tests/Test_MapClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -import unittest -from commons.launcher.MapClusterLauncher import MapClusterLauncher - - -class Test_MapClusterLauncher( unittest.TestCase ): - - - def setUp( self ): - self._i = MapClusterLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self._i.getGapSize() ) - exp += "\n -m: penalty for a mismatch (default='%i')" % ( self._i.getMismatchPenalty() ) - exp += "\n -O: penalty for a gap openning (default='%i')" % ( self._i.getGapOpenPenalty() ) - exp += "\n -e: penalty for a gap extension (default='%i')" % ( self._i.getGapExtendPenalty() ) - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "42" ) - self.assertEqual( 42, self._i.getGapSize() ) - - self._i.setASpecificAttributeFromCmdLine( "-m", "-7" ) - self.assertEqual( -7, self._i.getMismatchPenalty() ) - - self._i.setASpecificAttributeFromCmdLine( "-O", "15" ) - self.assertEqual( 15, self._i.getGapOpenPenalty() ) - - self._i.setASpecificAttributeFromCmdLine( "-e", "5" ) - self.assertEqual( 5, self._i.getGapExtendPenalty() ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_MapProgramLauncher.py --- a/commons/launcher/tests/Test_MapProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,115 +0,0 @@ -import unittest -from commons.launcher.MapProgramLauncher import MapProgramLauncher - -class Test_MapProgramLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = MapProgramLauncher() - - def tearDown( self ): - self._i = None - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self._i.getGapSize() ) - exp += "\n -m: penalty for a mismatch (default='%i', match=10)" % ( self._i.getMismatchPenalty() ) - exp += "\n -O: penalty for a gap opening (default='%i')" % ( self._i.getGapOpenPenalty()) - exp += "\n -e: penalty for a gap extension (default='%i')" % ( self._i.getGapExtendPenalty() ) - exp += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "40" ) - self.assertEqual( 40, self._i.getGapSize() ) - - self._i.setASpecificAttributeFromCmdLine( "-m", "-7" ) - self.assertEqual( -7, self._i.getMismatchPenalty() ) - - self._i.setASpecificAttributeFromCmdLine( "-O", "15" ) - self.assertEqual( 15, self._i.getGapOpenPenalty() ) - - self._i.setASpecificAttributeFromCmdLine( "-e", "5" ) - self.assertEqual( 5, self._i.getGapExtendPenalty() ) - - self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" ) - self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() ) - - def test_setWrapperCommandLine( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - exp = "MapProgramLauncher.py" - exp += " -i %s" % ( inFile ) - exp += " -s 50" - exp += " -m -8" - exp += " -O 16" - exp += " -e 4" - exp += " -o %s.fa_aln" % ( inFile ) - exp += " -v 0" - self._i.setWrapperCommandLine() - obs = self._i.getWrapperCommandLine() - self.assertEqual( exp, obs ) - - def test_setProgramCommandLine( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - exp = self._i.getProgramName() - exp += " %s.shortH" % ( inFile ) - exp += " 50" - exp += " -8" - exp += " 16" - exp += " 4" - exp += " > %s.shortH.fa_aln" % ( inFile ) - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - def test_setListFilesToKeep( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - self._i.setListFilesToKeep() - lExp = [ "dummyInFile.fa.fa_aln" ] - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - self._i._lFilesToKeep = [] - - outFile = "dummyOutFile.fa_aln" - self._i.setOutputFile( outFile ) - self._i.setListFilesToKeep() - lExp = [ outFile ] - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - def test_getListFilesToRemove( self ): - inFile = "dummyInFile.fa" - self._i.setInputFile( inFile ) - self._i.setListFilesToRemove() - lExp = [ "dummyInFile.fa.shortH", \ - "dummyInFile.fa.shortH.fa_aln", \ - "dummyInFile.fa.shortHlink" ] - lObs = self._i.getListFilesToRemove() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - def test_setSummary( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setGapSize( 104 ) - exp = "input file: %s" % ( "dummyInFile.fa" ) - exp += "\ngap size: %i" % ( self._i.getGapSize() ) - exp += "\nmismatch penalty: %i" % ( self._i.getMismatchPenalty() ) - exp += "\ngap openning penalty: %i" % ( self._i.getGapOpenPenalty() ) - exp += "\ngap extension penalty: %i" % ( self._i.getGapExtendPenalty() ) - exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_NWalignProgramLauncher.py --- a/commons/launcher/tests/Test_NWalignProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -import unittest -from commons.launcher.NWalignProgramLauncher import NWalignProgramLauncher - - -class Test_NWalignProgramLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = NWalignProgramLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (format='fasta')" - exp += "\n -p: parameters for 'NWalign'" - exp += "\n -o: name of the output file (format='align', default=inFile+'.align')" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - - self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" ) - self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() ) - - - def test_setWrapperCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "NWalignProgramLauncher.py" - exp += " -i %s" % ( "dummyInFile.fa" ) - exp += " -s %s" % ( "dummySubjectFile.fa" ) - exp += " -o %s.align" % ( "dummyInFile.fa" ) - exp += " -v 0" - self._i.setWrapperCommandLine() - obs = self._i.getWrapperCommandLine() - self.assertEqual( exp, obs ) - - - def test_setProgramCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - self._i.setProgramParameters( "-m 2" ) - exp = "NWalign -m 2 -o dummyInFile.fa.afa -v 0 dummySubjectFile.fa dummyInFile.fa" - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - - def test_setListFilesToKeep( self ): - self._i.setInputFile( "dummyInFile.fa" ) - lExp = [ "dummyInFile.fa.afa" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setSummary( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "input file: %s" % ( self._i.getInputFile() ) - exp += "\nsubject file: %s" % ( self._i.getSubjectFile() ) - exp += "\nparameters: %s" % ( self._i.getProgramParameters() ) - exp += "\noutput file: %s" % ( "dummyInFile.fa.align" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_RepeatMaskerClusterLauncher.py --- a/commons/launcher/tests/Test_RepeatMaskerClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -import unittest -from commons.launcher.RepeatMaskerClusterLauncher import RepeatMaskerClusterLauncher - - -class Test_RepeatmaskerClusterLauncher( unittest.TestCase ): - - - def setUp( self ): - self._i = RepeatMaskerClusterLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (repeats, format='fasta')" - exp += "\n -n: nb of processors to use in parallel (default=1)" - exp += "\n -g: calculate the GC content" - exp += "\n -b: skip bacterial insertion element check" - exp += "\n -l: mask low-complexity DNA or simple repeats" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - - self._i.setASpecificAttributeFromCmdLine( "-n", "2" ) - self.assertEqual( 2, self._i.getNbProcessors() ) - - self._i.setASpecificAttributeFromCmdLine( "-g" ) - self.assertTrue( self._i.getCalculateGCcontent() ) - - self._i.setASpecificAttributeFromCmdLine( "-b" ) - self.assertTrue( self._i.getSkipBacterialIsCheck() ) - - self._i.setASpecificAttributeFromCmdLine( "-l" ) - self.assertFalse( self._i.getMaskSsr() ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_RepeatMaskerProgramLauncher.py --- a/commons/launcher/tests/Test_RepeatMaskerProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,171 +0,0 @@ -import unittest -from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher - - -class Test_RepeatMaskerProgramLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = RepeatMaskerProgramLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (repeats, format='fasta')" - exp += "\n -n: nb of processors to use in parallel (default='%i')" % ( self._i.getNbProcessors() ) - exp += "\n -g: calculate the GC content" - exp += "\n -b: skip bacterial insertion element check" - exp += "\n -l: does not mask low-complexity DNA or simple repeats" - exp += "\n -m: only masks low complex/simple repeats (no interspersed repeats)" - exp += "\n -o: name of the output file" - exp += "\n with -s: format='align', default=inFile+'.cat.align')" - exp += "\n with -m: format='path', default=inFile+'.cat.path')" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - - self._i.setASpecificAttributeFromCmdLine( "-n", "2" ) - self.assertEqual( 2, self._i.getNbProcessors() ) - - self._i.setASpecificAttributeFromCmdLine( "-g" ) - self.assertEqual( True, self._i.getCalculateGCcontent() ) - - self._i.setASpecificAttributeFromCmdLine( "-b" ) - self.assertEqual( True, self._i.getSkipBacterialIsCheck() ) - - self._i.setASpecificAttributeFromCmdLine( "-l" ) - self.assertEqual( False, self._i.getMaskSsr() ) - - self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" ) - self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() ) - - - def test_setWrapperCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "RepeatMaskerProgramLauncher.py" - exp += " -i %s" % ( "dummyInFile.fa" ) - exp += " -s %s" % ( "dummySubjectFile.fa" ) - exp += " -n 1" - self._i.setWrapperCommandLine() - obs = self._i.getWrapperCommandLine() - self.assertEqual( exp, obs ) - - - def test_setProgramCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - self._i.setCalculateGCcontent() - self._i.setSkipBacterialIsCheck() - exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow -lib dummySubjectFile.fa dummyInFile.fa" - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - - def test_setProgramCommandLine_withoutSubjects_withMaskSsr( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setCalculateGCcontent() - self._i.setSkipBacterialIsCheck() - exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow dummyInFile.fa" - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - - def test_setListFilesToKeep_onlyInFile( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setOnlySsr() - lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.path" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setListFilesToKeep_withSubjectFile( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySbjFile.fa" ) - lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.align" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setListFilesToKeep_inFileAndOutFile( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setOutputFile( "dummyOutFile.align" ) - lExp = [ "dummyInFile.fa.cat", "dummyOutFile.align" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setListFilesToKeep_inFileAndOutFileAndSsr( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.unsetMaskSsr() - self._i.setOutputFile( "dummyOutFile.path" ) - lExp = [ "dummyInFile.fa.cat", "dummyOutFile.path" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setListFilesToRemove( self ): - self._i.setInputFile( "dummyInFile.fa" ) - lExp = [ "dummyInFile.fa.out", \ - "dummyInFile.fa.log", \ - "dummyInFile.fa.stderr", \ - "dummyInFile.fa.ori.out", \ - "dummyInFile.fa.masked", \ - "dummyInFile.fa.tbl", \ - "dummyInFile.fa.ref" ] - self._i.setListFilesToRemove() - lObs = self._i.getListFilesToRemove() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setSummary( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "input file: %s" % ( self._i.getInputFile() ) - exp += "\nsubject file: %s" % ( self._i.getSubjectFile() ) - exp += "\nnb processors: %i" % ( self._i.getNbProcessors() ) - exp += "\nmask low-complexity DNA or simple repeats" - exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.path" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - - - def test_setSummary_noMaskSsr( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - self._i.unsetMaskSsr() - exp = "input file: %s" % ( self._i.getInputFile() ) - exp += "\nsubject file: %s" % ( self._i.getSubjectFile() ) - exp += "\nnb processors: %i" % ( self._i.getNbProcessors() ) - exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.align" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_YassClusterLauncher.py --- a/commons/launcher/tests/Test_YassClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -import unittest -from commons.launcher.YassClusterLauncher import YassClusterLauncher - -class Test_YassClusterLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = YassClusterLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (format='fasta')" - exp += "\n -p: parameters for 'yass'" - exp += "\n -Z: concatenate output files" - exp += "\n -A: same sequences (all-by-all)" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_YassProgramLauncher.py --- a/commons/launcher/tests/Test_YassProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ -import unittest -from commons.launcher.YassProgramLauncher import YassProgramLauncher - - - -class Test_YassProgramLauncher( unittest.TestCase ): - - def setUp( self ): - self._i = YassProgramLauncher() - - - def tearDown( self ): - self._i = None - - - def test_getSpecificHelpAsString( self ): - exp = "" - exp += "\nspecific options:" - exp += "\n -s: name of the subject file (format='fasta')" - exp += "\n -p: parameters for 'yass'" - exp += "\n -A: same sequences (all-by-all)" - exp += "\n -o: name of the output file (format='align', default=inFile+'.align')" - obs = self._i.getSpecificHelpAsString() - self.assertEqual( exp, obs ) - - - def test_setASpecificAttributeFromCmdLine( self ): - self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" ) - self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() ) - - self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" ) - self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() ) - - - def test_setWrapperCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "YassProgramLauncher.py" - exp += " -i %s" % ( "dummyInFile.fa" ) - exp += " -s %s" % ( "dummySubjectFile.fa" ) - exp += " -o %s.align" % ( "dummyInFile.fa" ) - exp += " -v 0" - self._i.setWrapperCommandLine() - obs = self._i.getWrapperCommandLine() - self.assertEqual( exp, obs ) - - - def test_setProgramCommandLine( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "yass -d 2 -o dummyInFile.fa.blast dummyInFile.fa dummySubjectFile.fa" - self._i.setProgramCommandLine() - obs = self._i.getProgramCommandLine() - self.assertEqual( exp, obs ) - - - def test_setListFilesToKeep( self ): - self._i.setInputFile( "dummyInFile.fa" ) - lExp = [ "dummyInFile.fa.align" ] - self._i.setListFilesToKeep() - lObs = self._i.getListFilesToKeep() - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_setSummary( self ): - self._i.setInputFile( "dummyInFile.fa" ) - self._i.setSubjectFile( "dummySubjectFile.fa" ) - exp = "input file: %s" % ( self._i.getInputFile() ) - exp += "\nsubject file: %s" % ( self._i.getSubjectFile() ) - exp += "\nparameters: %s" % ( self._i.getProgramParameters() ) - exp += "\noutput file: %s" % ( "dummyInFile.fa.align" ) - self._i.setSummary() - obs = self._i.getSummary() - self.assertEqual( exp, obs ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/Test_launchTEclass.py --- a/commons/launcher/tests/Test_launchTEclass.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.launcher import launchTEclass - - -class Test_launchTEclass( unittest.TestCase ): - - def test_parseFastaFileFromTEclass( self ): - inFile = "dummyLibFile.fa" - inHandler = open( inFile, "w" ) - inHandler.write( ">1360|TEclass result: DNA|ORFs: 1360..2226:+1\n" ) - inHandler.write( "AGCATGACGCA\n" ) - inHandler.write( ">FB|TEclass result: unclear\n" ) - inHandler.write( "GCATGCAGCGACGCGAC\n" ) - inHandler.close() - - expFile = "dummyExpFile.map" - expHandler = open( expFile, "w" ) - expHandler.write( "DNA\t1360\t1\t11\n" ) - expHandler.write( "unclear\tFB\t1\t17\n" ) - expHandler.close() - - obsFile = "dummyObsFile.map" - - launchTEclass.parseFastaFileFromTEclass( inFile, obsFile ) - - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, expFile, obsFile ]: - os.remove( f ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/launcher/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/AlignList.py --- a/commons/pyRepetUnit/align/AlignList.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -## class of list of align object -# -class AlignList: - - list; - - def __init__( self ): - self.list = [] - - ## append align instance in the align instance list - # - # @param AlignInstance instance of align object - # - def append(self, AlignInstance): - self.list.append(AlignInstance) - - ## get length of list of align instance - # - #@return length integer length of list - # - def len(self): - return len(self.list) - - ## get list of align instance - # - #@return list of align instance - # - def getList(self): - return self.list - - ## get item in list of align instance according to index - # - #@param index integer index of list - #@return align instance item of list of align instance - # - def get(self, index): - return self.list[index] - - ## extend align instance in the align instance list - # - # @param AlignInstance instance of align object - # - def extend(self, AlignInstance): - self.list.extend(AlignInstance) - - ## take off an align instance from the align instance list - # - # @param AlignInstance instance of align object - # - def remove(self, AlignInstance): - self.list.remove(AlignInstance) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/AlignListUtils.py --- a/commons/pyRepetUnit/align/AlignListUtils.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -import os -import commons.core.coord.Align -import commons.pyRepetUnit.align.AlignList -from commons.core.utils.FileUtils import FileUtils - -class AlignListUtils: - - ##read a file in align format and return a AlignList - # - # @param inFileName string name of file - # @return listAlignInstance list list of align instance - # - def read( inFileName ): - alignInstance = commons.core.coord.Align.Align() - listAlignInstance = commons.pyRepetUnit.align.AlignList.AlignList() - f = open( inFileName , "r") - while alignInstance.read( f ): - listAlignInstance.append(alignInstance) - alignInstance = commons.core.coord.Align.Align() - f.close - return (listAlignInstance) - - read = staticmethod( read ) - - ## write a file in align format from an AlignList - # - # @param alignListInstance list list of align instance object - # @param inFileName string name of file - def write( alignListInstance, inFileName ): - f = open( inFileName , "w") - for alignInstance in alignListInstance.getList(): - alignInstance.write( f ) - f.close - - write = staticmethod( write ) - - ## Filter an AlignList by removing all is <= minScore - # - # @param listAlignInstance list list of align instance object - # @param minScore integer minimum score to keep in result - # - def filterOnAMinimalScore( listAlignInstance, minScore ): - listAlignInstanceOld = commons.pyRepetUnit.align.AlignList.AlignList() - for alignInstance in listAlignInstance.getList(): - listAlignInstanceOld.append(alignInstance) - for alignInstance in listAlignInstanceOld.getList(): - if alignInstance.score <= minScore: - listAlignInstance.remove(alignInstance) - - filterOnAMinimalScore = staticmethod( filterOnAMinimalScore ) - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/HmmpfamOutput2align.py --- a/commons/pyRepetUnit/align/hmmOutputParsing/HmmpfamOutput2align.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing - -##data processor : read an output from hmmpfam and transform it into .align file -# -class HmmpfamOutput2align( object ): - - ## constructor - # - def __init__(self): - self.hmmpfamOutputProcess = HmmpfamOutputProcessing() - self._inputFile = "" - self._outputFile = "" - - ## set input file - # - # @param input file input file - # - def setInputFile(self, input): - self._inputFile = input - - ## set output file - # - # @param output file output file - # - def setOutputFile(self, output): - self._outputFile = output - - - ##read a hmmpfam output file, parse it and, write the corresponding .align file - # - def run( self ): - self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/HmmscanOutput2align.py --- a/commons/pyRepetUnit/align/hmmOutputParsing/HmmscanOutput2align.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing -##data processor : read an output from hmmscan and transform it into .align file -# -class HmmscanOutput2align( object ): - - ## constructor - # - def __init__(self): - self.hmmscanOutputProcess = HmmscanOutputProcessing() - self._inputFile = "" - self._outputFile = "" - - ## set input file - # - # @param input file input file - # - def setInputFile(self, input): - self._inputFile = input - ## set output file - # @param output file output file - # - def setOutputFile(self, output): - self._outputFile = output - - ##read a hmmscan output file, parse it and, write the corresponding .align file - # - def run( self ): - self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/HmmpfamOutput2AlignTestSuite.py --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/HmmpfamOutput2AlignTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -import unittest -import sys -from Test_F_HmmpfamOutput2align import Test_F_HmmpfamOutput2align -from Test_F_HmmscanOutput2align import Test_F_HmmscanOutput2align -from Test_F_Hmmerpfam2align import Test_F_Hmmerpfam2align -from commons.tools.tests.Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script import Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script - -def main(): - - hmmerTestSuite = unittest.TestSuite() - hmmerTestSuite.addTest(unittest.makeSuite(Test_F_HmmpfamOutput2align,'test')) - hmmerTestSuite.addTest(unittest.makeSuite(Test_F_HmmscanOutput2align,'test')) - hmmerTestSuite.addTest(unittest.makeSuite(Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script,'test')) - hmmerTestSuite.addTest(unittest.makeSuite(Test_F_Hmmerpfam2align,'test')) - - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(hmmerTestSuite) - - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_Hmmerpfam2align.py --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_Hmmerpfam2align.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -import os -import unittest -import commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing -from commons.core.utils.FileUtils import FileUtils - -class Test_F_Hmmerpfam2align(unittest.TestCase): - - def setUp(self): - self.hmmpfamOutputProcess = commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing.HmmpfamOutputProcessing() - self._inputFile = "./datas/test_hmmpfam_output" - self._outputFile = "./datas/PostProcessResult.align" - - def testAcceptanceHmmpfam2align(self): - self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile ) - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._inputFile + ".align", self._outputFile)) - os.remove(self._outputFile) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_HmmpfamOutput2align.py --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_HmmpfamOutput2align.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align import HmmpfamOutput2align -from commons.core.utils.FileUtils import FileUtils - -class Test_F_HmmpfamOutput2align(unittest.TestCase): - - def setUp(self): - self.hmmpfamOutput2align = HmmpfamOutput2align() - self._inputFile = "./datas/test_hmmpfam_output" - self._outputFile = "./datas/hmmpfam_output.align" - - def testParseHmmpfamOutput2align(self): - self.hmmpfamOutput2align.setInputFile(self._inputFile) - self.hmmpfamOutput2align.setOutputFile(self._outputFile) - self.hmmpfamOutput2align.run() - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._inputFile + ".align", self._outputFile)) - os.remove( self._outputFile ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_HmmscanOutput2align.py --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/Test_F_HmmscanOutput2align.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.align.hmmOutputParsing.HmmscanOutput2align import HmmscanOutput2align -from commons.core.utils.FileUtils import FileUtils - -CURRENT_DIR = os.getcwd() - -class Test_F_HmmscanOutput2align(unittest.TestCase): - - def setUp(self): - self.hmmscanOutput2align = HmmscanOutput2align() - self._inputFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput" - self._outputFile = "./datas/test_hmmscanOutput.align" - os.chdir(CURRENT_DIR) - - def testParseHmmscanOutput2align(self): - self.hmmscanOutput2align.setInputFile(self._inputFile) - self.hmmscanOutput2align.setOutputFile(self._outputFile) - self.hmmscanOutput2align.run() - expectedFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align" - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(expectedFile, self._outputFile)) - os.remove( self._outputFile ) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/ConsensusTestFile_nt.fsa --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/ConsensusTestFile_nt.fsa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ ->blumeria_Grouper_590_20:NoCat -TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA -AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT -ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA -ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA -CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC -TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC -TCCATAATTTCAACACTNAAGAATATTTGTA ->blumeria_Grouper_4152_12:NoCat -GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA -AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC -GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC -GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC -TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT -TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT -GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG -CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC -ATATCTACCTCGGGGACATTG diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,406 +0,0 @@ -hmmpfam - search one or more sequences against HMM database -HMMER 2.3.2 (Oct 2003) -Copyright (C) 1992-2003 HHMI/Washington University School of Medicine -Freely distributed under the GNU General Public License (GPL) -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -HMM file: /home/choede/hmmer3/Pfam_fs -Sequence file: ConsensusTestFile_aaWithoutStop.fsa -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query sequence: blumeria_Grouper_590_20:NoCat_1 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -DUF234 Archaea bacterial proteins of unknown 3.2 1.5 1 -DUF1414 Protein of unknown function (DUF1414) 2.9 6.3 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -DUF234 1/1 91 108 .. 5 22 .. 3.2 1.5 -DUF1414 1/1 111 119 .. 1 9 [. 2.9 6.3 - -Alignments of top-scoring domains: -DUF234: domain 1 of 1, from 91 to 108: score 3.2, E = 1.5 - *->VyPNrseIEsGnikevle<-* - VyPN++ IEs ++k++++ - blumeria_G 91 VYPNIEIIESSTPKPLIN 108 - -DUF1414: domain 1 of 1, from 111 to 119: score 2.9, E = 6.3 - *->HkAPvDLSL<-* - H ++DLSL - blumeria_G 111 HXSSPDLSL 119 - -// - -Query sequence: blumeria_Grouper_590_20:NoCat_2 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- - [no hits above thresholds] - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- - [no hits above thresholds] - -Alignments of top-scoring domains: - [no hits above thresholds] -// - -Query sequence: blumeria_Grouper_590_20:NoCat_3 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -CPW_WPC Plasmodium falciparum domain of unknown func 1.5 7.7 1 -HECT HECT-domain (ubiquitin-transferase) 0.0 9.2 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -CPW_WPC 1/1 30 37 .. 1 9 [. 1.5 7.7 -HECT 1/1 55 69 .. 341 355 .] 0.0 9.2 - -Alignments of top-scoring domains: -CPW_WPC: domain 1 of 1, from 30 to 37: score 1.5, E = 7.7 - *->CerdYsisk<-* - C++dYs sk - blumeria_G 30 CQFDYS-SK 37 - -HECT: domain 1 of 1, from 55 to 69: score 0.0, E = 9.2 - *->LllAIneeteGFgle<-* - Ll+A+n+ + G+ ++ - blumeria_G 55 LLTAVNNANTGYTQS 69 - -// - -Query sequence: blumeria_Grouper_590_20:NoCat_4 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -DUF46 Putative integral membrane protein DUF46 6.4 0.11 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -DUF46 1/1 82 91 .. 173 182 .] 6.4 0.11 - -Alignments of top-scoring domains: -DUF46: domain 1 of 1, from 82 to 91: score 6.4, E = 0.11 - *->YkLGlKdVpW<-* - Y+LGlK V++ - blumeria_G 82 YLLGLKGVWY 91 - -// - -Query sequence: blumeria_Grouper_590_20:NoCat_5 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -POC4 POC4 chaperone -1.7 6.3 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -POC4 1/1 121 125 .. 276 280 .] -1.7 6.3 - -Alignments of top-scoring domains: -POC4: domain 1 of 1, from 121 to 125: score -1.7, E = 6.3 - *->SGLYI<-* - SGLYI - blumeria_G 121 SGLYI 125 - -// - -Query sequence: blumeria_Grouper_590_20:NoCat_6 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- - [no hits above thresholds] - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- - [no hits above thresholds] - -Alignments of top-scoring domains: - [no hits above thresholds] -// - -Query sequence: blumeria_Grouper_4152_12:NoCat_1 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -Peptidase_S29 Hepatitis C virus NS3 protease 4.7 1.1 1 -DGOK 2-keto-3-deoxy-galactonokinase 0.5 1.3 1 -TNV_CP Satellite tobacco necrosis virus coat p 0.1 7.9 1 -TrbL TrbL/VirB6 plasmid conjugal transfer pr 0.8 8 1 -Amino_oxidase Flavin containing amine oxidoreductase -0.6 9.1 1 -DUF1301 Protein of unknown function (DUF1301) 0.4 9.9 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -Amino_oxidase 1/1 27 38 .. 471 482 .] -0.6 9.1 -TrbL 1/1 33 67 .. 231 285 .] 0.8 8 -TNV_CP 1/1 58 80 .. 167 189 .. 0.1 7.9 -DGOK 1/1 94 109 .. 283 298 .] 0.5 1.3 -Peptidase_S29 1/1 113 127 .. 1 15 [. 4.7 1.1 -DUF1301 1/1 148 157 .. 1 10 [. 0.4 9.9 - -Alignments of top-scoring domains: -Amino_oxidase: domain 1 of 1, from 27 to 38: score -0.6, E = 9.1 - CS HHHHHHHHHHHH - *->veSGlrAAaril<-* - veSG rAA +l - blumeria_G 27 VESGXRAASTLL 38 - -TrbL: domain 1 of 1, from 33 to 67: score 0.8, E = 8 - *->ksstiesfnlfvllaivllslvlilllkqipgiAqglvgavvtlgga - ++st+ + +++ ++ +++++l+l++ ++iA - blumeria_G 33 AASTLLI-----AVEHIVNCAAFCLALRSSASIA------------- 61 - - vaaalaGG<-* - a+ +GG - blumeria_G 62 --ASNSGG 67 - -TNV_CP: domain 1 of 1, from 58 to 80: score 0.1, E = 7.9 - CS SSSGGGB-TTEEEEEEEES-SS- - *->AdvAaSNgpgAvFvLeigdkvag<-* - A++AaSN g vF+L +++ g - blumeria_G 58 ASIAASNSGGCVFFLPAASSAGG 80 - -DGOK: domain 1 of 1, from 94 to 109: score 0.5, E = 1.3 - *->VdGDeAvrAGLseiAr<-* - VdG A AGL ++ r - blumeria_G 94 VDGVSALFAGLTSAGR 109 - -Peptidase_S29: domain 1 of 1, from 113 to 127: score 4.7, E = 1.1 - *->GevqvLgTaTqsflG<-* - G+v++ + aT+ flG - blumeria_G 113 GTVMRFSGATTVFLG 127 - -DUF1301: domain 1 of 1, from 148 to 157: score 0.4, E = 9.9 - *->gVKvFSlSTS<-* - ++vFS+STS - blumeria_G 148 SARVFSFSTS 157 - -// - -Query sequence: blumeria_Grouper_4152_12:NoCat_2 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -DUF1602 Protein of unknown function (DUF1602) 5.0 0.39 1 -Toxin_18 Conotoxin O-superfamily 4.2 4.4 1 -ABC_transp_aux ABC-type uncharacterized transport sys 1.1 5.2 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -Toxin_18 1/1 21 26 .. 50 55 .] 4.2 4.4 -ABC_transp_aux 1/1 126 137 .. 276 287 .] 1.1 5.2 -DUF1602 1/1 143 159 .. 23 39 .] 5.0 0.39 - -Alignments of top-scoring domains: -Toxin_18: domain 1 of 1, from 21 to 26: score 4.2, E = 4.4 - *->gfCLpr<-* - +fCL+r - blumeria_G 21 NFCLHR 26 - -ABC_transp_aux: domain 1 of 1, from 126 to 137: score 1.1, E = 5.2 - *->wGvrldpdlVlD<-* - wG+r+dp+l+l - blumeria_G 126 WGIRWDPRLALR 137 - -DUF1602: domain 1 of 1, from 143 to 159: score 5.0, E = 0.39 - *->kPPlSSsGalfanplrP<-* - +P l + G+l + +lrP - blumeria_G 143 MPKLNRRGFLASRLLRP 159 - -// - -Query sequence: blumeria_Grouper_4152_12:NoCat_3 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -zf-P11 P-11 zinc finger 3.6 1.8 1 -V-ATPase_G Vacuolar (H+)-ATPase G subunit 2.4 5.3 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -zf-P11 1/1 102 122 .. 1 20 [. 3.6 1.8 -V-ATPase_G 1/1 126 135 .. 1 10 [. 2.4 5.3 - -Alignments of top-scoring domains: -zf-P11: domain 1 of 1, from 102 to 122: score 3.6, E = 1.8 - *->GplnCKs..CWfkdknLveCsd<-* - Gp +C+s+ CW + + L C d - blumeria_G 102 GPHFCRSrxCW-NRDALLGCDD 122 - -V-ATPase_G: domain 1 of 1, from 126 to 135: score 2.4, E = 5.3 - *->sqsqGIQqLL<-* - ++s+GIQ LL - blumeria_G 126 GGSGGIQDLL 135 - -// - -Query sequence: blumeria_Grouper_4152_12:NoCat_4 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -XhoI Restriction endonuclease XhoI 9.9 0.014 1 -Endomucin Endomucin 0.1 6 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -XhoI 1/1 92 122 .. 172 202 .] 9.9 0.014 -Endomucin 1/1 113 119 .. 261 267 .] 0.1 6 - -Alignments of top-scoring domains: -XhoI: domain 1 of 1, from 92 to 122: score 9.9, E = 0.014 - *->klvlerfytrpasllrdaqavlqGiikeprk<-* - ++++ ++yt ++ +d++++ qG k+ ++ - blumeria_G 92 RSSRQKKYTPSRIACSDRSGGAQGKTKSRAI 122 - -Endomucin: domain 1 of 1, from 113 to 119: score 0.1, E = 6 - *->AQGKtKN<-* - AQGKtK - blumeria_G 113 AQGKTKS 119 - -// - -Query sequence: blumeria_Grouper_4152_12:NoCat_5 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -SLT Transglycosylase SLT domain 4.5 1.2 1 -DUF881 Bacterial protein of unknown function 4.0 1.6 1 -DUF2346 Uncharacterized conserved protein (DUF 3.2 2.8 1 -DUF1798 Bacterial domain of unknown function ( 3.0 3.3 1 -LBP_BPI_CETP LBP / BPI / CETP family, N-terminal do 1.8 3.8 1 -Jun Jun-like transcription factor -0.7 6.5 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -DUF1798 1/1 2 19 .. 35 52 .. 3.0 3.3 -DUF881 1/1 46 69 .. 214 237 .] 4.0 1.6 -Jun 1/1 77 93 .. 264 284 .. -0.7 6.5 -SLT 1/1 89 108 .. 1 20 [. 4.5 1.2 -DUF2346 1/1 93 115 .. 63 85 .] 3.2 2.8 -LBP_BPI_CETP 1/1 124 139 .. 191 209 .] 1.8 3.8 - -Alignments of top-scoring domains: -DUF1798: domain 1 of 1, from 2 to 19: score 3.0, E = 3.3 - *->KPfvdevdqllaeWkelA<-* - +P+vd+vd++++++k+lA - blumeria_G 2 VPEVDMVDAEVEKLKTLA 19 - -DUF881: domain 1 of 1, from 46 to 69: score 4.0, E = 1.6 - *->VeksdditiPAydgplklrYAkPv<-* - V + +it+PA++ p +r Ak++ - blumeria_G 46 VAPEKRITVPALPRPAEVRPAKRA 69 - -Jun: domain 1 of 1, from 77 to 93: score -0.7, E = 6.5 - *->qHheNPpgfqhsavgpPRlaa<-* - +++eNPp+ a++pP+l a - blumeria_G 77 AGAENPPL----APQPPALEA 93 - -SLT: domain 1 of 1, from 89 to 108: score 4.5, E = 1.2 - CS HHHHHHHHHHTS-HHHHHHH - *->dliikaaekygidpsllaAi<-* - ++ ++a+ k+ ++p llaAi - blumeria_G 89 PALEAAGRKNTHPPELLAAI 108 - -DUF2346: domain 1 of 1, from 93 to 115: score 3.2, E = 2.8 - *->AtKRrEkhdneLlealeeeEaKk<-* - A R+ h eLl+a+e eE+ - blumeria_G 93 AAGRKNTHPPELLAAIEAEERRA 115 - -LBP_BPI_CETP: domain 1 of 1, from 124 to 139: score 1.8, E = 3.8 - CS HHHHHHHCHHHH...HTTS - *->lCPviessVnslNvhLstl<-* - +C +++ssV++ L++l - blumeria_G 124 ICSTAISSVEAA---LQPL 139 - -// - -Query sequence: blumeria_Grouper_4152_12:NoCat_6 -Accession: [none] -Description: [none] - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -DUF258 Protein of unknown function, DUF258 1.5 3.8 1 -TRAP_alpha Translocon-associated protein (TRAP), alph 0.1 4.1 1 -DUF1289 Protein of unknown function (DUF1289) 2.8 5.3 1 -SOCS_box SOCS box 2.4 9.7 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -DUF258 1/1 50 62 .. 293 305 .] 1.5 3.8 -SOCS_box 1/1 85 90 .. 1 6 [. 2.4 9.7 -DUF1289 1/1 95 115 .. 36 56 .] 2.8 5.3 -TRAP_alpha 1/1 106 116 .. 317 327 .] 0.1 4.1 - -Alignments of top-scoring domains: -DUF258: domain 1 of 1, from 50 to 62: score 1.5, E = 3.8 - CS -HHHHHHHHHHHH - *->seeRYesYlklle<-* - s++R+++Y+ l++ - blumeria_G 50 SASRFQHYRDLQK 62 - -SOCS_box: domain 1 of 1, from 85 to 90: score 2.4, E = 9.7 - *->prSLqh<-* - prSLqh - blumeria_G 85 PRSLQH 90 - -DUF1289: domain 1 of 1, from 95 to 115: score 2.8, E = 5.3 - *->dERravlqllpqRlaalglkp<-* - +E+ + lq+++qR +++++ + - blumeria_G 95 AEKIHTLQNCLQRSKRRSAGQ 115 - -TRAP_alpha: domain 1 of 1, from 106 to 116: score 0.1, E = 4.1 - *->kRkvKRsvGdD<-* - +R +Rs+G+D - blumeria_G 106 QRSKRRSAGQD 116 - -// diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/PostPostProcessTestFiltered.align --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/PostPostProcessTestFiltered.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -blumeria_Grouper_590_20:NoCat 271 324 DUF234 5 22 1.5 3 0.000000 -blumeria_Grouper_590_20:NoCat 331 357 DUF1414 1 9 6.3 2 0.000000 -blumeria_Grouper_590_20:NoCat 90 113 CPW_WPC 1 9 7.7 1 0.000000 -blumeria_Grouper_590_20:NoCat 119 148 DUF46 182 173 0.11 6 0.000000 -blumeria_Grouper_4152_12:NoCat 97 201 TrbL 231 285 8 0 0.000000 -blumeria_Grouper_4152_12:NoCat 172 240 TNV_CP 167 189 7.9 0 0.000000 -blumeria_Grouper_4152_12:NoCat 280 327 DGOK 283 298 1.3 0 0.000000 -blumeria_Grouper_4152_12:NoCat 337 381 Peptidase_S29 1 15 1.1 4 0.000000 -blumeria_Grouper_4152_12:NoCat 442 471 DUF1301 1 10 9.9 0 0.000000 -blumeria_Grouper_4152_12:NoCat 62 79 Toxin_18 50 55 4.4 4 0.000000 -blumeria_Grouper_4152_12:NoCat 377 412 ABC_transp_aux 276 287 5.2 1 0.000000 -blumeria_Grouper_4152_12:NoCat 428 478 DUF1602 23 39 0.39 5 0.000000 -blumeria_Grouper_4152_12:NoCat 306 368 zf-P11 1 20 1.8 3 0.000000 -blumeria_Grouper_4152_12:NoCat 378 407 V-ATPase_G 1 10 5.3 2 0.000000 -blumeria_Grouper_4152_12:NoCat 136 228 XhoI 202 172 0.014 9 0.000000 -blumeria_Grouper_4152_12:NoCat 145 165 Endomucin 267 261 6 0 0.000000 -blumeria_Grouper_4152_12:NoCat 444 497 DUF1798 52 35 3.3 3 0.000000 -blumeria_Grouper_4152_12:NoCat 294 365 DUF881 237 214 1.6 4 0.000000 -blumeria_Grouper_4152_12:NoCat 177 236 SLT 20 1 1.2 4 0.000000 -blumeria_Grouper_4152_12:NoCat 156 224 DUF2346 85 63 2.8 3 0.000000 -blumeria_Grouper_4152_12:NoCat 84 131 LBP_BPI_CETP 209 191 3.8 1 0.000000 -blumeria_Grouper_4152_12:NoCat 314 352 DUF258 305 293 3.8 1 0.000000 -blumeria_Grouper_4152_12:NoCat 230 247 SOCS_box 6 1 9.7 2 0.000000 -blumeria_Grouper_4152_12:NoCat 155 217 DUF1289 56 36 5.3 2 0.000000 -blumeria_Grouper_4152_12:NoCat 152 184 TRAP_alpha 327 317 4.1 0 0.000000 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscanTransformedExpected.align --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscanTransformedExpected.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Polinton-1_DY:classII:Polinton 2974 3642 DNA_pol_B_2 13 252 3.7e-06 24 0.000000 -Polinton-1_DY:classII:Polinton 7897 7944 ASFV_p27 59 74 6 4 0.000000 -Polinton-1_DY:classII:Polinton 9022 9123 Ribosomal_S4 39 72 18 4 0.000000 -Polinton-1_DY:classII:Polinton 11896 11955 Homo_sperm_syn 49 68 8.8 2 0.000000 -Polinton-1_DY:classII:Polinton 5480 5932 rve 168 4 6.7e-30 103 0.000000 -Polinton-1_DY:classII:Polinton 5099 5191 Chromo 51 4 8.5e-06 24 0.000000 -Polinton-1_DY:classII:Polinton 8408 8434 GARS_A 204 196 11 2 0.000000 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/repetHmmscan.fa --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/repetHmmscan.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,314 +0,0 @@ ->SAR:satellite:satellite -acagtatataatatatattttgggtactttgatattttatgtacagtatataatatatat -tttgggtactttgatattttatgt ->BARI_DM:classII:TIR -acagtcatggtcaaaattattttcacaaagtgcatttttgtgcatgggtcacaaacagtt -gcttgtgcagcaagtggggggaggtgaaatgcaaaaaaacttttgcttttgcaaattcaa -acctatgcagagtcagatgaaagaagaattgaaaaaataactgttcctatgcgcaaggaa -gaggcaaatgaagagatctttatcagttgtcagaagtatttgcacacggtttcgtcgcat -cacaattattttcacaacgcaatttcttcttcagtgattggtttagagtgacaagtgccg -gtttgtttgcttaaatacatttaaattattgaataaaaattagatttaatcattttccta -ttacagttattaaataaaatgcccaaaacaaaagagttaacagttgaggcccgggctggt -attgttgctaggtttaaagccggtacacctgcggccaaaatagctgaaatatatcaaatt -tcgcgtagaactgtctactacttaataaaaaagtttgatacagttggcacattaaaaaat -aaaaaaagatcaggccgaaaacctgtgctggaccaaaggcaatgcaggcaaatacttgga -gttgtggcgaagaatcctagtgccagtccggtaaaaattgccttagaatcaaaaaataca -attggcaaacaagttagtagttctacaattcgtcgcaggctaaaagaagctgattttaag -acatacgttgttcgcaaaacgattgagatcacaccaaccaacaaaacaaaacgtcttcga -tttgcgttggaatatgttaagaagcctcttgacttttggtttaatattttatggactgat -gagtctgcatttcagtaccaggggtcatacagcaagcattttatgcatttgaaaaataat -caaaagcatttggcagcccagccaaccaatagatttggtgggggcacagtcatgttttgg -ggatgtctttcctattatggattcggagacttggtaccgatagaaggaactttaaatcag -aacggataccttcttatcttaaacaaccatgcttttacgtctggaaatagactttttcca -actactgaatggattcttcagcaggacaatgctccatgccataagggtaggataccaaca -aaatttttaaacgaccttaatctggcggttcttccgtggcccccccaaagcccagacctt -aatatcattgaaaacgtttgggcttttattaaaaaccaacgaactattgataaaaataga -aaacgagagggagccatcattgaaatagcggagatttggtccaaattgacattagaattt -gcacaaactttggtaaggtcaataccaaaaagacttcaagcagttattgatgccaaaggt -ggtgttacaaaatattagtattgtatttatataaaataaagaaattcttatgttgaaatt -agatgttaagctgaaatttactaaattaagttgagtgaaaatacttttgaagcgcaataa -acatgtgaaaatactattgacaacttgcatgcatattttcttttgctttaagctttgtac -tatgaaccgttatctttcgtatttcttttcgactaccttctgcatagatcaagctaagcg -ataagaactatttcaggcaaatcggacaacaacaagaagaaatataacaaaaagaagttg -aagtttgcaaatattgtgcgttgtgaaaatacttttgaccacctctgt ->MOLLY_SN:classII:TIR -acgtacctcacgggttggccggacacacggtttggccggacacttttgccaagcccccac -caaattctacctctcaacgtgatgcctcaacaacaacaccagatagacccttctagcgaa -cgtcatatacagactgcccttcaagctcttaaacaagacgcgacactgtccttgcgacgc -gctgcagctatctataacgtctctcgagcaacactaagcgatcgacgcgctggacggcct -tcacaagcagattgctggcctaaaacaaagaatctaactaagactgaggaggacgtagtt -gttaagcatatacttgagctggttacgcgtggatttcctcctaggctcgcagctgtggct -gatatggctaattccctgcgcgctgagcgcggtctgggccaagttggctcaaactggccc 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-ttaattacataaaaccacttttcatttcgggtttaaatgctataaaaaatcaagctgcag -agactggaaaagctgtaattaatgaatttggtagaaagccattaagaaatattattcaag -aacagagtaaaattgctttacaaaacctatcaaataaagcaataaataaaatgacacggt -ttcaaaatggcagtggaaaaagaaataaaaagcgaggtggtagaaaaaaacgaaatcatt -taacatctaaacgacaacgtaaacatacccaaccgtctcataaaaraaaaaaatcatcaa -ggaaattaaatattacggatattttttctaacacaaaatgagtaaccatatagaatgtat -gaaaggcgaattggatttgtttgcaccacaccctacgcaaagttcaattctacgaaccga -agaggtttcttataatccaattgcatccttggatggtgcctcctcaatcgaatttgtttg -tttaggaaatggtgaaacatatcgagatctatcaagtgtttatttacgacttgtggtgca -attgaaaaaaaatgataacagcgtcattgaaggaaatgctgtcggtgtagtaaacaatat -cttacattcaatatttagaagttcatcagtatatttaaataacatattagtttcgcagag -tgataataattatcattatagagcatatctgcaaacagttttaaactatgggagtgacgc -ctcggaaagccacttggcctcgcaaggttattttccaaatttcggacgattaacatcagg -aaaatacgtttatccgagctctaatgaaactctgaaaaatatatttcaaaatagtaataa -ggtagaactatttggaaaaattcatggtgatatatttaatcaaacgaaacttcttgtcaa -taatgttgacttaagaattaattttaatattgaaaaaactgcattttatttaatggaaaa -ggatagcgaatcaaatttaaagatattagaagcacaacttttcatgaatcatgtaactgt -gaacccaagcattttattggctcatcatcatgttttacaaacaaaaaatgctctttaccc -attcagtaaagtagaagtaaaatcgtttacaatttacccaggaaacaatacgctatcaat -agacaatgctgtaattggacaattaccaaattttctagctttttgtatgattaaaaaccg -ttcatactcaggcaacagaggactagatccatttaattttgaacattttaaaatgcaacg -ctttaatctaatggtgaatggagttcaagttccttcgcaagctctggaatttgactactc -gaactctgaaaacgttcaaagctcaagaggctataatatgctattcagatcaagcggaat -aaaacattatgatcggggtcttcaaattaccaaggaaatgtttgatacgaacagttttat -attagcctttgatttaactgctgatcagtcaaataccaccatatgttcaaatttgatgtc -gcaaggcacaataagaatcgaaggaagattttcagaacctcttagtgaagccgttacttg -tctggtatattgtgaatacgattccatgattgatattgataagcatagaaatattcgaac -ccttttttaaaatgaatactttacaaattcacaatttgcttacaaaacatatatacacaa -aatcaatttttaaaggagttttcccttcagaccagcttccaaaaactatttcaaagtatc -cggctttaattattgcaaacaccgacacttcagatcaaccaggaactcattggattgcat -tctatttcgaaagtcgcaaatcagcagaattttttgattcctatggacaatttccccaaa -acaaggaattcgtgacatttttaaaatctaacgcaaataaatattgctataacaagcaac -aactacaaggatatttttctaatacgtgtggtcattattgcataatgtatggtcttttta -aatgtaaaaagaaaacgctaaaatatttattaacaaattttaagagaaatgacttttcat -ataacgataaattaatacttaaaatgtttaagtctaattttaaaaaataaaatgcaagat -atttaagaaaatcaatgtagtttatttattaagtcgtttgtttagcttataatattttaa -cataatattgaaggcctcgtctcttaaaattggaagcctatgacactggcacgtatcggg -tccttccgaagcgtcatcatcactccagggacaaagcttgtagtggaatccatatttaga -atggatcagttctttatcctctaagtcctccagagtgctcttcaaatatataagctgcgt -tacgtgctcctcaaatatcatgtcttcgaactgcatcaagaagagctcaatttgtttgga -gtccattttcgttatggttcttttaaggttttttaaagactgatgttggatttagaaaac -tcaaacctttatattggaaaatttcatttacttatttatttactgataaaaattcaattc -gtgcagaactatatctatttacatccttccccttatataccatatgggtaataccattct -catttaatttcctaaaaggtgtcttagtacagaatttgtttacataactcttaggtagaa -aaatccaaacatctttttcgtccttgtctgctaaataaagagctaccttagttccataag -gtgtctttttcagcttacaaccagtgatcttatactcaaatccaatacatagatcttcag -tttttgtataaccaatcacaggcttcgattcattcagagtctctaggaaatcctagaaat -tcaataaaatttgaacaggatttatttattaatgtcctatatgcataccatttctgacca -acgtgagatttgattcgttatgctcttgtaactattcgtattatactaatgcatttactt -acaattacgagacttttatactgttcagcactacatatatatatatatatatatatatta -caagaacaaaatactacgtgaaagagataccaatatatctgttatgctctttatatacat -aaactcagttaagcctatgtagaatatttttatatacttgagtatatctatctcattttg -tataaatatataacttcatatgaaataaaaggttactacaaacctaatataagacagcac -ttttctcgaaaactcagattcaatttttactctcagaatgacaaagttgtattgtgagtt -gtgttcggaaacaaaatcgtttgcttcacgcagcggtttaaaaaaacataccttaaaagt -gcataacttcagctatcaaaaatcaaaatcttcttattattgttgctttttctgtcccaa -tgaacgaaaattctggttgcgatataattacaatgttcatctcttgctgatgcacgatgc -agaattaaagagtatgcgtaaatcaatggaaagttatcaaataaagataaaacaagtttg -agaatttaattttgtaaaatagttttatttaataaatttctgtataatatagacaaatta -aaaacctagatcaaataaaacgtctagtaatgaatggtcatcttcatccttcattattcg -taaataaatgttgggttgacttggctcgatgaactgatcaaaaatatgatcatcatcagg -aaactcatagattataggatctgtgtgcagtatatccatatcgaaatgctgtgcacattg -catttcttgatcgtctccattgcctcgtataagatcatttaaaacgtcctgcgttgccgc -tccaaaaggaaaatcgctccactcaagagacgcaaattcacttccaatttttgtagtggg -ggtagatgacatagaagggtcaaatactcctcttaagaagcgatctatcgaatcctctgt -gtcgatagcctccacataaccttccttcgagccttcaattatttcgacatcagagtcttg -agttaatggaacatttattccatttactgagtcaacaaactctacagtaagatccattgg -tatgcagtgctgaggtattataagaactgatcctgagcaatttaaggggatccattttta -tacacgaggattagagagtttgacatctacagggggtgtctactcttagaatccacctga -ttggttctcgatttaaggagccttcacagactgcagactgcacagactgcaatggggaag -tcagaaaaggagggcgagctatgggtttggatgcaggtaaatagccgcttgactttctcg -ataataggttcaaagagtcataaatatttgattttatggggtctcctagcataatgaaaa -tggagacagatcacagataatctgaaatacatatctctgtagggaattatttcggatgac -cgcagtcagggatcatgaaattattggtgactactagtcattgttactttataagtaaca -ttttgcaaggcatacatttaaaacgtgggtagccttaagctgaaagtcgctatgacttca -gattgtttagattttcttctcaacggctccatagcttttagctgaaagtagctggaatat -acgggaacgacggttttttaacggttttatgattatatgattttttatatatacgtatac -acgaccctataaccagtttgtttgatatttctaaatatttctcaactaataatccaacca -ccagttaccttcccagaaaattgaggacacagtaaggtgcatagccttgaacagaaatct -cacccccacccttgcgatcatc diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,321 +0,0 @@ -hmmpfam - search one or more sequences against HMM database -HMMER 2.3.2 (Oct 2003) -Copyright (C) 1992-2003 HHMI/Washington University School of Medicine -Freely distributed under the GNU General Public License (GPL) -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -HMM file: myhmms -Sequence file: test.fa -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query sequence: pkinase_full -Accession: [none] -Description: Dario rerio - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain 266.6 3.3e-80 1 -pkinase Protein kinase domain 265.4 7.6e-80 1 -rrm -42.5 2.5 1 -rrm -8.7 3.7 1 -fn3 Fibronectin type III domain -45.8 3.7 1 -fn3 Fibronectin type III domain -9.0 3.8 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -rrm 1/1 169 180 .. 66 77 .] -8.7 3.7 -fn3 1/1 197 200 .. 81 84 .] -9.0 3.8 -rrm 1/1 256 319 .. 1 77 [] -42.5 2.5 -pkinase 1/1 258 540 .. 1 294 [] 266.6 3.3e-80 -pkinase 1/1 258 537 .. 1 289 [. 265.4 7.6e-80 -fn3 1/1 434 506 .. 1 84 [] -45.8 3.7 - -Alignments of top-scoring domains: -rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7 - *->nGkelggrklrv<-* - n++ ++l v - pkinase_fu 169 NKQDPHQHRLSV 180 - -fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8 - CS CCCC - *->GpeS<-* - G eS - pkinase_fu 197 GGES 200 - -rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5 - *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks - +N++ +d+ e + F+ + +++ + - pkinase_fu 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285 - - kGfaFVeFeseedAekAlealnG.kelggrklrv<-* - + V++ +ee+ ++ ++++ + l++ + - pkinase_fu 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319 - -pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - ng........................gplsekeakkialQilrGleYLHs - + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + - pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402 - - ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY - +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p + - pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451 - - mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev - +m+PE ++++ y+s++DvW++Gv+L+E++++g - pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483 - - dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd - ++P+++ + ee+ + +++ g l +p+nc+ el+ - pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517 - - LlkkcLnkDPskRpGsatakeilnhpwf<-* - L++ c+ P++Rp ++ i h + - pkinase_fu 518 LMRLCWSGHPTDRP---SFASI--HRIL 540 - -pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - ng........................gplsekeakkialQilrGleYLHs - + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + - pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402 - - ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY - +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p + - pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451 - - mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev - +m+PE ++++ y+s++DvW++Gv+L+E++++g - pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483 - - dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd - ++P+++ + ee+ + +++ g l +p+nc+ el+ - pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517 - - LlkkcLnkDPskRpGsatakeil<-* - L++ c+ P++Rp ++ i+ - pkinase_fu 518 LMRLCWSGHPTDRP---SFASIH 537 - -fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.E - *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq - a ++++ + + ++W pp++ ++ + +++ Y v + + - pkinase_fu 434 IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477 - - CS CCCCCC CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC - pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-* - + + + ++ + ++V+ +g+ S - pkinase_fu 478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS 506 - -// - -Query sequence: pkinase_part -Accession: [none] -Description: Dario rerio - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain 101.5 1.7e-30 1 -pkinase Protein kinase domain -94.7 1.5e-05 1 -rrm -42.5 2.5 1 -rrm -8.7 3.7 1 -fn3 Fibronectin type III domain -9.0 3.8 1 -fn3 Fibronectin type III domain -52.2 5.9 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -rrm 1/1 169 180 .. 66 77 .] -8.7 3.7 -fn3 1/1 197 200 .. 81 84 .] -9.0 3.8 -fn3 1/1 233 299 .. 1 84 [] -52.2 5.9 -rrm 1/1 256 319 .. 1 77 [] -42.5 2.5 -pkinase 1/1 258 400 .] 1 116 [. 101.5 1.7e-30 -pkinase 1/1 258 400 .] 1 294 [] -94.7 1.5e-05 - -Alignments of top-scoring domains: -rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7 - *->nGkelggrklrv<-* - n++ ++l v - pkinase_pa 169 NKQDPHQHRLSV 180 - -fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8 - CS CCCC - *->GpeS<-* - G eS - pkinase_pa 197 GGES 200 - -fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9 - CS CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC - *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew - P + ++l ++ +s ls + p + i++ +R + ++g - pkinase_pa 233 PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267 - - CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC - neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-* - g ++ gL P + ++ + + ++S - pkinase_pa 268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS 299 - -rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5 - *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks - +N++ +d+ e + F+ + +++ + - pkinase_pa 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285 - - kGfaFVeFeseedAekAlealnG.kelggrklrv<-* - + V++ +ee+ ++ ++++ + l++ + - pkinase_pa 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319 - -pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - ng........................gplsekeakkialQilrGleYL<- - + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL - pkinase_pa 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL 400 - - * - - pkinase_pa - - - -pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi - + - pkinase_pa 353 RC------------------------------------------------ 354 - - aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL - A++ s + +t++ ++ PE - pkinase_pa 355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377 - - yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee - +P s - pkinase_pa 378 --------------------------------YPPLS------------- 382 - - lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp - + + ++S+ + + - pkinase_pa 383 -----CQ------EQLSISKQVAAGM-----------A------------ 398 - - wf<-* - ++ - pkinase_pa 399 YL 400 - -// - -Query sequence: S13421 -Accession: [none] -Description: S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum. - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain -171.6 0.19 1 -rrm -32.5 0.26 1 -rrm -6.1 0.92 1 -fn3 Fibronectin type III domain -39.7 1.2 1 -pkinase Protein kinase domain -9.2 1.8 1 -fn3 Fibronectin type III domain -7.5 1.9 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -fn3 1/1 143 224 .. 1 84 [] -39.7 1.2 -pkinase 1/1 233 241 .. 1 9 [. -9.2 1.8 -rrm 1/1 440 456 .. 1 17 [. -6.1 0.92 -rrm 1/1 669 731 .. 1 77 [] -32.5 0.26 -pkinase 1/1 906 1127 .. 1 294 [] -171.6 0.19 -fn3 1/1 923 934 .. 1 12 [. -7.5 1.9 - -Alignments of top-scoring domains: -fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2 - CS C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC - *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew - + ++t+l++ dv ++ sWs+ +g+ + tg v R + ng + - S13421 143 IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185 - - CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - +++ ++ + + l L + + V v ++ +G - S13421 186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH 224 - -pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8 - *->yelleklGe<-* - +l+klGe - S13421 233 VSTLKKLGE 241 - -rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92 - *->lfVgNLppdvteedLkd<-* - + ++ L++ + d+ d - S13421 440 VIISFLNEGLRQADIVD 456 - -rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26 - *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG - V L+++d+ + + f i k++ D + - S13421 669 --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699 - - faFVeFeseedAekAlealnGkelggr.klrv<-* - + FV ++ + e+ ++ l k+++ +l++ - S13421 700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI 731 - -pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19 - *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes - ++l G++ ++ + ++ ++ ++ + ++VAv + ++ - S13421 906 FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942 - - ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy - + + L+ ++ fe + + v++ +d - S13421 943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980 - - lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde - l + +++ +s ++ Q+ lde - S13421 981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007 - - ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l - + ++ + LAr+l +++ + + +++++f+ +++ ++++l - S13421 1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047 - - egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif - +r s ++ W++++ vi+ ++ g - S13421 1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073 - - vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL - l++ +++ dp + + k l + ++++ ++l+ L +k++ - S13421 1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113 - - nkDPskRpGsatakeilnhpwf<-* - +k +k p +i f - S13421 1114 TKVFTKHP----DYQI----LF 1127 - -fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9 - CS CCCCCEEEEEEC - *->PsaPtnltvtdv<-* - + t+l++++v - S13421 923 INPITGLSAREV 934 - -// - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output.align --- a/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -pkinase_full 169 180 rrm 66 77 3.7 -8.7 0 -pkinase_full 197 200 fn3 81 84 3.8 -9.0 0 -pkinase_full 256 319 rrm 1 77 2.5 -42.5 0 -pkinase_full 258 540 pkinase 1 294 3.3e-80 266.6 0 -pkinase_full 258 537 pkinase 1 289 7.6e-80 265.4 0 -pkinase_full 434 506 fn3 1 84 3.7 -45.8 0 -pkinase_part 169 180 rrm 66 77 3.7 -8.7 0 -pkinase_part 197 200 fn3 81 84 3.8 -9.0 0 -pkinase_part 233 299 fn3 1 84 5.9 -52.2 0 -pkinase_part 256 319 rrm 1 77 2.5 -42.5 0 -pkinase_part 258 400 pkinase 1 116 1.7e-30 101.5 0 -pkinase_part 258 400 pkinase 1 294 1.5e-05 -94.7 0 -S13421 143 224 fn3 1 84 1.2 -39.7 0 -S13421 233 241 pkinase 1 9 1.8 -9.2 0 -S13421 440 456 rrm 1 17 0.92 -6.1 0 -S13421 669 731 rrm 1 77 0.26 -32.5 0 -S13421 906 1127 pkinase 1 294 0.19 -171.6 0 -S13421 923 934 fn3 1 12 1.9 -7.5 0 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/tests/Test_AlignListUtils.py --- a/commons/pyRepetUnit/align/tests/Test_AlignListUtils.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.align.AlignList import AlignList -from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.coord.Range import Range -from commons.core.coord.Align import Align - -class Test_AlignListUtils (unittest.TestCase): - - def setUp(self): - self.inputFileName = "dummyAlignFile.align" - self.outputFileName = "dummyAlignFile.out" - - def testRead(self): - f = open(self.inputFileName, "w") - f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t2.6e-60\t0\t3.2\n") - f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t0\t2.9\n") - f.close() - alignRead = AlignListUtils() - tableauAlignInstance = alignRead.read(self.inputFileName) - self.assertEquals(tableauAlignInstance.get(0).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1") - self.assertEquals(tableauAlignInstance.get(0).range_query.start, 91) - self.assertEquals(tableauAlignInstance.get(0).range_query.end, 108) - self.assertEquals(tableauAlignInstance.get(0).range_subject.seqname, "DUF234") - self.assertEquals(tableauAlignInstance.get(0).range_subject.start, 5) - self.assertEquals(tableauAlignInstance.get(0).range_subject.end, 22) - self.assertEquals(tableauAlignInstance.get(0).e_value, 2.6e-60) - self.assertEquals(tableauAlignInstance.get(0).score, 0) - self.assertEquals(tableauAlignInstance.get(0).identity, 3.2) - self.assertEquals(tableauAlignInstance.get(1).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1") - self.assertEquals(tableauAlignInstance.get(1).range_query.start, 111) - self.assertEquals(tableauAlignInstance.get(1).range_query.end, 119) - self.assertEquals(tableauAlignInstance.get(1).range_subject.seqname, "DUF1414") - self.assertEquals(tableauAlignInstance.get(1).range_subject.start, 1) - self.assertEquals(tableauAlignInstance.get(1).range_subject.end, 9) - self.assertEquals(tableauAlignInstance.get(1).e_value, 6.3) - self.assertEquals(tableauAlignInstance.get(1).score, 0) - self.assertEquals(tableauAlignInstance.get(1).identity, 2.9) - os.system("rm " + self.inputFileName) - - def testWrite(self): - f = open("expectedAlignFile.align", "w") - f.write("biduleChouetteQuery\t20\t55\tbiduleChouetteSubject\t2\t15\t0.005\t20\t0.000000\n") - f.write("trucBiduleQuery\t110\t155\ttrucBiduleSubject\t1\t35\t2\t1\t0.000000\n") - f.write("dummyQuery\t1\t65\tdummySubject\t1\t25\t2.6e-60\t50\t0.000000\n") - f.close() - listAlignInstance = AlignList() - align1 = Align() - align1.range_query = Range("biduleChouetteQuery", 20, 55) - align1.range_subject = Range("biduleChouetteSubject", 2, 15) - align1.e_value = 0.005 - align1.score = 20 - listAlignInstance.append(align1) - align2 = Align() - align2.range_query = Range("trucBiduleQuery", 110, 155) - align2.range_subject = Range("trucBiduleSubject", 1, 35) - align2.e_value = 2 - align2.score = 1.5 - listAlignInstance.append(align2) - align3 = Align() - align3.range_query = Range("dummyQuery", 1, 65) - align3.range_subject = Range("dummySubject", 1, 25) - align3.e_value = 2.6e-60 - align3.score = 50 - listAlignInstance.append(align3) - f = open(self.outputFileName, "w") - alignUtils = AlignListUtils() - alignUtils.write(listAlignInstance, self.outputFileName) - self.assertTrue(FileUtils.are2FilesIdentical(self.outputFileName, "expectedAlignFile.align")) - os.system("rm " + self.outputFileName) - os.system("rm expectedAlignFile.align") - - def testFilterOnAMinimalScore(self): - listAlignInstance = AlignList() - align1 = Align() - align1.range_query = Range("biduleChouetteQuery", 20, 55) - align1.range_subject = Range("biduleChouetteSubject", 2, 15) - align1.e_value = 5 - align1.score = -0.5 - listAlignInstance.append(align1) - align2 = Align() - align2.range_query = Range("trucBiduleQuery", 110, 155) - align2.range_subject = Range("trucBiduleSubject", 1, 35) - align2.e_value = 2 - align2.score = -2.0 - listAlignInstance.append(align2) - align3 = Align() - align3.range_query = Range("dummyQuery", 1, 65) - align3.range_subject = Range("dummySubject", 1, 25) - align3.e_value = 2.6e-60 - align3.score = 50 - listAlignInstance.append(align3) - expectedAlignInstance = align3 - alignUtils = AlignListUtils() - alignUtils.filterOnAMinimalScore(listAlignInstance, 0) - self.assertEquals(listAlignInstance.get(0), expectedAlignInstance) - -if __name__ == "__main__" : - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/tests/hmmpfamOutputParsingTestSuite.py --- a/commons/pyRepetUnit/align/tests/hmmpfamOutputParsingTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -''' -Created on 29 mai 2009 - -@author: oinizan -''' -import unittest -import sys -from commons.pyRepetUnit.align.tests.Test_AlignListUtils import Test_AlignListUtils - - -def main(): - - hmmpfamOutputParsingTestSuite = unittest.TestSuite() - hmmpfamOutputParsingTestSuite.addTest(unittest.makeSuite(Test_AlignListUtils,'test')) - - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(hmmpfamOutputParsingTestSuite) - - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/TransformAACoordIntoNtCoordInAlignFormat.py --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/TransformAACoordIntoNtCoordInAlignFormat.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,133 +0,0 @@ -import os -import sys -from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils -from commons.core.seq.BioseqUtils import BioseqUtils -from commons.core.checker.RepetException import RepetException - -### Transform amino acid query coord in an align format to nucleotide coord -### according to the frame specified at the end of seqName -# -class TransformAACoordIntoNtCoordInAlignFormat( object ): - - def __init__(self): - self._inFileName = None - self._clean = False - self._outFileName = None - self._consensusFileName = None - self._IsFiltered = True - - ## read input file, transform it and write the output file - # - def run(self): - alignUtils = AlignListUtils() - listAlignInstance = alignUtils.read(self._inFileName) - self.transformQueryCoord(listAlignInstance) - #self.getOriginalQueryNameForAlignList(listAlignInstance) - if self._IsFiltered: - alignUtils.filterOnAMinimalScore(listAlignInstance, 0) - alignUtils.write(listAlignInstance, self._outFileName) - if self._clean: - self.clean() - - ## Transform the amino acid query coord into nucleotides and switch subject coord if the strand is reversed - # @param listAlignInstance list of align object instance - # - def transformQueryCoord(self, listAlignInstance): - bioseqList = BioseqUtils.extractBioseqListFromFastaFile( self._consensusFileName ) - for alignInstance in listAlignInstance.getList(): - try: - frame = self.extractFrameFromSeqName(alignInstance) - except RepetException, e: - raise e - previousEnd = alignInstance.range_query.end - previousStart = alignInstance.range_query.start - alignInstance.range_query.seqname = self._getOriginalQueryNameForAlignInstance(alignInstance) - if frame < 4: - self._changeStartInAAIntoNtInPositiveFrame(alignInstance, frame, previousStart) - self._changeEndInAAIntoNtInPositiveFrame(alignInstance, frame, previousEnd) - else: - self._checkIfSeqNameIsInDNASeqFile(bioseqList, alignInstance.range_query.seqname) - consensusLength = BioseqUtils.getSeqLengthWithSeqName(bioseqList, alignInstance.range_query.seqname) - self._changeStartInAAIntoNtInNegativeFrame(alignInstance, frame, consensusLength, previousEnd) - self._changeEndInAAIntoNtInNegativeFrame(alignInstance, frame, consensusLength, previousStart) - self._invertedSubjectCoord(alignInstance) - - ## remove the input file - # - def clean(self): - os.remove(self._inFileName) - - ## set input file name - # - # @param fileName string name of file - # - def setInFileName(self, fileName): - self._inFileName = fileName - - ## set output file name - # - # @param fileName string name of file - # - def setOutFileName(self, fileName): - self._outFileName = fileName - - ## set consensus file name - # - # @param fileName string name of file - # - def setConsensusFileName(self, fileName): - self._consensusFileName = fileName - - ## set is clean will be done - # - # @param clean boolean clean - # - def setIsClean(self, clean): - self._clean = clean - - ## get input file name - # - def getInFileName(self): - return self._inFileName - - ## set is negativ score filter will be done - # - # @param isFiltered boolean isFiltered - # - def setIsFiltered(self, isFiltered): - self._IsFiltered = isFiltered - - def _getOriginalQueryNameForAlignInstance(self, alignInstance): - return alignInstance.range_query.seqname[0:len(alignInstance.range_query.seqname) - 2] - - def _invertedSubjectCoord(self, alignInstance): - return alignInstance.range_subject.reverse() - - def _changeEndInAAIntoNtInPositiveFrame(self, alignInstance, frame, previousEnd): - alignInstance.range_query.end = 3 * previousEnd + frame - 1 - - def _changeStartInAAIntoNtInPositiveFrame(self, alignInstance, frame, previousStart): - alignInstance.range_query.start = 3 * (previousStart - 1) + frame - - def _changeEndInAAIntoNtInNegativeFrame(self, alignInstance, frame, consensusLength, previousStart): - alignInstance.range_query.end = consensusLength - 3 * (previousStart - 1) - frame + 4 - - def _changeStartInAAIntoNtInNegativeFrame(self, alignInstance, frame, consensusLength, previousEnd): - alignInstance.range_query.start = consensusLength - 3 * (previousEnd - 1) - frame + 2 - - def extractFrameFromSeqName(self, alignInstance): - try: - frame = int(alignInstance.range_query.seqname[len(alignInstance.range_query.seqname) - 1]) - except ValueError: - raise RepetException("Unable to extract frame from sequence name") - return frame - - def _checkIfSeqNameIsInDNASeqFile(self, bioseqList, seqName): - isSeqNameInBioseqList = False - for bioseq in bioseqList: - if seqName == bioseq.header: - isSeqNameInBioseqList = True - if not isSeqNameInBioseqList: - sys.stderr.write("seqName : " + seqName + " is not in the consensus file " + self._consensusFileName + "\n") - sys.exit(1) - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/Test_F_TransformAACoordIntoNtCoordAndScoreFiltering.py --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/Test_F_TransformAACoordIntoNtCoordAndScoreFiltering.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat -from commons.core.utils.FileUtils import FileUtils - -class Test_F_TransformAACoordIntoNtCoordAndScoreFiltering (unittest.TestCase): - - def setUp(self): - self._inputFile = "./datas/OutputHmmpfamTest.align" - self._consensusFile = "./datas/ConsensusTestFile_nt.fsa" - self._outputFile = "./datas/alignTransformedToTest.align" - self._expectedFile = "./datas/PostPostProcessTest.align" - self._expectedFileFiltered = "./datas/PostPostProcessTestFiltered.align" - self._alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - - def testRun_with_no_filter(self): - self._alignTransformation.setInFileName(self._inputFile) - self._alignTransformation.setOutFileName(self._outputFile) - self._alignTransformation.setConsensusFileName(self._consensusFile) - self._alignTransformation.setIsFiltered(False) - self._alignTransformation.run() - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile)) - os.remove(self._outputFile) - - def testRun_with_filter(self): - self._alignTransformation.setInFileName(self._inputFile) - self._alignTransformation.setOutFileName(self._outputFile) - self._alignTransformation.setConsensusFileName(self._consensusFile) - self._alignTransformation.setIsFiltered(True) - self._alignTransformation.run() - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFileFiltered, self._outputFile)) - os.remove(self._outputFile) - - -if __name__ == "__main__" : - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/Test_TransformAACoordIntoNtCoordInAlignFormat.py --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/Test_TransformAACoordIntoNtCoordInAlignFormat.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,237 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils -from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat -from commons.core.utils.FileUtils import FileUtils -from commons.core.coord.Align import Align -from commons.core.coord.Range import Range -from commons.core.checker.RepetException import RepetException - -class Test_TransformAACoordIntoNtCoordInAlignFormat(unittest.TestCase): - - def setUp(self): - self.inputFileName = "alignFile.align" - self.consensusFile = "consensus.fa" - self.outputFileName = "outputFile.align" - self._expFileName = "expFile.align" - - def tearDown(self): - if FileUtils.isRessourceExists(self.inputFileName): - os.remove(self.inputFileName) - if FileUtils.isRessourceExists(self.consensusFile): - os.remove(self.consensusFile) - if FileUtils.isRessourceExists(self.outputFileName): - os.remove(self.outputFileName) - if FileUtils.isRessourceExists(self._expFileName): - os.remove(self._expFileName) - - def test_transformQueryCoord(self): - f = open(self.inputFileName, "w") - f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n") - f.close() - f = open(self.consensusFile, "w") - f.write(">blumeria_Grouper_590_20:NoCat\n") - f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n") - f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n") - f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n") - f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n") - f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n") - f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n") - f.write("TCCATAATTTCAACACTNAAGAATATTTGTA") - f.close() - alignRead = AlignListUtils() - tableauAlignInstance = alignRead.read(self.inputFileName) - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setConsensusFileName(self.consensusFile) - alignTransformation.transformQueryCoord(tableauAlignInstance) - #check query coord - self.assertEquals(tableauAlignInstance.get(0).range_query.start, 271) - self.assertEquals(tableauAlignInstance.get(0).range_query.end, 324) - self.assertEquals(tableauAlignInstance.get(1).range_query.start, 331) - self.assertEquals(tableauAlignInstance.get(1).range_query.end, 357) - self.assertEquals(tableauAlignInstance.get(2).range_query.start, 90) - self.assertEquals(tableauAlignInstance.get(2).range_query.end, 113) - self.assertEquals(tableauAlignInstance.get(3).range_query.start, 165) - self.assertEquals(tableauAlignInstance.get(3).range_query.end, 209) - self.assertEquals(tableauAlignInstance.get(4).range_query.start, 119) - self.assertEquals(tableauAlignInstance.get(4).range_query.end, 148) - self.assertEquals(tableauAlignInstance.get(5).range_query.start, 16) - self.assertEquals(tableauAlignInstance.get(5).range_query.end, 30) - #check subject (profiles) coord - #positive frame : they don't change - self.assertEquals(tableauAlignInstance.get(0).range_subject.start, 5) - self.assertEquals(tableauAlignInstance.get(0).range_subject.end, 22) - self.assertEquals(tableauAlignInstance.get(1).range_subject.start, 1) - self.assertEquals(tableauAlignInstance.get(1).range_subject.end, 9) - self.assertEquals(tableauAlignInstance.get(2).range_subject.start, 1) - self.assertEquals(tableauAlignInstance.get(2).range_subject.end, 9) - self.assertEquals(tableauAlignInstance.get(3).range_subject.start, 341) - self.assertEquals(tableauAlignInstance.get(3).range_subject.end, 355) - #negative frame : they must be inverted - self.assertEquals(tableauAlignInstance.get(4).range_subject.start, 182) - self.assertEquals(tableauAlignInstance.get(4).range_subject.end, 173) - self.assertEquals(tableauAlignInstance.get(5).range_subject.start, 280) - self.assertEquals(tableauAlignInstance.get(5).range_subject.end, 276) - - def test_transformQueryCoord_with_seqName_not_in_consensus_file(self): - f = open(self.inputFileName, "w") - f.write("dummy_Grouper_590_20:NoCat_4\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("dummy_Grouper_590_20:NoCat_4\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.close() - f = open(self.consensusFile, "w") - f.write(">blumeria_Grouper_590_20:NoCat\n") - f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n") - f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n") - f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n") - f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n") - f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n") - f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n") - f.write("TCCATAATTTCAACACTNAAGAATATTTGTA") - f.close() - alignRead = AlignListUtils() - tableauAlignInstance = alignRead.read(self.inputFileName) - - isSystemExitRaised = False - try: - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setConsensusFileName(self.consensusFile) - alignTransformation.transformQueryCoord(tableauAlignInstance) - except SystemExit: - isSystemExitRaised = True - self.assertTrue(isSystemExitRaised) - - def test_run(self): - f = open(self.inputFileName, "w") - f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n") - f.close() - f = open(self.consensusFile, "w") - f.write(">blumeria_Grouper_590_20:NoCat\n") - f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n") - f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n") - f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n") - f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n") - f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n") - f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n") - f.write("TCCATAATTTCAACACTNAAGAATATTTGTA") - f.close() - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setInFileName(self.inputFileName) - alignTransformation.setOutFileName(self.outputFileName) - alignTransformation.setConsensusFileName(self.consensusFile) - alignTransformation.run() - f = open(self._expFileName, "w") - f.write("blumeria_Grouper_590_20:NoCat\t271\t324\tDUF234\t5\t22\t1.5\t3\t0.000000\n") - f.write("blumeria_Grouper_590_20:NoCat\t331\t357\tDUF1414\t1\t9\t6.3\t2\t0.000000\n") - f.write("blumeria_Grouper_590_20:NoCat\t90\t113\tCPW_WPC\t1\t9\t7.7\t1\t0.000000\n") - f.write("blumeria_Grouper_590_20:NoCat\t119\t148\tDUF46\t182\t173\t0.11\t6\t0.000000\n") - f.close() - self.assertTrue(FileUtils.isRessourceExists(self.outputFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, self.outputFileName)) - - #TODO: is it normal ? - def test_run_header_without_frame(self): - f = open(self.inputFileName, "w") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t186\t218\tPF02022.11_Integrase_Zn_INT_13.5\t1\t40\t8.9\t-20.4\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t209\t266\tPF04236.7_Transp_Tc5_C_Tase_25.0\t1\t61\t8.5\t-38.8\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t256\t266\tPF04236.7_Transp_Tc5_C_Tase_30.0\t51\t61\t2.3\t-0.2\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t388\t395\tPF10576.1_EndIII_4Fe-2S_EN_17.5\t10\t17\t3.9\t-0.0\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t425\t433\tPF05410.5_Peptidase_C31_CYP_25.0\t98\t106\t1.9\t-2.0\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t487\t497\tPF09225.2_Endonuc-PvuII_EN_25.0\t127\t137\t4.9\t-3.5\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t574\t581\tPF02093.8_Gag_p30_GAG_10.5\t1\t8\t7.3\t-4.5\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t693\t706\tPF00910.14_RNA_helicase_HEL_20.0\t1\t14\t3.8\t-1.0\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t735\t743\tPF09569.2_RE_ScaI_EN_25.0\t1\t9\t7.1\t-3.3\t0\n") - f.write("BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\t737\t743\tPF03577.7_Peptidase_C69_CYP_25.0\t459\t465\t6.2\t-4.8\t0\n") - f.close() - f = open(self.consensusFile, "w") - f.write(">BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp\n") - f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n") - f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n") - f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n") - f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n") - f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n") - f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n") - f.write("TCCATAATTTCAACACTNAAGAATATTTGTA") - f.close() - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setInFileName(self.inputFileName) - alignTransformation.setOutFileName(self.outputFileName) - alignTransformation.setConsensusFileName(self.consensusFile) - self.assertRaises(RepetException, alignTransformation.run) - - def test_extractFrameFromSeqName(self): - alignInstance = Align() - rangeQuery = Range() - rangeQuery.seqname = "BlastclustCluster251Mb1_Jr945-B-R1176-Map4_classII-Helitron-incomp" - alignInstance.range_query = rangeQuery - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - self.assertRaises(RepetException, alignTransformation.extractFrameFromSeqName, alignInstance) - - def test_run_no_filter(self): - f = open(self.inputFileName, "w") - f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n") - f.close() - f = open(self.consensusFile, "w") - f.write(">blumeria_Grouper_590_20:NoCat\n") - f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n") - f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n") - f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n") - f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n") - f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n") - f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n") - f.write("TCCATAATTTCAACACTNAAGAATATTTGTA") - f.close() - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setInFileName(self.inputFileName) - alignTransformation.setOutFileName(self.outputFileName) - alignTransformation.setConsensusFileName(self.consensusFile) - alignTransformation.setIsFiltered(False) - alignTransformation.run() - self.assertTrue(FileUtils.getNbLinesInSingleFile(self.outputFileName), 6) - self.assertTrue(FileUtils.isRessourceExists(self.inputFileName)) - - def test_run_no_filter_clean_option(self): - f = open(self.inputFileName, "w") - f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2\t0.0\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("blumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n") - f.close() - f = open(self.consensusFile, "w") - f.write(">blumeria_Grouper_590_20:NoCat\n") - f.write("TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA\n") - f.write("AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT\n") - f.write("ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA\n") - f.write("ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA\n") - f.write("CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC\n") - f.write("TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC\n") - f.write("TCCATAATTTCAACACTNAAGAATATTTGTA") - f.close() - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setInFileName(self.inputFileName) - alignTransformation.setOutFileName(self.outputFileName) - alignTransformation.setConsensusFileName(self.consensusFile) - alignTransformation.setIsFiltered(True) - alignTransformation.setIsClean(True) - alignTransformation.run() - self.assertTrue(FileUtils.getNbLinesInSingleFile(self.outputFileName), 6) - self.assertFalse(FileUtils.isRessourceExists(self.inputFileName)) - -if __name__ == "__main__" : - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/TransformAACoordIntoNtCoordTestSuite.py --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/TransformAACoordIntoNtCoordTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -import unittest -import sys -import TestTransformAACoordIntoNtCoordInAlignFormat -import TestAcceptanceTransformAACoordIntoNtCoordAndScoreFiltering - -def main(): - - TransformAlignTestSuite = unittest.TestSuite() - TransformAlignTestSuite.addTest(unittest.makeSuite(TestTransformAACoordIntoNtCoordInAlignFormat.TestTransformAACoordIntoNtCoordInAlignFormat,'test')) - TransformAlignTestSuite.addTest(unittest.makeSuite(TestAcceptanceTransformAACoordIntoNtCoordAndScoreFiltering.TestAcceptanceTransformAACoordIntoNtCoordAndScoreFiltering,'test')) - - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(TransformAlignTestSuite) - - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/ConsensusTestFile_nt.fsa --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/ConsensusTestFile_nt.fsa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ ->blumeria_Grouper_590_20:NoCat -TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA -AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT -ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA -ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA -CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC -TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC -TCCATAATTTCAACACTNAAGAATATTTGTA ->blumeria_Grouper_4152_12:NoCat -GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA -AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC -GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC -GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC -TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT -TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT -GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG -CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC -ATATCTACCTCGGGGACATTG diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/OutputHmmpfamTest.align --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/OutputHmmpfamTest.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -blumeria_Grouper_590_20:NoCat_1 91 108 DUF234 5 22 1.5 3.2 0 -blumeria_Grouper_590_20:NoCat_1 111 119 DUF1414 1 9 6.3 2.9 0 -blumeria_Grouper_590_20:NoCat_3 30 37 CPW_WPC 1 9 7.7 1.5 0 -blumeria_Grouper_590_20:NoCat_3 55 69 HECT 341 355 9.2 0.0 0 -blumeria_Grouper_590_20:NoCat_4 82 91 DUF46 173 182 0.11 6.4 0 -blumeria_Grouper_590_20:NoCat_5 121 125 POC4 276 280 6.3 -1.7 0 -blumeria_Grouper_4152_12:NoCat_1 27 38 Amino_oxidase 471 482 9.1 -0.6 0 -blumeria_Grouper_4152_12:NoCat_1 33 67 TrbL 231 285 8 0.8 0 -blumeria_Grouper_4152_12:NoCat_1 58 80 TNV_CP 167 189 7.9 0.1 0 -blumeria_Grouper_4152_12:NoCat_1 94 109 DGOK 283 298 1.3 0.5 0 -blumeria_Grouper_4152_12:NoCat_1 113 127 Peptidase_S29 1 15 1.1 4.7 0 -blumeria_Grouper_4152_12:NoCat_1 148 157 DUF1301 1 10 9.9 0.4 0 -blumeria_Grouper_4152_12:NoCat_2 21 26 Toxin_18 50 55 4.4 4.2 0 -blumeria_Grouper_4152_12:NoCat_2 126 137 ABC_transp_aux 276 287 5.2 1.1 0 -blumeria_Grouper_4152_12:NoCat_2 143 159 DUF1602 23 39 0.39 5.0 0 -blumeria_Grouper_4152_12:NoCat_3 102 122 zf-P11 1 20 1.8 3.6 0 -blumeria_Grouper_4152_12:NoCat_3 126 135 V-ATPase_G 1 10 5.3 2.4 0 -blumeria_Grouper_4152_12:NoCat_4 92 122 XhoI 172 202 0.014 9.9 0 -blumeria_Grouper_4152_12:NoCat_4 113 119 Endomucin 261 267 6 0.1 0 -blumeria_Grouper_4152_12:NoCat_5 2 19 DUF1798 35 52 3.3 3.0 0 -blumeria_Grouper_4152_12:NoCat_5 46 69 DUF881 214 237 1.6 4.0 0 -blumeria_Grouper_4152_12:NoCat_5 77 93 Jun 264 284 6.5 -0.7 0 -blumeria_Grouper_4152_12:NoCat_5 89 108 SLT 1 20 1.2 4.5 0 -blumeria_Grouper_4152_12:NoCat_5 93 115 DUF2346 63 85 2.8 3.2 0 -blumeria_Grouper_4152_12:NoCat_5 124 139 LBP_BPI_CETP 191 209 3.8 1.8 0 -blumeria_Grouper_4152_12:NoCat_6 50 62 DUF258 293 305 3.8 1.5 0 -blumeria_Grouper_4152_12:NoCat_6 85 90 SOCS_box 1 6 9.7 2.4 0 -blumeria_Grouper_4152_12:NoCat_6 95 115 DUF1289 36 56 5.3 2.8 0 -blumeria_Grouper_4152_12:NoCat_6 106 116 TRAP_alpha 317 327 4.1 0.1 0 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/PostPostProcessTest.align --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/PostPostProcessTest.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -blumeria_Grouper_590_20:NoCat 271 324 DUF234 5 22 1.5 3 0.000000 -blumeria_Grouper_590_20:NoCat 331 357 DUF1414 1 9 6.3 2 0.000000 -blumeria_Grouper_590_20:NoCat 90 113 CPW_WPC 1 9 7.7 1 0.000000 -blumeria_Grouper_590_20:NoCat 165 209 HECT 341 355 9.2 0 0.000000 -blumeria_Grouper_590_20:NoCat 119 148 DUF46 182 173 0.11 6 0.000000 -blumeria_Grouper_590_20:NoCat 16 30 POC4 280 276 6.3 -1 0.000000 -blumeria_Grouper_4152_12:NoCat 79 114 Amino_oxidase 471 482 9.1 0 0.000000 -blumeria_Grouper_4152_12:NoCat 97 201 TrbL 231 285 8 0 0.000000 -blumeria_Grouper_4152_12:NoCat 172 240 TNV_CP 167 189 7.9 0 0.000000 -blumeria_Grouper_4152_12:NoCat 280 327 DGOK 283 298 1.3 0 0.000000 -blumeria_Grouper_4152_12:NoCat 337 381 Peptidase_S29 1 15 1.1 4 0.000000 -blumeria_Grouper_4152_12:NoCat 442 471 DUF1301 1 10 9.9 0 0.000000 -blumeria_Grouper_4152_12:NoCat 62 79 Toxin_18 50 55 4.4 4 0.000000 -blumeria_Grouper_4152_12:NoCat 377 412 ABC_transp_aux 276 287 5.2 1 0.000000 -blumeria_Grouper_4152_12:NoCat 428 478 DUF1602 23 39 0.39 5 0.000000 -blumeria_Grouper_4152_12:NoCat 306 368 zf-P11 1 20 1.8 3 0.000000 -blumeria_Grouper_4152_12:NoCat 378 407 V-ATPase_G 1 10 5.3 2 0.000000 -blumeria_Grouper_4152_12:NoCat 136 228 XhoI 202 172 0.014 9 0.000000 -blumeria_Grouper_4152_12:NoCat 145 165 Endomucin 267 261 6 0 0.000000 -blumeria_Grouper_4152_12:NoCat 444 497 DUF1798 52 35 3.3 3 0.000000 -blumeria_Grouper_4152_12:NoCat 294 365 DUF881 237 214 1.6 4 0.000000 -blumeria_Grouper_4152_12:NoCat 222 272 Jun 284 264 6.5 0 0.000000 -blumeria_Grouper_4152_12:NoCat 177 236 SLT 20 1 1.2 4 0.000000 -blumeria_Grouper_4152_12:NoCat 156 224 DUF2346 85 63 2.8 3 0.000000 -blumeria_Grouper_4152_12:NoCat 84 131 LBP_BPI_CETP 209 191 3.8 1 0.000000 -blumeria_Grouper_4152_12:NoCat 314 352 DUF258 305 293 3.8 1 0.000000 -blumeria_Grouper_4152_12:NoCat 230 247 SOCS_box 6 1 9.7 2 0.000000 -blumeria_Grouper_4152_12:NoCat 155 217 DUF1289 56 36 5.3 2 0.000000 -blumeria_Grouper_4152_12:NoCat 152 184 TRAP_alpha 327 317 4.1 0 0.000000 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/PostPostProcessTestFiltered.align --- a/commons/pyRepetUnit/align/transformAACoordIntoNtCoord/tests/datas/PostPostProcessTestFiltered.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -blumeria_Grouper_590_20:NoCat 271 324 DUF234 5 22 1.5 3 0.000000 -blumeria_Grouper_590_20:NoCat 331 357 DUF1414 1 9 6.3 2 0.000000 -blumeria_Grouper_590_20:NoCat 90 113 CPW_WPC 1 9 7.7 1 0.000000 -blumeria_Grouper_590_20:NoCat 119 148 DUF46 182 173 0.11 6 0.000000 -blumeria_Grouper_4152_12:NoCat 97 201 TrbL 231 285 8 0 0.000000 -blumeria_Grouper_4152_12:NoCat 172 240 TNV_CP 167 189 7.9 0 0.000000 -blumeria_Grouper_4152_12:NoCat 280 327 DGOK 283 298 1.3 0 0.000000 -blumeria_Grouper_4152_12:NoCat 337 381 Peptidase_S29 1 15 1.1 4 0.000000 -blumeria_Grouper_4152_12:NoCat 442 471 DUF1301 1 10 9.9 0 0.000000 -blumeria_Grouper_4152_12:NoCat 62 79 Toxin_18 50 55 4.4 4 0.000000 -blumeria_Grouper_4152_12:NoCat 377 412 ABC_transp_aux 276 287 5.2 1 0.000000 -blumeria_Grouper_4152_12:NoCat 428 478 DUF1602 23 39 0.39 5 0.000000 -blumeria_Grouper_4152_12:NoCat 306 368 zf-P11 1 20 1.8 3 0.000000 -blumeria_Grouper_4152_12:NoCat 378 407 V-ATPase_G 1 10 5.3 2 0.000000 -blumeria_Grouper_4152_12:NoCat 136 228 XhoI 202 172 0.014 9 0.000000 -blumeria_Grouper_4152_12:NoCat 145 165 Endomucin 267 261 6 0 0.000000 -blumeria_Grouper_4152_12:NoCat 444 497 DUF1798 52 35 3.3 3 0.000000 -blumeria_Grouper_4152_12:NoCat 294 365 DUF881 237 214 1.6 4 0.000000 -blumeria_Grouper_4152_12:NoCat 177 236 SLT 20 1 1.2 4 0.000000 -blumeria_Grouper_4152_12:NoCat 156 224 DUF2346 85 63 2.8 3 0.000000 -blumeria_Grouper_4152_12:NoCat 84 131 LBP_BPI_CETP 209 191 3.8 1 0.000000 -blumeria_Grouper_4152_12:NoCat 314 352 DUF258 305 293 3.8 1 0.000000 -blumeria_Grouper_4152_12:NoCat 230 247 SOCS_box 6 1 9.7 2 0.000000 -blumeria_Grouper_4152_12:NoCat 155 217 DUF1289 56 36 5.3 2 0.000000 -blumeria_Grouper_4152_12:NoCat 152 184 TRAP_alpha 327 317 4.1 0 0.000000 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/blastnForClassifierStep1/RepbaseBLRnForClassifierStep1.py --- a/commons/pyRepetUnit/blastnForClassifierStep1/RepbaseBLRnForClassifierStep1.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,186 +0,0 @@ -""" -Launch Blaster and then Matcher to compare the input sequences with known TEs via blastn and record the results into a MySQL table. -""" - -import os -import ConfigParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.LoggerFactory import LoggerFactory - -LOG_DEPTH = "repet.tools" - -class RepbaseBLRnForClassifierStep1( object ): - - """ - Launch Blaster and then Matcher to compare the input sequences with known TEs via blastn and record the results into a MySQL table. - - @param inFileName: name of the input fasta file - @type inFileName: string - - @param launch_1: generic command at the beginning of a specific command - @type launch_1: string - - @param launch_2: generic command at the end of a specific command - @type launch_2: string - - @return: all the commands to run the job - @rtype: string - - @param cDir: current directory (where to retrieve the result files) - @ype cDir: string - - @param tmpDir: temporary directory (where the job will run) - @type tmpDir: string - - @param configFileName: configuration file name - @type configFileName: string - - @param logger: a logger Instance - @type logger: logger - - @param verbose: verbose(0/1/2) - @type verbose: int - - @param pL: program launcher - @type pL: programLauncher Instance - - @param project: project name - @type project: string - - """ - - def __init__(self, inFileName, launch_1, launch_2, cDir, tmpDir, configFileName, verbose, pL, project): - """ - Constructor - """ - self._inFileName = inFileName - self._launch_1 = launch_1 - self._launch_2 = launch_2 - self._cDir = cDir - self._tmpDir = tmpDir - self._verbose = verbose - self._pL = pL - self._project = project - self._fileUtils = FileUtils() - self._config = ConfigParser.ConfigParser() - self._configFileName = configFileName - self._config.readfp( open(self._configFileName) ) - self._bank = self._config.get("detect_features","TE_nucl_bank") - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbose) - - def formatRepbase_ntIfNecessary( self ): - """ - Format Repbase (make 'cut' files). - """ - if not os.path.exists( "%s_cut" % ( self._bank ) ): - self._log.debug("prepare bank '%s'..." % ( self._bank )) - prg = os.environ["REPET_PATH"] + "/bin/blaster" - cmd = prg - cmd += " -s %s" % ( self._bank ) - cmd += " -n blastn" - if self._config.get("detect_features","wublast") == "yes": - cmd += " -W" - cmd += " -r" - cmd += " -P" - self._pL.launch( prg, cmd ) - os.system( "rm -f %s-blastn-*.param" % ( self._bank ) ) - - def createCmdToLaunch( self ): - cmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster" - cmd += " -q %s" % ( self._inFileName ) - cmd += " -s %s/%s" % ( self._cDir, self._bank ) - cmd += " -B %s_BLRn_%s" % ( self._inFileName, self._bank ) - cmd += " -n blastn" - if self._config.get("detect_features","wublast") == "yes": - cmd += " -W" - cmd += " -r" - cmd += " -v 1" - cmd += self._launch_2 - - cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, self._bank ) - cmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, self._bank, self._cDir ) - cmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName ) - cmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName ) - cmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName ) - cmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName ) - cmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, self._bank ) - cmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, self._bank ) - cmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, self._bank ) - cmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, self._bank ) - - cmd += self._launch_1 - cmd += os.environ["REPET_PATH"] + "/bin/matcher" - cmd += " -m %s_BLRn_%s.align" % ( self._inFileName, self._bank ) - cmd += " -q %s" % ( self._inFileName ) - cmd += " -s %s/%s" % ( self._cDir, self._bank ) - cmd += " -j" - cmd += " -v 1" - cmd += self._launch_2 - - cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, self._bank ) - cmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, self._bank, self._cDir ) - cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, self._bank ) - cmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, self._bank, self._cDir ) - cmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, self._bank ) - cmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, self._bank ) - cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, self._bank ) - cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, self._bank ) - cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, self._bank ) - cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, self._bank ) - cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, self._bank ) - cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, self._bank ) - - if self._tmpDir != self._cDir: - cmd += "if os.path.exists( \"%s\" ):\n" % ( self._bank ) - cmd += "\tos.remove( \"%s\" )\n" % ( self._bank ) - - return cmd - - def collectRepbaseBLRn( self ): - """ - Concatenate the outputs of blastn, adapt the ID and load the results into a table. - """ - bankFull = self._bank - bankPath, bank = os.path.split( bankFull ) - self._concatPathFile(bank) - self._adaptIDInPathFile(bank) - self._loadPathFileInTable(bank) - self._findAndRemoveUselessFiles(bank) - - def _concatPathFile(self, bank): - FileUtils.catFilesByPattern("../batch_*.fa_BLRn_%s.align.clean_match.path" % bank, - "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)) - - def _adaptIDInPathFile(self, bank): - if os.path.exists(os.environ["REPET_PATH"] + "/bin/pathnum2id"): - prg = os.environ["REPET_PATH"] + "/bin/pathnum2id" - cmd = prg - cmd += " -i %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank) - cmd += " -o %s_BLRn_%s.align.clean_match.path" % (self._project, bank) - cmd += " -v %i" % (self._verbose - 1) - self._pL.launch(prg, cmd) - else: - prg = os.environ["REPET_PATH"] + "/bin/pathnum2id.py" - cmd = prg - cmd += " -i %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank) - cmd += " -o %s_BLRn_%s.align.clean_match.path" % (self._project, bank) - self._pL.launch(prg, cmd) - - def _loadPathFileInTable(self, bank): - prg = os.environ["REPET_PATH"] + "/bin/srptCreateTable.py" - cmd = prg - cmd += " -f %s_BLRn_%s.align.clean_match.path" % (self._project, bank) - cmd += " -n %s_TE_BLRn_path" % (self._project) - cmd += " -t path" - cmd += " -c ../%s" % (self._configFileName) - self._pL.launch(prg, cmd) - - def _findAndRemoveUselessFiles(self, bank): - prg = "find" - cmd = prg - cmd += " .. -name \"batch_*.fa_BLRn_%s.*\" -exec rm {} \;" % (bank) - self._pL.launch(prg, cmd) - prg = "rm" - cmd = prg - cmd += " %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank) - self._pL.launch(prg, cmd) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/blastnForClassifierStep1/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/blastnForClassifierStep1/tests/Test_RepbaseBLRnForClassifierStep1.py --- a/commons/pyRepetUnit/blastnForClassifierStep1/tests/Test_RepbaseBLRnForClassifierStep1.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,343 +0,0 @@ -import unittest -import os -import shutil -import ConfigParser -import sys -from commons.pyRepetUnit.blastnForClassifierStep1.RepbaseBLRnForClassifierStep1 import RepbaseBLRnForClassifierStep1 -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.coord.Path import Path -import pyRepet.launcher.programLauncher - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -NB_EXPECTED_LINES_IN_PATH_FILE = 10 -CURRENT_DIR = os.getcwd() - - -class Test_RepbaseBLRnForClassifierStep1( unittest.TestCase ): - - - def setUp( self ): - os.chdir(CURRENT_DIR) - self._inFileName = "dummyFileName" - self._launch_1 = "log = os.system( \"" - self._launch_2 = "\" )\n" - self._launch_2 += "if log != 0:\n" - self._launch_2 += "\tsys.exit(1)\n" - self._cDir = "/home/user/dummy_cdir" - self._tmpDir = "/home/user/dummy_tmpDir" - self._configFileName = "configFile" - self._repbaseName = "dummyRepbase_nt.fa" - f = open(self._configFileName, "w") - f.write("[repet_env]\n") - f.write("repet_host: %s\n" % os.environ["REPET_HOST"]) - f.write("repet_user: %s\n" % os.environ["REPET_USER"]) - f.write("repet_pw: %s\n" % os.environ["REPET_PW"]) - f.write("repet_db: %s\n" % os.environ["REPET_DB"]) - f.write("repet_port: %s\n" % os.environ["REPET_PORT"]) - f.write("[detect_features]\n") - f.write("TE_BLRn: yes\n") - f.write("TE_nucl_bank: %s\n" % self._repbaseName) - f.write("wublast: yes\n") - f.close() - self._verbose = 0 - self._config = ConfigParser.ConfigParser() - self._config.readfp( open(self._configFileName) ) - self._pL = pyRepet.launcher.programLauncher.programLauncher() - self._project = "dummyProject" - self._repbaseBLRn = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project) - self._expFileName = "expFile" - self._bank = self._config.get("detect_features","TE_nucl_bank") - self._db = DbFactory.createInstance() - - - def tearDown( self ): - self._db.dropTable("%s_TE_BLRn_path" % (self._project)) - os.chdir(CURRENT_DIR) - self._repbaseBLRn = None - os.remove(self._configFileName) - if os.path.isfile("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)): - os.remove("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)) - if os.path.isfile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)): - os.remove("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)) - if os.path.isfile("batch_1.fa_BLRn_%s.*" % (self._bank)): - os.remove("batch_1.fa_BLRn_%s.*" % (self._bank)) - if os.path.isfile("batch_2.fa_BLRn_%s.*" % (self._bank)): - os.remove("batch_2.fa_BLRn_%s.*" % (self._bank)) - if os.path.isfile("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank)): - os.remove("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank)) - if os.path.isfile("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank)): - os.remove("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank)) - if os.path.isfile(self._repbaseName): - os.remove(self._repbaseName) - os.remove(self._repbaseName + "_cut") - os.remove(self._repbaseName + "_cut.xnd") - os.remove(self._repbaseName + "_cut.xns") - os.remove(self._repbaseName + "_cut.xnt") - os.remove(self._repbaseName + ".Nstretch.map") - os.remove("last_time_stamp.log") - if os.path.isdir( "TE_BLRn" ): - os.chdir( "TE_BLRn" ) - os.chdir(CURRENT_DIR) - shutil.rmtree("TE_BLRn") - if os.path.isfile(self._expFileName): - os.remove(self._expFileName) - - - def test_formatRepbase_ntIfNecessaryWithoutLog( self ): - f = open(self._repbaseName, "w") - f.write(">seq1\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.write(">seq2\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.close() - f = open(self._expFileName, "w") - f.write(">1 seq1 {Cut} 1..180\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.write(">2 seq2 {Cut} 1..180\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.close() - self._repbaseBLRn.formatRepbase_ntIfNecessary() - obsFileName = self._repbaseName + "_cut" - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) - - - def test_formatRepbase_ntIfNecessary_withLogFile( self ): - f = open(self._repbaseName, "w") - f.write(">seq1\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.write(">seq2\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.close() - f = open(self._expFileName, "w") - f.write(">1 seq1 {Cut} 1..180\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.write(">2 seq2 {Cut} 1..180\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") - f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") - f.close() - repbaseBLRnWithLog = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project) - repbaseBLRnWithLog.formatRepbase_ntIfNecessary() - obsFileName = self._repbaseName + "_cut" - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) - - - def test_createCmdToLaunch( self ): - bank = self._config.get("detect_features","TE_nucl_bank") - obsCmd = self._repbaseBLRn.createCmdToLaunch() - expCmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster" - expCmd += " -q %s" % ( self._inFileName ) - expCmd += " -s %s/%s" % ( self._cDir, bank ) - expCmd += " -B %s_BLRn_%s" % ( self._inFileName, bank ) - expCmd += " -n blastn" - if self._config.get("detect_features","wublast") == "yes": - expCmd += " -W" - expCmd += " -r" - expCmd += " -v 1" - expCmd += self._launch_2 - expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, bank ) - expCmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, bank, self._cDir ) - expCmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName ) - expCmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName ) - expCmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName ) - expCmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName ) - expCmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, bank ) - expCmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, bank ) - expCmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, bank ) - expCmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, bank ) - expCmd += self._launch_1 - expCmd += os.environ["REPET_PATH"] + "/bin/matcher" - expCmd += " -m %s_BLRn_%s.align" % ( self._inFileName, bank ) - expCmd += " -q %s" % ( self._inFileName ) - expCmd += " -s %s/%s" % ( self._cDir, bank ) - expCmd += " -j" - expCmd += " -v 1" - expCmd += self._launch_2 - expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, bank ) - expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, bank, self._cDir ) - expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, bank ) - expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, bank, self._cDir ) - expCmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, bank ) - expCmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, bank ) - expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, bank ) - expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, bank ) - expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, bank ) - expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, bank ) - expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, bank ) - expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, bank ) - if self._tmpDir != self._cDir: - expCmd += "if os.path.exists( \"%s\" ):\n" % ( bank ) - expCmd += "\tos.remove( \"%s\" )\n" % ( bank ) - self.assertEquals( expCmd, obsCmd ) - - - def test_concatPathFile( self ): - os.chdir(CURRENT_DIR) - if not FileUtils.isRessourceExists("TE_BLRn"): - os.mkdir( "TE_BLRn" ) - self._createPathFiles(self._bank) - os.chdir( "TE_BLRn" ) - f = open(self._expFileName, "w") - f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.close() - FileUtils.sortFileContent(self._expFileName) - obsFileName = "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank) - self._repbaseBLRn._concatPathFile(self._bank) - FileUtils.sortFileContent(obsFileName) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) - - - def test_adaptIDInPathFile( self ): - f = open("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank), "w") - f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.close() - self._repbaseBLRn._adaptIDInPathFile(self._bank) - f = open(self._expFileName, "w") - f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.close() - obsFileName = "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) - - - def test_loadPathFileInTable( self ): - os.chdir(CURRENT_DIR) - if not FileUtils.isRessourceExists("TE_BLRn"): - os.mkdir( "TE_BLRn" ) - self._createPathFiles(self._bank) - os.chdir( "TE_BLRn" ) - f = open("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank), "w") - f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.close() - self._repbaseBLRn._loadPathFileInTable(self._bank) - resultFromFilePathList = self._readPathResultsFromFileAndFillList() - resultFromTablePathList = self._readPathResultsFromTableAndFillList() - self.assertEquals(resultFromFilePathList, resultFromTablePathList) - - - def test_findAndRemoveUselessFiles( self ): - self._createFile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)) - self._createFile("batch_1.fa_BLRn_%s.*" % (self._bank)) - self._createFile("batch_2.fa_BLRn_%s.*" % (self._bank)) - self._repbaseBLRn._findAndRemoveUselessFiles(self._bank) - self.assertFalse(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank))) - self.assertFalse(FileUtils.isRessourceExists("batch_1.fa_BLRn_%s.*" % (self._bank))) - self.assertFalse(FileUtils.isRessourceExists("batch_2.fa_BLRn_%s.*" % (self._bank))) - - - def test_collectRepbaseBLRn( self ): - os.chdir(CURRENT_DIR) - if not FileUtils.isRessourceExists("TE_BLRn"): - os.mkdir( "TE_BLRn" ) - self._createPathFiles(self._bank) - os.chdir( "TE_BLRn" ) - self._repbaseBLRn.collectRepbaseBLRn() - self.assertTrue(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank ))) - self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, FileUtils.getNbLinesInSingleFile("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank ))) - self.assertTrue(self._db.doesTableExist("%s_TE_BLRn_path" % (self._project))) - self._db.execute('select * from %s_TE_BLRn_path' % (self._project)) - self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, len(self._db.fetchall())) - self._db.dropTable("%s_TE_BLRn_path" % (self._project)) - - - def _createPathFiles( self, bankFull ): - bank = os.path.split(bankFull)[1] - fileName = "batch_1.fa_BLRn_" + bank + ".align.clean_match.path" - f = open(fileName, "w") - f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.close() - fileName = "batch_2.fa_BLRn_" + bank + ".align.clean_match.path" - f = open(fileName, "w") - f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") - f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") - f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") - f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") - f.close() - - - def _readPathResultsFromTableAndFillList( self ): - tablePathAdaptatorInstance = TablePathAdaptator (self._db, "%s_TE_BLRn_path" % (self._project)) - pathList = tablePathAdaptatorInstance.getListOfAllPaths() - return pathList - - - def _readPathResultsFromFileAndFillList( self ): - pathInstance = Path() - pathList = [] - f = open( "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank) , "r") - while pathInstance.read( f ): - pathList.append(pathInstance) - pathInstance = Path() - f.close() - return pathList - - - def _createFile( self, nameFile ): - f = open(nameFile, "w") - f.close() - - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_RepbaseBLRnForClassifierStep1 ) ) -if __name__ == "__main__": - unittest.TextTestRunner(verbosity=2).run( test_suite ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/blastnForClassifierStep1/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/AbstractClusterLauncher.py --- a/commons/pyRepetUnit/components/AbstractClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,606 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import getopt -import time -import glob -import sys -import os - -from commons.core.checker.CheckerException import CheckerException -from commons.core.sql.RepetJob import RepetJob -from commons.core.sql.Job import Job -from commons.core.stat.Stat import Stat -from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher - -GENERIC_IN_FILE = "zDUMMYz" - - -## Abstract class to launch a program in parallel on a cluster. -# -class AbstractClusterLauncher( object ): #( IClusterLauncher ) - - def __init__( self ): - """ - Constructor. - """ - self._inputDir = "" # path to the directory with input files - self._queueName = "" # name of the queue on the cluster - self._groupId = "" # identifier of the group of jobs (groupid) - self._inputFileSuffix = "fa" # suffix of the input files (default='fa') - self._prgAcronym = "" # acronym of the program to launch - self._configFile = "" # name of the configuration file (connect to MySQL) - self._currentDir = os.getcwd() # path to the current directory - self._tmpDir = "" # path to the temporary directory - self._jobTable = "jobs" # name of the table recording the jobs - self._catOutFiles = False # concatenate output files of all jobs - self._clean = False # clean job file, job stdout, job table... - self._verbose = 1 # verbosity level - self.jobdb = None # RepetJob instance - self.job = Job() # Job instance - - self._nbJobs = 0 - self._cmdLineGenericOptions = "hi:Q:g:S:a:C:d:j:Zcv:" - self._cmdLineSpecificOptions = "" - - self._exeWrapper = "AbstractProgramLauncher.py" - self._prgLauncher = None - # list of instances derived from AbstractProgramLauncher() - # If several program are launched successively in the same job, - # 'lPrgLaunchers' has to be filled before run(). - self.lPrgLaunchers = [] - - def setProgramLauncherAttributeFromCmdLine(self, o, a=""): - self.getProgramLauncherInstance().setASpecificAttributeFromCmdLine(o, a) - - def setClusterLauncherAttributeFromCmdLine(self, o, a=""): - if o == "-h": - print self.getHelpAsString() - sys.exit(0) - elif o == "-i": - self.setInputDirectory(a) - elif o == "-Q": - self.setQueueName(a) - elif o == "-g": - self.setGroupIdentifier(a) - elif o == "-S": - self.setInputFileSuffix(a) - elif o == "-a": - self.setAcronym(a) - elif o == "-C": - self.setConfigFile(a) - elif o == "-d": - self.setTemporaryDirectory(a) - elif o == "-j": - self.setJobTableName(a) - elif o == "-Z": - self.setCatOutputFiles() - elif o == "-c": - self.setClean() - elif o == "-v": - self.setVerbosityLevel(a) - - def setAttributesFromCmdLine(self): - try: - opts, args = getopt.getopt(sys.argv[1:], self.getCmdLineOptions()) - except getopt.GetoptError, err: - print str(err); - print self.getHelpAsString() - sys.exit(1) - for o, a in opts: - self.setClusterLauncherAttributeFromCmdLine(o, a) - self.setProgramLauncherAttributeFromCmdLine(o, a) - - def setAGenericAttributeFromCmdLine( self, o, a="" ): - self.setClusterLauncherAttributeFromCmdLine(o, a) - - def setASpecificAttributeFromCmdLine( self, o, a="" ): - self.setProgramLauncherAttributeFromCmdLine(o, a) - - def setInputDirectory( self, arg ): - self._inputDir = arg - - def setQueueName( self, arg ): - self._queueName = arg - - def setGroupIdentifier( self, arg ): - self._groupId = arg - - def setInputFileSuffix( self, arg ): - self._inputFileSuffix = arg - - def setAcronym( self, arg ): - self._prgAcronym = arg - - def setConfigFile( self, arg ): - if os.path.dirname( arg ) == "": - self._configFile = "%s/%s" % ( os.getcwd(), arg ) - else: - self._configFile = arg - - def setCurrentDirectory( self, arg =os.getcwd()): - self._currentDir = arg - - def setTemporaryDirectory( self, arg ): - self._tmpDir = arg - - def setJobTableName( self, arg ): - self._jobTable = arg - - def setCatOutputFiles( self ): - self._catOutFiles = True - - def setClean( self): - self._clean = True - - def setVerbosityLevel( self, arg ): - self._verbose = int(arg) - - def setExecutableWrapper( self, arg = "AbstractProgramLauncher.py" ): - self._exeWrapper = arg - - def setSingleProgramLauncher( self ): - """ - Set the wrapper and program command-lines of the program launcher. - Append the program launcher to 'self.lPrgLaunchers'. - """ - self.getProgramLauncherInstance().setWrapperCommandLine() - self.getProgramLauncherInstance().setProgramCommandLine() - self.lPrgLaunchers.append( self.getProgramLauncherInstance() ) - - def getGenericHelpAsString( self ): - string = "" - string += "usage: %s.py [options]" % (type(self).__name__ ) - string += "\ngeneric options:" - string += "\n -h: this help" - string += "\n -i: directory with input files (absolute path)" - string += "\n -Q: name of the queue on the cluster" - string += "\n -g: identifier of the group of jobs (groupid)" - string += "\n -S: suffix of the input files (default='fa')" - string += "\n -a: acronym of the program to be launched (default='%s')" % ( self.getAcronym() ) - string += "\n -C: configuration file to connect to MySQL (absolute path or in current dir)" - string += "\n -d: temporary directory (absolute path, default=None)" - string += "\n -j: table recording the jobs (default='jobs')" - string += "\n -c: clean the temporary data" - string += "\n -v: verbosity level (default=0/1/2)" - return string - - def getSpecificHelpAsString( self ): - pass - - def getHelpAsString(self): - return self.getGenericHelpAsString() + self.getSpecificHelpAsString() - - def getInputDirectory( self ): - return self._inputDir - - def getQueueName( self ): - return self._queueName - - def getGroupIdentifier( self ): - return self._groupId - - def getInputFileSuffix( self ): - return self._inputFileSuffix - - def getAcronym( self ): - return self._prgAcronym - - def getConfigFile( self ): - return self._configFile - - def getCurrentDirectory( self ): - return self._currentDir - - def getTemporaryDirectory( self ): - return self._tmpDir - - def getJobTableName( self ): - return self._jobTable - - def getCatOutputFiles( self ): - return self._catOutFiles - - def getClean( self ): - return self._clean - - def getVerbosityLevel( self ): - return self._verbose - - def getWrapperName( self ): - return self.getProgramLauncherInstance().getWrapperName() - - def getProgramName( self ): - return self.getProgramLauncherInstance().getProgramName() - - def getPatternToConcatenate( self ): - return self.getProgramLauncherInstance().getOutputFile().replace( GENERIC_IN_FILE, "*" ) - - def getProgramLauncherInstance( self ): - if self._prgLauncher == None: - self._prgLauncher = AbstractProgramLauncher() - return self._prgLauncher - - def getInputFilesList(self): - lInFiles = glob.glob("%s/*.%s" % (self._inputDir, self._inputFileSuffix)) - return lInFiles - - def getCmdLineOptions(self): - return "hi:Q:g:S:a:C:d:j:Zcv:" - - - def getProgramCommandLineAsString( self ): - """ - Return the command-line to launch in each job. - Specified in each wrapper. - """ - pass - - - def getListFilesToKeep( self ): - """ - Return the list of files to keep at the end of each job. - Specified in each wrapper. - """ - pass - - - def getListFilesToRemove( self ): - """ - Return the list of files to remove at the end of each job. - Specified in each wrapper. - """ - pass - - - def getJobFileNameAsString( self, count ): - """ - Return the name of the job file as a string. - @param count: job number (e.g. '1') or '*' - @type count: integer or string - """ - jobFile = "ClusterLauncher" - jobFile += "_groupid%s" % ( self.getGroupIdentifier() ) - if count != "*": - jobFile += "_job%i" % ( count ) - jobFile += "_time%s" % ( time.strftime("%Y-%m-%d-%H-%M-%S") ) - else: - jobFile += "_job*" - jobFile += "_time%s-*" % ( time.strftime("%Y-%m") ) - jobFile += ".py" - return jobFile - - - def getCmdUpdateJobStatusAsString( self, newStatus ): - """ - Return the command to update the job status in the table. - """ - prg = os.environ["REPET_PATH"] + "/bin/srptChangeJobStatus.py" - cmd = prg - cmd += " -t %s" % ( self.job.tablename ) - if str(self.job.jobid).isdigit(): - cmd += " -j %s" % ( self.job.jobname ) - else: - cmd += " -j %s" % ( self.job.jobid ) - cmd += " -g %s" % ( self.job.groupid ) - if self.job.queue != "": - cmd += " -q %s" % ( self.job.queue ) - cmd += " -s %s" % ( newStatus ) - cmd += " -c %s" % ( self.getConfigFile() ) - cmd += " -v %i" % ( self._verbose ) - return "os.system( \"%s\" )\n" % ( cmd ) - - - def getCmdToLaunchWrapper( self, fileName, genericCmd, exeWrapper ): - """ - Return the launching command as a string. - Launch the wrapper, retrieve its exit status, update status if error. - """ - specificCmd = genericCmd.replace( GENERIC_IN_FILE, fileName ) - cmd = "" - cmd += "print \"LAUNCH: %s\"\n" % ( specificCmd ) - cmd += "sys.stdout.flush()\n" - cmd += "exitStatus = os.system ( \"%s\" )\n" % ( specificCmd ) - cmd += "if exitStatus != 0:\n" - cmd += "\tprint \"ERROR: wrapper '%s'" % ( exeWrapper ) - cmd += " returned exit status '%i'\" % ( exitStatus )\n" - cmd += "\tos.chdir( \"%s\" )\n" % ( self.getTemporaryDirectory() ) - cmd += "\tshutil.move( newDir, '%s' )\n" % ( self.getCurrentDirectory() ) - cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) ) - cmd += "\tsys.exit(1)\n" - return cmd - - - def getCmdToKeepFiles( self, fileName, lFilesToKeep ): - """ - Return the commands to keep the output files. - """ - cmd = "" - for f in lFilesToKeep: - f = f.replace( GENERIC_IN_FILE, fileName ) - cmd += "if not os.path.exists( \"%s\" ):\n" % ( f ) - cmd += "\tprint \"ERROR: output file '%s' doesn't exist\"\n" % ( f ) - cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) ) - cmd += "\tsys.exit(1)\n" - cmd += "if not os.path.exists( \"%s/%s\" ):\n" \ - % ( self._currentDir, f ) - cmd += "\tshutil.copy( \"%s\", \"%s/%s\" )\n" % ( f, self.getCurrentDirectory(), f ) - return cmd - - - def getCmdToRemoveFiles( self, fileName, lFilesToRemove ): - """ - Return the commands to remove the temporary files. - """ - cmd = "" - if lFilesToRemove != []: - for f in lFilesToRemove: - f = f.replace( GENERIC_IN_FILE, fileName ) - cmd += "if os.path.exists( \"%s\" ):\n" % ( f ) - cmd += "\tos.remove( \"%s\" )\n" % ( f ) - return cmd - - - def getJobCommandsAsString( self, fileName, jobName, minFreeGigaInTmpDir=1 ): - """ - Return all the job commands as a string. - """ - cmd = "#!/usr/bin/env python\n" - cmd += "\n" - cmd += "import os\n" - cmd += "import sys\n" - cmd += "import shutil\n" - cmd += "import time\n" - cmd += "\n" - cmd += "print \"system:\", os.uname()\n" - cmd += "beginTime = time.time()\n" - cmd += "print 'beginTime=%f' % ( beginTime )\n" - cmd += "\n" - cmd += self.getCmdUpdateJobStatusAsString( "running" ) - cmd += "\n" - cmd += "if not os.path.exists( \"%s\" ):\n" % ( self.getTemporaryDirectory() ) - cmd += "\tprint \"ERROR: working dir '%s' doesn't exist\"\n" % ( \ - self.getTemporaryDirectory() ) - cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) ) - cmd += "\tsys.exit(1)\n" - cmd += "freeSpace = os.statvfs( \"%s\" )\n" % ( self.getTemporaryDirectory() ) - cmd += "if ( freeSpace.f_bavail * freeSpace.f_frsize ) / 1073741824.0 < %i:\n" % ( minFreeGigaInTmpDir ) # nb blocs * bloc size in bytes > 1 GigaByte ? - cmd += "\tprint \"ERROR: less than %iGb in '%s'\"\n" % ( minFreeGigaInTmpDir, self.getTemporaryDirectory() ) - cmd += "\t%s" % ( self.getCmdUpdateJobStatusAsString( "error" ) ) - cmd += "\tsys.exit(1)\n" - cmd += "print \"working dir: %s\"\n" % ( self.getTemporaryDirectory() ) - cmd += "sys.stdout.flush()\n" - cmd += "os.chdir( \"%s\" )\n" % ( self.getTemporaryDirectory() ) - cmd += "\n" - cmd += "newDir = \"%s_%s_%s\"\n" % ( self.getGroupIdentifier(), jobName, time.strftime("%Y%m%d-%H%M%S") ) - cmd += "if os.path.exists( newDir ):\n" - cmd += "\tshutil.rmtree( newDir )\n" - cmd += "os.mkdir( newDir )\n" - cmd += "os.chdir( newDir )\n" - cmd += "\n" - cmd += "if not os.path.exists( \"%s\" ):\n" % ( fileName ) - cmd += "\tos.symlink( \"%s/%s\", \"%s\" )\n" % \ - ( self._inputDir, fileName, fileName ) - cmd += "\n" - - for pL in self.lPrgLaunchers: - cmd += self.getCmdToLaunchWrapper( \ - fileName, \ - pL.getWrapperCommandLine(), \ - "%s.py" % ( type(pL).__name__ ) ) - cmd += "\n" - cmd += self.getCmdToKeepFiles( fileName, pL.getListFilesToKeep() ) - cmd += "\n" - cmd += self.getCmdToRemoveFiles( fileName, \ - pL.getListFilesToRemove() ) - - cmd += "if os.path.exists( \"%s\" ):\n" % ( fileName ) - cmd += "\tos.remove( \"%s\" )\n" % ( fileName ) - cmd += "os.chdir( \"..\" )\n" - cmd += "shutil.rmtree( newDir )\n" - cmd += self.getCmdUpdateJobStatusAsString( "finished" ) - cmd += "\n" - cmd += "endTime = time.time()\n" - cmd += "print 'endTime=%f' % ( endTime)\n" - cmd += "print 'executionTime=%f' % ( endTime - beginTime )\n" - cmd += "print \"system:\", os.uname()\n" - cmd += "sys.exit(0)\n" - return cmd - - def getStatsOfExecutionTime( self ): - """ - Return a Stat object about the execution time of each job as a - float expressed in seconds since the epoch, in UTC. - """ - stat = Stat() - pattern = "%s/%s*.o*" % ( self.getCurrentDirectory(), \ - self.getAcronym() ) - lJobFiles = glob.glob( pattern ) - for f in lJobFiles: - fH = open( f, "r" ) - while True: - line = fH.readline() - if line == "": - break - if "executionTime" in line: - stat.add( float(line[:-1].split("=")[1] ) ) - break - fH.close() - return stat - - - def formatGroupidAndTime(self): - return self.job.groupid + " " + time.strftime("%Y-%m-%d %H:%M:%S") + "" - - def submitJob(self, lInFiles): - count = 0 - for inFile in lInFiles: - count += 1 - fileName = os.path.basename(inFile) - if self._verbose > 1: - print "processing '%s' # %i..." % (fileName, count) - sys.stdout.flush() - - self.initializeJob(fileName, count) - time.sleep(0.5) - exitStatus = self.jobdb.submitJob(self.job) - if exitStatus != 0: - print "ERROR while submitting job '%i' to the cluster" % (count) - sys.exit(1) - - def checkClusterLauncherAttributes( self ): - if self.getInputDirectory() == "": - message = "ERROR: missing input directory" - raise CheckerException(message) - if not os.path.exists( self.getInputDirectory() ): - message = "ERROR: input directory '%s' doesn't exist" % ( self.getInputDirectory() ) - raise CheckerException(message) - if self.getGroupIdentifier() == "": - message = "ERROR: missing group identifier" - raise CheckerException(message) - if self.getAcronym() == "": - message = "ERROR: missing program acronym" - raise CheckerException(message) - if self.getConfigFile() == "": - message = "ERROR: missing config file to access MySQL" - raise CheckerException(message) - if not os.path.exists( self.getConfigFile() ): - message = "ERROR: config file '%s' doesn't exist" % ( self.getConfigFile() ) - raise CheckerException(message) - if self.getTemporaryDirectory() == "": - self.setTemporaryDirectory(self._currentDir) - - def checkGenericAttributes( self ): - self.checkClusterLauncherAttributes() - - def checkProgramLauncherAttributes( self ): - self.getProgramLauncherInstance().checkSpecificAttributes() - - def checkSpecificAttributes( self ): - self.checkProgramLauncherAttributes() - - def start( self ): - - if self.lPrgLaunchers == []: - self.setSingleProgramLauncher() - for pL in self.lPrgLaunchers: - if pL.getWrapperCommandLine() == "": - string = "ERROR: wrapper command is empty !" - print string - sys.exit(1) - if pL.getProgramCommandLine() == "": - string = "ERROR: program command is empty !" - print string - sys.exit(1) - self.checkProgramAvailability() - - try: - self.checkProgramLauncherAttributes() - except CheckerException, msg: - print msg - print self.getHelpAsString() - sys.exit(1) - - if self.getVerbosityLevel() > 0: - string = "START %s" % ( type(self).__name__ ) - print string - self.job.tablename = self.getJobTableName() - self.job.groupid = self.getGroupIdentifier() - tokens = self.getQueueName().replace("'","").split(" ") - self.job.setQueue( tokens[0] ) - if len(tokens) > 1: - lResources = tokens[1:] - self.job.lResources = lResources - if self.getVerbosityLevel() > 0: - print "groupid: %s" % ( self.getGroupIdentifier() ) - self.jobdb = RepetJob( cfgFileName=self.getConfigFile() ) - if self.jobdb.hasUnfinishedJob( self.job.tablename, \ - self.job.groupid ): - self.jobdb.waitJobGroup( self.job.tablename, self.job.groupid ) - return - self.jobdb.cleanJobGroup( self.job.tablename, self.job.groupid ) - sys.stdout.flush() - - def end( self ): - if self.getClean(): - self.removeAllJobFiles() - self.removeAllJobStdouts() - self.removeAllJobStderrs() - - if self.getCatOutputFiles(): - self.catOutputFiles() - - self.jobdb.close() - - if self.getVerbosityLevel() > 0: - string = "END %s" % ( type(self).__name__ ) - print string - sys.stdout.flush() - - def run( self ): - try: - self.checkClusterLauncherAttributes() - except CheckerException, msg: - print msg - print self.getHelpAsString() - sys.exit(1) - - self.start() - - lInFiles = self.getInputFilesList() - self._nbJobs = len(lInFiles) - - if self._verbose > 0: - string = "submitting " + str(self._nbJobs) + " jobs... " + self.formatGroupidAndTime() - print string; sys.stdout.flush() - - self.submitJob(lInFiles) - - if self._verbose > 0: - string = "waiting for jobs... " + self.formatGroupidAndTime() - print string; sys.stdout.flush() - - self.jobdb.waitJobGroup( self.job.tablename, self.job.groupid ) - - if self._verbose > 0: - string = "all jobs completed ! " + self.formatGroupidAndTime() - print string; sys.stdout.flush() - statsExecutionTime = self.getStatsOfExecutionTime() - print "execution time of all jobs (seconds): %f" % statsExecutionTime.getSum() - print "execution time per job: %s" % statsExecutionTime.string() - sys.stdout.flush() - - self.jobdb.cleanJobGroup( self.job.tablename, self.job.groupid ) - - self.end() - - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/AbstractProgramLauncher.py --- a/commons/pyRepetUnit/components/AbstractProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -#!/usr/bin/env python -##@file -# Abstract class to launch a program. - -import getopt -import sys -import os -import pyRepet.launcher.AbstractProgramLauncher - -class AbstractProgramLauncher( pyRepet.launcher.AbstractProgramLauncher.AbstractProgramLauncher ): #( IProgramLauncher ) - - def getHelpAsString( self ): - """ - Return the generic help as a string. - """ - string = "" - string += "usage: %s.py [options]" % ( type(self).__name__ ) - string += "\ngeneric options:" - string += "\n -h: this help" - string += "\n -i: name of the input file (format='%s')" % ( self.getFormatInputFile() ) - string += "\n -c: clean" - string += "\n -v: verbosity level (default=0/1)" - return string - - def setAttributesFromCmdLine( self, o, a="" ): - """ - Set a generic attribute from the command-line arguments. - """ - if o == "-h": - print self.getHelpAsString() - sys.exit(0) - elif o == "-i": - self.setInputFile( a ) - elif o == "-c": - self.setClean() - elif o == "-v": - self.setVerbosityLevel( a ) - - def checkAttributesFromCmdLine( self ): - """ - Set the attributes from the command-line arguments. - """ - try: - opts, args = getopt.getopt( sys.argv[1:], "%s" % (self.getCmdLineOptions()) ) - except getopt.GetoptError, err: - print str(err); - print self.getHelpAsString() - sys.exit(1) - for o, a in opts: - self.setAttributesFromCmdLine( o, a ) - - def getCmdLineOptions(self): - return self._cmdLineGenericOptions - - def check( self ): - """ - Check the generic attributes before running the program. - """ - self._checkProgramName() - self.checkInput() - - def checkInput(self): - if self.getInputFile() == "": - string = "ERROR: missing input file" - print string - print self.getHelpAsString() - sys.exit(1) - - if not os.path.exists(self.getInputFile()): - string = "ERROR: input file '%s' doesn't exist" % (self.getInputFile()) - print string - print self.getHelpAsString() - sys.exit(1) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/IClusterLauncher.py --- a/commons/pyRepetUnit/components/IClusterLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,290 +0,0 @@ - -## Interface for AbstractClusterLauncher -# -class IClusterLauncher(object): - - ## Constructor. - # - def __init__( self ): - pass - - ## Useful commands before running the program (check, open database connector...). - # - def start(self): - pass - - ## Useful commands after the program was run (clean, close database connector...). - # - def end(self): - pass - - ## Launch jobs in parallel on each file in the query directory. - # - def run(self): - pass - - ## Initialize the job (jobname, command, launcher). - # - def initializeJob(self, fileName, count): - pass - - ## Return all the job commands as a string. - # - def getJobCommandsAsString(self, fileName, jobName, minFreeGigaInTmpDir=1): - pass - - ## Return the generic help as a string. - # - def getGenericHelpAsString(self): - pass - - ## Check the generic attributes before running the program. - # - def checkGenericAttributes(self): - pass - - ## Check the specific attributes of each program launcher. - # - def checkSpecificAttributes(self): - pass - - ## Check that all required programs are in the user's PATH. - # - def checkProgramAvailability(self): - pass - - ## Return the command-line to launch in each job. Specified in each wrapper. - # - def getProgramCommandLineAsString(self): - pass - - ## Return the list of files to keep at the end of each job. Specified in each wrapper. - # - def getListFilesToKeep(self): - pass - - ## Return the list of files to remove at the end of each job. Specified in each wrapper. - # - def getListFilesToRemove(self): - pass - - ## Return the name of the job file as a string. - # - def getJobFileNameAsString(self, count): - pass - - ## Return the command to update the job status in the table. - # - def getCmdUpdateJobStatusAsString(self, newStatus): - pass - - ## Return the launching command as a string. Launch the wrapper, retrieve its exit status, update status if error. - # - def getCmdToLaunchWrapper(self, fileName, genericCmd, exeWrapper): - pass - - ## Return the commands to keep the output files. - # - def getCmdToKeepFiles( self, fileName, lFilesToKeep ): - pass - - ## Return the commands to remove the temporary files. - # - def getCmdToRemoveFiles( self, fileName, lFilesToRemove ): - pass - - ## Remove all job files. - # - def removeAllJobFiles( self ): - pass - - ## Remove all job stdout. - # - def removeAllJobStdouts( self ): - pass - - ## Remove all job stderr. - # - def removeAllJobStderrs( self ): - pass - - ## Process the output file if necessary. - # - def processOutputFile( self, tmpFile, outFile ): - pass - - ## Concatenate output files from all jobs. - # - def catOutputFiles( self ): - pass - - ## Return the specific help as a string. - # - def getSpecificHelpAsString( self ): - pass - - ## Return the help as a string. - # - def getHelpAsString( self ): - pass - - ##Set a generic attribute from the command-line arguments. - # - def setAGenericAttributeFromCmdLine( self, o, a="" ): - pass - - ## Set the specific attributes from the command-line arguments. - # - def setASpecificAttributeFromCmdLine( self, o, a="" ): - pass - - ## Set the attributes from the command-line arguments. - # - def setAttributesFromCmdLine( self ): - pass - - ## - # - def setInputDirectory( self, arg ): - pass - - ## - # - def setQueueName( self, arg ): - pass - - ## - # - def setGroupIdentifier( self, arg ): - pass - - ## - # - def setInputFileSuffix( self, arg ): - pass - - ## - # - def setAcronym( self, arg ): - pass - - ## - # - def setConfigFile( self, arg ): - pass - - ## - # - def setCurrentDirectory( self ): - pass - - ## - # - def setTemporaryDirectory( self, arg ): - pass - - ## - # - def setJobTableName( self, arg ): - pass - - ## - # - def setCatOutputFiles( self ): - pass - - ## - # - def setClean( self ): - pass - - ## - # - def setVerbosityLevel( self, arg ): - pass - - ## - # - def setExecutableWrapper( self, arg ): - pass - - ## Set the wrapper and program command-lines of the program launcher. Append the program launcher to 'self.lPrgLaunchers'. - # - def setSingleProgramLauncher( self ): - pass - - ## - # - def getInputDirectory( self ): - pass - - ## - # - def getQueueName( self ): - pass - - ## - # - def getGroupIdentifier( self ): - pass - - ## - # - def getInputFileSuffix( self ): - pass - - ## - # - def getAcronym( self ): - pass - - ## - # - def getConfigFile( self ): - pass - - ## - # - def getCurrentDirectory( self ): - pass - - ## - # - def getTemporaryDirectory( self ): - pass - - ## - # - def getJobTableName( self ): - pass - - ## - # - def getCatOutputFiles( self ): - pass - - ## - # - def getClean( self ): - pass - - ## - # - def getVerbosityLevel( self ): - pass - - ## - # - def getWrapperName( self ): - pass - - ## - # - def getProgramName( self ): - pass - - ## - # - def getPatternToConcatenate( self ): - pass - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/blastx2GFFTestSuite.py --- a/commons/pyRepetUnit/components/blastx2GFF/tests/blastx2GFFTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -import unittest -import sys -import Test_BlasterClusterLauncher -import Test_BlasterProgramLauncher -import Test_F_BlasterClusterLauncher -import Test_F_BlasterComponent -import Test_F_BlasterMatcher2GFF3 -import Test_F_BlasterMatcherComponent -import Test_F_BlasterProgramLauncher - -def main(): - - commonsTestSuite = unittest.TestSuite() - commonsTestSuite.addTest( unittest.makeSuite( Test_BlasterClusterLauncher.Test_BlasterClusterLauncher, "test" ) ) - commonsTestSuite.addTest( unittest.makeSuite( Test_BlasterProgramLauncher.Test_BlasterProgramLauncher, "test" ) ) - commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterClusterLauncher.Test_F_BlasterClusterLauncher, "test" ) ) - commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterComponent.Test_F_BlasterComponent, "test" ) ) - commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterMatcher2GFF3.Test_F_BlasterMatcher2GFF3, "test" ) ) - commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterMatcherComponent.Test_F_BlasterMatcherComponent, "test" ) ) - commonsTestSuite.addTest( unittest.makeSuite( Test_F_BlasterProgramLauncher.Test_F_BlasterProgramLauncher, "test" ) ) - runner = unittest.TextTestRunner( sys.stderr, 2, 2 ) - runner.run( commonsTestSuite ) - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/dummy.align.match.path --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/dummy.align.match.path Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -1 lm_SuperContig_30_v2 35498 35914 mito_010 NADH dehydrogenase (ubiquinone) chain 5 307 445 1e-62 244 82.73 -1 lm_SuperContig_30_v2 37314 37823 mito_010 NADH dehydrogenase (ubiquinone) chain 5 494 663 8e-67 258 67.65 -161 lm_SuperContig_29_v2 193781 194212 1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 228 85 1e-40 84 30.56 -161 lm_SuperContig_29_v2 192832 193704 1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 522 229 1e-40 106 23.99 -174 lm_SuperContig_29_v2 78031 78588 xnc164_090 related to multidrug resistance protein 19 209 3e-21 101 30.89 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/dummy.align.match.tab --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/dummy.align.match.tab Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -lm_SuperContig_30_v2 35498 37823 927 0.00598594 1.29469 mito_010 307 663 309 0.431564 8e-67 424 74.4336 1 -lm_SuperContig_29_v2 192832 194212 1305 0.00649448 2.13934 1nc550_030 522 85 438 0.718033 1e-40 99 26.1649 161 -lm_SuperContig_29_v2 78031 78588 558 0.00277695 0.980668 xnc164_090 19 209 191 0.335677 3e-21 101 30.89 174 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/exp_dummy.gff --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/exp_dummy.gff Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -##gff-version 3 -lm_SuperContig_30_v2 blastx_ProtBank match 35498 37823 8e-67 + . ID=BlastBank_lm_SuperContig_30_v2_mito_010_m0001;Target=mito_010+307+663;Name=lm_SuperContig_30_v2_mito_010;target_pcover=43.15;target_pident=74.43;evalue=8e-67;target_description=NADH dehydrogenase (ubiquinone) chain 5;target_length=716;lib=BlastBank;program=blastx -lm_SuperContig_30_v2 blastx_ProtBank match_part 35498 35914 1e-62 + 0 ID=BlastBank_lm_SuperContig_30_v2_mito_010_m0001mp0001;Target=mito_010+307+445;Parent=BlastBank_lm_SuperContig_30_v2_mito_010_m0001 -lm_SuperContig_30_v2 blastx_ProtBank match_part 37314 37823 8e-67 + 2 ID=BlastBank_lm_SuperContig_30_v2_mito_010_m0001mp0002;Target=mito_010+494+663;Parent=BlastBank_lm_SuperContig_30_v2_mito_010_m0001 -lm_SuperContig_29_v2 blastx_ProtBank match 192832 194212 1e-40 - . ID=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002;Target=1nc550_030+85+522;Name=lm_SuperContig_30_v2_1nc550_030;target_pcover=71.80;target_pident=26.16;evalue=1e-40;target_description=related to putative multidrug transporter Mfs1.1 (major facilitator family protein);target_length=610;lib=BlastBank;program=blastx -lm_SuperContig_29_v2 blastx_ProtBank match_part 193781 194212 1e-40 - 0 ID=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002mp0002;Target=1nc550_030+85+228;Parent=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002 -lm_SuperContig_29_v2 blastx_ProtBank match_part 192832 193704 1e-40 - 2 ID=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002mp0001;Target=1nc550_030+229+522;Parent=BlastBank_lm_SuperContig_30_v2_1nc550_030_m0002 -lm_SuperContig_29_v2 blastx_ProtBank match 78031 78588 3e-21 + . ID=BlastBank_lm_SuperContig_30_v2_xnc164_090_m0003;Target=xnc164_090+19+209;Name=lm_SuperContig_30_v2_xnc164;target_pcover=33.56;target_pident=30.89;evalue=3e-21;target_description=related to multidrug resistance protein;target_length=569;lib=BlastBank;program=blastx -lm_SuperContig_29_v2 blastx_ProtBank match_part 78031 78588 3e-21 + 1 ID=BlastBank_lm_SuperContig_30_v2_xnc164_090_m0003mp0001;Target=xnc164_090+19+209;Parent=BlastBank_lm_SuperContig_30_v2_xnc164_090_m0003 \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,456 +0,0 @@ -lm_SuperContig_30_v2 23817 24089 mito_010 NADH dehydrogenase (ubiquinone) chain 5 1 91 7e-25 119 63.74 -lm_SuperContig_30_v2 27615 28001 mito_010 NADH dehydrogenase (ubiquinone) chain 5 109 237 1e-53 214 77.52 -lm_SuperContig_30_v2 29503 29673 mito_010 NADH dehydrogenase (ubiquinone) chain 5 254 310 3e-21 107 92.98 -lm_SuperContig_30_v2 35498 35914 mito_010 NADH dehydrogenase (ubiquinone) chain 5 307 445 1e-62 244 82.73 -lm_SuperContig_30_v2 37314 37823 mito_010 NADH dehydrogenase (ubiquinone) chain 5 494 663 8e-67 258 67.65 -lm_SuperContig_30_v2 23817 24089 mito_020 predicted ND5 intron 2 protein 1 91 7e-25 119 63.74 -lm_SuperContig_30_v2 27615 28001 mito_020 predicted ND5 intron 2 protein 109 237 1e-53 214 77.52 -lm_SuperContig_30_v2 28681 29418 mito_020 predicted ND5 intron 2 protein 303 540 4e-37 159 41.2 -lm_SuperContig_30_v2 94306 95085 mito_020 predicted ND5 intron 2 protein 544 279 2e-22 110 28.46 -lm_SuperContig_30_v2 18181 19317 mito_030 predicted ND5 intron 1 protein 167 528 3e-57 226 37.76 -lm_SuperContig_30_v2 22437 23375 mito_030 predicted ND5 intron 1 protein 219 528 1e-43 181 32.59 -lm_SuperContig_30_v2 23817 24089 mito_030 predicted ND5 intron 1 protein 1 91 7e-25 119 63.74 -lm_SuperContig_30_v2 26190 27509 mito_030 predicted ND5 intron 1 protein 84 525 0 666 76.52 -lm_SuperContig_30_v2 32527 33390 mito_030 predicted ND5 intron 1 protein 236 518 6e-40 169 36.15 -lm_SuperContig_30_v2 35963 37213 mito_030 predicted ND5 intron 1 protein 114 525 4e-62 242 38.08 -lm_SuperContig_30_v2 55780 56187 mito_030 predicted ND5 intron 1 protein 492 357 1e-34 96 36.96 -lm_SuperContig_30_v2 56292 56582 mito_030 predicted ND5 intron 1 protein 351 255 1e-34 74 38.78 -lm_SuperContig_30_v2 61805 62656 mito_030 predicted ND5 intron 1 protein 528 241 3e-55 219 38.89 -lm_SuperContig_30_v2 63837 64676 mito_030 predicted ND5 intron 1 protein 511 232 1e-35 155 35.21 -lm_SuperContig_30_v2 80861 81706 mito_030 predicted ND5 intron 1 protein 525 242 5e-44 182 35.66 -lm_SuperContig_30_v2 82749 83615 mito_030 predicted ND5 intron 1 protein 525 236 3e-47 193 35.27 -lm_SuperContig_30_v2 86928 87770 mito_030 predicted ND5 intron 1 protein 525 242 3e-47 193 36.14 -lm_SuperContig_30_v2 90399 91238 mito_030 predicted ND5 intron 1 protein 528 249 1e-37 161 32.52 -lm_SuperContig_30_v2 109092 109925 mito_030 predicted ND5 intron 1 protein 525 243 2e-49 200 38.16 -lm_SuperContig_30_v2 115228 116103 mito_030 predicted ND5 intron 1 protein 236 528 6e-48 195 35.93 -lm_SuperContig_30_v2 116645 117925 mito_030 predicted ND5 intron 1 protein 121 526 6e-60 235 37.12 -lm_SuperContig_30_v2 117965 119308 mito_030 predicted ND5 intron 1 protein 87 525 1e-63 248 35.79 -lm_SuperContig_30_v2 141039 141308 mito_030 predicted ND5 intron 1 protein 250 342 8e-47 58 34.41 -lm_SuperContig_30_v2 141292 141858 mito_030 predicted ND5 intron 1 protein 337 525 8e-47 155 42.11 -lm_SuperContig_30_v2 146223 147503 mito_030 predicted ND5 intron 1 protein 114 528 2e-64 250 37.61 -lm_SuperContig_30_v2 149559 149744 mito_030 predicted ND5 intron 1 protein 233 296 6e-40 41 35.94 -lm_SuperContig_30_v2 149749 150444 mito_030 predicted ND5 intron 1 protein 299 530 6e-40 149 37.02 -lm_SuperContig_30_v2 150994 152199 mito_030 predicted ND5 intron 1 protein 121 525 4e-58 229 36.3 -lm_SuperContig_30_v2 21984 22220 mito_040 NADH dehydrogenase (ubiquinone) chain 4L 1 79 3e-30 136 84.81 -lm_SuperContig_30_v2 18466 19329 mito_050 predicted ND4L intron protein 145 438 6e-54 215 40.53 -lm_SuperContig_30_v2 21984 22229 mito_050 predicted ND4L intron protein 1 82 8e-31 138 82.93 -lm_SuperContig_30_v2 22509 23387 mito_050 predicted ND4L intron protein 145 438 7e-81 305 49 -lm_SuperContig_30_v2 26661 27530 mito_050 predicted ND4L intron protein 145 438 1e-43 181 35.67 -lm_SuperContig_30_v2 32542 33390 mito_050 predicted ND4L intron protein 145 424 6e-43 179 38.91 -lm_SuperContig_30_v2 36323 37234 mito_050 predicted ND4L intron protein 145 438 4e-49 199 40.39 -lm_SuperContig_30_v2 61793 62650 mito_050 predicted ND4L intron protein 438 145 3e-49 200 40.33 -lm_SuperContig_30_v2 63768 64748 mito_050 predicted ND4L intron protein 438 111 4e-45 186 37.09 -lm_SuperContig_30_v2 80849 81703 mito_050 predicted ND4L intron protein 435 145 1e-45 188 39.6 -lm_SuperContig_30_v2 82737 83594 mito_050 predicted ND4L intron protein 435 145 1e-45 188 37.46 -lm_SuperContig_30_v2 86916 87767 mito_050 predicted ND4L intron protein 435 145 4e-45 186 36.49 -lm_SuperContig_30_v2 90387 91259 mito_050 predicted ND4L intron protein 438 144 2e-39 167 33.33 -lm_SuperContig_30_v2 109071 109925 mito_050 predicted ND4L intron protein 438 145 7e-42 175 35.67 -lm_SuperContig_30_v2 115249 116115 mito_050 predicted ND4L intron protein 145 438 1e-43 181 38.41 -lm_SuperContig_30_v2 117050 117943 mito_050 predicted ND4L intron protein 145 438 1e-42 178 37.62 -lm_SuperContig_30_v2 118442 119320 mito_050 predicted ND4L intron protein 145 435 3e-44 183 38.64 -lm_SuperContig_30_v2 141021 141260 mito_050 predicted ND4L intron protein 146 228 6e-38 52 40.96 -lm_SuperContig_30_v2 141295 141879 mito_050 predicted ND4L intron protein 241 438 6e-38 131 39.51 -lm_SuperContig_30_v2 146610 147515 mito_050 predicted ND4L intron protein 149 438 4e-37 159 34.18 -lm_SuperContig_30_v2 149583 149747 mito_050 predicted ND4L intron protein 145 199 3e-39 58 47.27 -lm_SuperContig_30_v2 149743 150450 mito_050 predicted ND4L intron protein 199 438 3e-39 130 35.34 -lm_SuperContig_30_v2 151234 152220 mito_050 predicted ND4L intron protein 118 438 2e-35 154 34.72 -lm_SuperContig_30_v2 53343 53696 mito_060 probable NADH dehydrogenase (ubiquinone) chain 3 117 1 2e-26 121 50 -lm_SuperContig_30_v2 5079 5582 mito_080 NADH dehydrogenase (ubiquinone) chain 2 403 582 7e-41 172 49.73 -lm_SuperContig_30_v2 53703 54143 mito_080 NADH dehydrogenase (ubiquinone) chain 2 582 425 3e-30 134 46.91 -lm_SuperContig_30_v2 55010 55561 mito_080 NADH dehydrogenase (ubiquinone) chain 2 423 242 1e-47 191 57.22 -lm_SuperContig_30_v2 59011 59799 mito_080 NADH dehydrogenase (ubiquinone) chain 2 271 1 1e-68 264 52.71 -lm_SuperContig_30_v2 64707 65165 mito_110 cytochrome-c oxidase chain III 227 74 2e-55 220 68.18 -lm_SuperContig_30_v2 103508 103711 mito_150 H+-transporting ATP synthase protein 6 261 194 7e-26 122 85.29 -lm_SuperContig_30_v2 108494 108691 mito_150 H+-transporting ATP synthase protein 6 179 114 3e-23 113 77.27 -lm_SuperContig_30_v2 110007 110387 mito_150 H+-transporting ATP synthase protein 6 134 6 2e-31 140 54.96 -lm_SuperContig_30_v2 17614 18054 mito_170 probable NADH dehydrogenase (ubiquinone) chain 4 83 229 3e-56 223 70.75 -lm_SuperContig_30_v2 19465 20481 mito_170 probable NADH dehydrogenase (ubiquinone) chain 4 195 536 3e-130 469 67.54 -lm_SuperContig_30_v2 17614 19341 mito_180 predicted ND4 intron protein 83 666 0 664 57.81 -lm_SuperContig_30_v2 22509 23405 mito_180 predicted ND4 intron protein 372 668 3e-57 226 39 -lm_SuperContig_30_v2 26640 27542 mito_180 predicted ND4 intron protein 365 666 9e-53 211 40.46 -lm_SuperContig_30_v2 32542 33390 mito_180 predicted ND4 intron protein 372 648 6e-64 248 44.14 -lm_SuperContig_30_v2 36329 37252 mito_180 predicted ND4 intron protein 374 668 2e-62 243 43.91 -lm_SuperContig_30_v2 42209 42388 mito_180 predicted ND4 intron protein 319 380 2e-21 26 30.16 -lm_SuperContig_30_v2 42457 42879 mito_180 predicted ND4 intron protein 384 528 2e-21 101 37.24 -lm_SuperContig_30_v2 55774 56199 mito_180 predicted ND4 intron protein 624 480 9e-27 79 32.41 -lm_SuperContig_30_v2 56307 56585 mito_180 predicted ND4 intron protein 473 383 9e-27 64 43.01 -lm_SuperContig_30_v2 61781 62653 mito_180 predicted ND4 intron protein 666 371 3e-63 246 42.62 -lm_SuperContig_30_v2 63756 64718 mito_180 predicted ND4 intron protein 666 347 2e-57 227 42.25 -lm_SuperContig_30_v2 80825 81706 mito_180 predicted ND4 intron protein 667 371 1e-57 228 41.28 -lm_SuperContig_30_v2 82716 83615 mito_180 predicted ND4 intron protein 666 365 1e-60 237 41.45 -lm_SuperContig_30_v2 86895 87770 mito_180 predicted ND4 intron protein 666 371 4e-57 226 41.47 -lm_SuperContig_30_v2 90384 91256 mito_180 predicted ND4 intron protein 663 372 4e-43 179 32.55 -lm_SuperContig_30_v2 109059 109979 mito_180 predicted ND4 intron protein 666 354 3e-58 229 37.7 -lm_SuperContig_30_v2 115189 116127 mito_180 predicted ND4 intron protein 352 666 8e-59 231 37.85 -lm_SuperContig_30_v2 117050 117955 mito_180 predicted ND4 intron protein 372 666 9e-54 215 41.5 -lm_SuperContig_30_v2 118439 119344 mito_180 predicted ND4 intron protein 371 667 3e-54 216 41.56 -lm_SuperContig_30_v2 125743 126138 mito_180 predicted ND4 intron protein 384 515 4e-23 113 41.67 -lm_SuperContig_30_v2 141030 141308 mito_180 predicted ND4 intron protein 376 469 3e-54 65 38.3 -lm_SuperContig_30_v2 141292 141897 mito_180 predicted ND4 intron protein 464 668 3e-54 173 43.9 -lm_SuperContig_30_v2 146610 147527 mito_180 predicted ND4 intron protein 376 666 6e-48 195 39.23 -lm_SuperContig_30_v2 149580 149747 mito_180 predicted ND4 intron protein 371 426 7e-54 59 44.64 -lm_SuperContig_30_v2 149743 150465 mito_180 predicted ND4 intron protein 425 667 7e-54 178 39.18 -lm_SuperContig_30_v2 151309 152232 mito_180 predicted ND4 intron protein 369 666 3e-50 203 40.76 -lm_SuperContig_30_v2 44197 44541 mito_190 NADH dehydrogenase (ubiquinone) chain 1 98 212 3e-43 180 76.52 -lm_SuperContig_30_v2 46832 47305 mito_190 NADH dehydrogenase (ubiquinone) chain 1 213 370 5e-44 182 59.01 -lm_SuperContig_30_v2 89139 89414 mito_210 cytochrome-c oxidase chain I 533 442 1e-22 111 58.7 -lm_SuperContig_30_v2 89713 89913 mito_210 cytochrome-c oxidase chain I 441 375 6e-24 116 79.1 -lm_SuperContig_30_v2 93858 94202 mito_210 cytochrome-c oxidase chain I 364 250 6e-51 205 87.83 -lm_SuperContig_30_v2 102101 102604 mito_210 cytochrome-c oxidase chain I 169 2 4e-74 282 80.36 -lm_SuperContig_30_v2 6405 6605 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 1 67 2e-23 114 76.12 -lm_SuperContig_30_v2 9733 9936 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 68 136 2e-27 127 89.86 -lm_SuperContig_30_v2 14626 15192 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 194 384 8e-78 295 73.82 -lm_SuperContig_30_v2 15860 16315 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 228 384 3e-37 160 56.25 -lm_SuperContig_30_v2 6405 6605 mito_230 related to cob intron2 maturase/endonuclease 1 67 2e-23 114 76.12 -lm_SuperContig_30_v2 9733 9936 mito_230 related to cob intron2 maturase/endonuclease 68 136 2e-27 127 89.86 -lm_SuperContig_30_v2 6405 6605 mito_240 related to cob intron1 maturase 1 67 2e-23 114 76.12 -lm_SuperContig_30_v2 9733 9927 mito_240 related to cob intron1 maturase 68 132 6e-27 126 90.77 -lm_SuperContig_30_v2 18442 19341 mito_155 predicted ATP6 intron maturase 56 357 3e-68 263 45.07 -lm_SuperContig_30_v2 22509 23387 mito_155 predicted ATP6 intron maturase 64 353 2e-37 161 31.19 -lm_SuperContig_30_v2 26607 27542 mito_155 predicted ATP6 intron maturase 46 357 7e-50 202 37.34 -lm_SuperContig_30_v2 32494 33504 mito_155 predicted ATP6 intron maturase 46 360 4e-52 209 37.64 -lm_SuperContig_30_v2 36323 37249 mito_155 predicted ATP6 intron maturase 64 358 2e-63 247 45.02 -lm_SuperContig_30_v2 61781 62650 mito_155 predicted ATP6 intron maturase 357 64 2e-58 230 41.75 -lm_SuperContig_30_v2 63756 64655 mito_155 predicted ATP6 intron maturase 357 60 1e-47 194 38.64 -lm_SuperContig_30_v2 80828 81703 mito_155 predicted ATP6 intron maturase 357 64 3e-51 206 39.6 -lm_SuperContig_30_v2 82716 83594 mito_155 predicted ATP6 intron maturase 357 64 1e-50 204 38.8 -lm_SuperContig_30_v2 86895 87767 mito_155 predicted ATP6 intron maturase 357 64 7e-50 202 37.92 -lm_SuperContig_30_v2 90381 91256 mito_155 predicted ATP6 intron maturase 355 64 8e-32 142 31 -lm_SuperContig_30_v2 109056 110081 mito_155 predicted ATP6 intron maturase 358 11 4e-91 338 51.85 -lm_SuperContig_30_v2 115198 116127 mito_155 predicted ATP6 intron maturase 47 357 1e-50 204 37.78 -lm_SuperContig_30_v2 116981 117955 mito_155 predicted ATP6 intron maturase 36 357 4e-53 213 37.01 -lm_SuperContig_30_v2 118442 119341 mito_155 predicted ATP6 intron maturase 64 357 7e-42 175 35.5 -lm_SuperContig_30_v2 125740 126240 mito_155 predicted ATP6 intron maturase 75 237 3e-30 136 46.11 -lm_SuperContig_30_v2 141021 141311 mito_155 predicted ATP6 intron maturase 65 161 2e-51 79 42.86 -lm_SuperContig_30_v2 141292 141891 mito_155 predicted ATP6 intron maturase 155 357 2e-51 150 40 -lm_SuperContig_30_v2 146610 147533 mito_155 predicted ATP6 intron maturase 68 359 2e-52 210 42.22 -lm_SuperContig_30_v2 149583 149747 mito_155 predicted ATP6 intron maturase 64 117 6e-49 55 45.45 -lm_SuperContig_30_v2 149746 150462 mito_155 predicted ATP6 intron maturase 117 357 6e-49 165 38.93 -lm_SuperContig_30_v2 151258 152232 mito_155 predicted ATP6 intron maturase 42 357 2e-52 210 39.34 -lm_SuperContig_30_v2 44996 45490 mito_195 predicted ND1 intron protein 39 206 3e-48 196 57.74 -lm_SuperContig_30_v2 45636 45911 mito_195 predicted ND1 intron protein 209 300 2e-21 107 58.7 -lm_SuperContig_30_v2 46058 46228 mito_195 predicted ND1 intron protein 44 100 1e-70 58 51.72 -lm_SuperContig_30_v2 46230 46769 mito_195 predicted ND1 intron protein 101 304 1e-70 235 58.54 -lm_SuperContig_30_v2 14662 15189 SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual 206 381 1e-42 178 48.86 -lm_SuperContig_30_v2 15941 16303 SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual 260 378 1e-22 111 48.76 -lm_SuperContig_30_v2 64752 65204 SPMIT.04 |cox3||cytochrome c oxidase 3|Schizosaccharomyces pombe|chr mitochondrial|||Manual 215 65 2e-34 150 50.98 -lm_SuperContig_30_v2 94345 95262 SPMIT.03 |||hypothetical protein|Schizosaccharomyces pombe|chr mitochondrial||Partial|Manual 312 3 1e-94 350 57.68 -lm_SuperContig_30_v2 93876 94202 SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual 360 251 3e-30 136 58.56 -lm_SuperContig_30_v2 102098 102580 SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual 171 10 3e-48 196 54.94 -lm_SuperContig_29_v2 77989 78369 Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 3 126 2e-22 105 40.94 -lm_SuperContig_29_v2 193985 194365 Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 126 3 1e-21 105 40.94 -lm_SuperContig_29_v2 78109 78582 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 20 177 7e-59 207 58.86 -lm_SuperContig_29_v2 78662 78817 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 180 231 7e-59 42 30.77 -lm_SuperContig_29_v2 192760 193692 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 485 180 2e-128 275 41.8 -lm_SuperContig_29_v2 193772 194245 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 177 20 2e-128 207 58.86 -lm_SuperContig_29_v2 78010 78567 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 21 208 5e-23 100 29.79 -lm_SuperContig_29_v2 78662 78808 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 216 261 5e-23 28 26.53 -lm_SuperContig_29_v2 192766 193692 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 535 216 3e-40 88 22.53 -lm_SuperContig_29_v2 193787 194344 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 208 21 3e-40 100 29.79 -lm_SuperContig_29_v2 78109 78588 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 45 204 1e-39 144 43.75 -lm_SuperContig_29_v2 78662 78817 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 205 258 1e-39 40 45.61 -lm_SuperContig_29_v2 192754 193692 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 521 205 2e-83 188 33.33 -lm_SuperContig_29_v2 193766 194245 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 204 45 2e-83 144 43.75 -lm_SuperContig_29_v2 78061 78573 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 15 189 3e-22 87 29.71 -lm_SuperContig_29_v2 78662 78814 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 195 242 3e-22 39 39.22 -lm_SuperContig_29_v2 192760 193692 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 506 195 1e-49 133 27.85 -lm_SuperContig_29_v2 193781 194293 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 189 15 1e-49 87 29.71 -lm_SuperContig_29_v2 78007 78576 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 48 237 2e-59 198 47.37 -lm_SuperContig_29_v2 78662 78817 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 242 293 2e-59 52 46.15 -lm_SuperContig_29_v2 193288 193692 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 375 242 1e-79 122 43.7 -lm_SuperContig_29_v2 193778 194347 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 237 48 1e-79 198 47.37 -lm_SuperContig_29_v2 78133 78576 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 77 224 2e-44 159 51.35 -lm_SuperContig_29_v2 78662 78817 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 229 282 2e-44 41 41.07 -lm_SuperContig_29_v2 192760 193692 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 541 229 3e-91 200 35.65 -lm_SuperContig_29_v2 193778 194221 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 224 77 3e-91 159 51.35 -lm_SuperContig_29_v2 10942 11625 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 1 2e-29 132 35.06 -lm_SuperContig_29_v2 16462 17082 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 208 2 4e-30 135 37.2 -lm_SuperContig_29_v2 31597 31836 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 147 6e-25 46 33.73 -lm_SuperContig_29_v2 31868 32272 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 136 4 6e-25 95 38.52 -lm_SuperContig_29_v2 41484 42080 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 200 2 8e-32 142 38.69 -lm_SuperContig_29_v2 91888 92562 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 4 3e-27 126 35.53 -lm_SuperContig_29_v2 101404 102000 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 200 2 3e-31 140 38.69 -lm_SuperContig_29_v2 133669 134343 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 226 2 3e-37 159 37.78 -lm_SuperContig_29_v2 167776 168372 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 200 2 9e-34 145 38.69 -lm_SuperContig_29_v2 178590 179264 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 4 1e-29 133 35.96 -lm_SuperContig_29_v2 78184 78585 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 53 186 2e-25 96 35.07 -lm_SuperContig_29_v2 78644 78814 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 186 239 2e-25 41 40.35 -lm_SuperContig_29_v2 192964 193710 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 430 186 3e-59 156 35.74 -lm_SuperContig_29_v2 193769 194170 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 186 53 3e-59 96 35.07 -lm_SuperContig_29_v2 78049 78567 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 19 191 3e-23 101 27.75 -lm_SuperContig_29_v2 78659 78775 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 198 236 3e-23 28 28.21 -lm_SuperContig_29_v2 192904 193695 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 459 198 9e-43 96 26.12 -lm_SuperContig_29_v2 193787 194305 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 191 19 9e-43 101 27.75 -lm_SuperContig_29_v2 78151 78576 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 93 235 3e-31 124 41.96 -lm_SuperContig_29_v2 78662 78814 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 242 293 3e-31 32 30.77 -lm_SuperContig_29_v2 192760 193692 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 552 242 6e-83 207 32.69 -lm_SuperContig_29_v2 193778 194203 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 235 93 6e-83 124 41.96 -lm_SuperContig_29_v2 78109 78576 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 34 189 3e-49 169 50 -lm_SuperContig_29_v2 78650 78814 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 190 245 3e-49 48 35.71 -lm_SuperContig_29_v2 192772 193704 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 501 190 2e-97 210 32.27 -lm_SuperContig_29_v2 193778 194245 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 189 34 2e-97 169 50 -lm_SuperContig_29_v2 78115 78576 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 51 204 6e-62 204 58.44 -lm_SuperContig_29_v2 78662 78817 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 209 260 6e-62 55 40.38 -lm_SuperContig_29_v2 192754 193692 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 520 209 1e-132 293 43.77 -lm_SuperContig_29_v2 193778 194239 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 204 51 1e-132 204 58.44 -lm_SuperContig_29_v2 192868 193695 Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92 482 201 1e-31 70 21.48 -lm_SuperContig_29_v2 193784 194323 Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92 195 16 1e-31 89 25 -lm_SuperContig_29_v2 193303 193707 fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5 308 174 6e-29 54 28.06 -lm_SuperContig_29_v2 193793 194221 fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5 169 27 6e-29 97 32.87 -lm_SuperContig_29_v2 192877 193695 fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168 483 215 7e-40 109 24.18 -lm_SuperContig_29_v2 193784 194221 fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168 205 60 7e-40 78 27.4 -lm_SuperContig_29_v2 77956 78576 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 2 220 7e-35 126 34.25 -lm_SuperContig_29_v2 78650 78814 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 221 272 7e-35 42 34.55 -lm_SuperContig_29_v2 192883 193704 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 490 221 7e-62 135 29.2 -lm_SuperContig_29_v2 193778 194398 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 220 2 7e-62 126 34.25 -lm_SuperContig_29_v2 78124 78576 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 62 212 4e-45 166 52.32 -lm_SuperContig_29_v2 78662 78718 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 217 236 4e-45 36 65 -lm_SuperContig_29_v2 192769 193692 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 537 217 1e-92 197 32.61 -lm_SuperContig_29_v2 193778 194230 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 212 62 1e-92 166 52.32 -lm_SuperContig_29_v2 193222 193707 fg12717 related to putative multidrug transporter, Contig fg_contig_1.37 402 218 2e-26 66 25 -lm_SuperContig_29_v2 193778 194383 fg12717 related to putative multidrug transporter, Contig fg_contig_1.37 219 15 2e-26 76 25.85 -lm_SuperContig_29_v2 193036 193695 b13o8_150 conserved hypothetical protein 460 238 3e-31 73 23.35 -lm_SuperContig_29_v2 193784 194248 b13o8_150 conserved hypothetical protein 232 73 3e-31 85 28.12 -lm_SuperContig_29_v2 78010 78585 b18d24_100 related to tetracycline efflux protein (otrb) 9 199 2e-27 99 28.12 -lm_SuperContig_29_v2 78644 78814 b18d24_100 related to tetracycline efflux protein (otrb) 197 250 2e-27 43 42.11 -lm_SuperContig_29_v2 192916 193710 b18d24_100 related to tetracycline efflux protein (otrb) 457 197 4e-60 155 33.96 -lm_SuperContig_29_v2 193769 194344 b18d24_100 related to tetracycline efflux protein (otrb) 199 9 4e-60 99 28.12 -lm_SuperContig_29_v2 78184 78576 b5k2_230 related to major facilitator (MFS1) transporter 211 341 4e-42 141 50.38 -lm_SuperContig_29_v2 78662 78814 b5k2_230 related to major facilitator (MFS1) transporter 346 396 4e-42 51 49.06 -lm_SuperContig_29_v2 192760 193692 b5k2_230 related to major facilitator (MFS1) transporter 657 346 7e-99 243 38.1 -lm_SuperContig_29_v2 193778 194170 b5k2_230 related to major facilitator (MFS1) transporter 341 211 7e-99 141 50.38 -lm_SuperContig_29_v2 192832 193704 1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 522 229 1e-40 106 23.99 -lm_SuperContig_29_v2 193781 194212 1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 228 85 1e-40 84 30.56 -lm_SuperContig_29_v2 77941 78576 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 28 241 1e-30 111 28.97 -lm_SuperContig_29_v2 78662 78736 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 246 270 1e-30 42 56 -lm_SuperContig_29_v2 192760 193692 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 559 246 5e-62 149 28.3 -lm_SuperContig_29_v2 193778 194413 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 241 28 5e-62 111 28.97 -lm_SuperContig_29_v2 192817 193695 6nc360_090 related to DHA14-like major facilitator 491 194 8e-44 132 28.9 -lm_SuperContig_29_v2 193778 194086 6nc360_090 related to DHA14-like major facilitator 188 86 8e-44 69 38.83 -lm_SuperContig_29_v2 78112 78576 29e8_240 probable aflatoxin efflux pump AFLT 62 216 1e-56 190 55.48 -lm_SuperContig_29_v2 78662 78817 29e8_240 probable aflatoxin efflux pump AFLT 221 272 1e-56 50 40.38 -lm_SuperContig_29_v2 192769 193692 29e8_240 probable aflatoxin efflux pump AFLT 535 221 2e-117 256 41.14 -lm_SuperContig_29_v2 193778 194242 29e8_240 probable aflatoxin efflux pump AFLT 216 62 2e-117 190 55.48 -lm_SuperContig_29_v2 192940 193695 7nc450_010 related to multidrug resistance protein 484 228 3e-24 79 25 -lm_SuperContig_29_v2 193787 194218 7nc450_010 related to multidrug resistance protein 221 78 3e-24 57 20.83 -lm_SuperContig_29_v2 192865 193692 4nc446_010 related to putative multidrug transporter 530 259 3e-48 134 28.26 -lm_SuperContig_29_v2 193781 194218 4nc446_010 related to putative multidrug transporter 253 106 3e-48 82 29.73 -lm_SuperContig_29_v2 192904 193704 b11e5_230 related to multidrug resistance protein fnx1 518 253 1e-40 93 25.27 -lm_SuperContig_29_v2 193766 194239 b11e5_230 related to multidrug resistance protein fnx1 254 97 1e-40 97 29.75 -lm_SuperContig_29_v2 77935 78576 xnc126_050 probable DHA14-like major facilitator; ABC transporter 38 241 7e-60 190 46.26 -lm_SuperContig_29_v2 78662 78817 xnc126_050 probable DHA14-like major facilitator; ABC transporter 246 298 7e-60 62 43.4 -lm_SuperContig_29_v2 192757 193692 xnc126_050 probable DHA14-like major facilitator; ABC transporter 559 246 2e-130 299 45.08 -lm_SuperContig_29_v2 193778 194419 xnc126_050 probable DHA14-like major facilitator; ABC transporter 241 38 2e-130 190 46.26 -lm_SuperContig_29_v2 78109 78576 4nc135_070 related to aflatoxin efflux pump AFLT 17 172 2e-53 184 53.85 -lm_SuperContig_29_v2 78662 78817 4nc135_070 related to aflatoxin efflux pump AFLT 177 238 2e-53 46 38.71 -lm_SuperContig_29_v2 192751 193692 4nc135_070 related to aflatoxin efflux pump AFLT 494 177 4e-99 201 34.46 -lm_SuperContig_29_v2 193778 194245 4nc135_070 related to aflatoxin efflux pump AFLT 172 17 4e-99 184 53.85 -lm_SuperContig_29_v2 78031 78588 xnc164_090 related to multidrug resistance protein 19 209 3e-21 101 30.89 -lm_SuperContig_29_v2 192802 193692 xnc164_090 related to multidrug resistance protein 509 210 1e-42 95 26.77 -lm_SuperContig_29_v2 193766 194323 xnc164_090 related to multidrug resistance protein 209 19 1e-42 101 30.89 -lm_SuperContig_29_v2 192916 193704 YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane 384 116 3e-23 74 23.53 -lm_SuperContig_29_v2 193766 194107 YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane 117 6 3e-23 57 27.19 -lm_SuperContig_29_v2 192985 193692 YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane 335 66 7e-28 95 28.04 -lm_SuperContig_29_v2 193778 193954 YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane 61 3 7e-28 52 38.98 -lm_SuperContig_29_v2 197021 197416 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 282 151 3e-22 107 39.39 -lm_SuperContig_29_v2 197024 197422 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 298 166 5e-24 113 45.52 -lm_SuperContig_29_v2 197027 197413 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 292 164 2e-23 111 46.56 -lm_SuperContig_29_v2 197039 197437 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 310 170 2e-22 108 46.1 -lm_SuperContig_29_v2 16081 17274 YGR109w-b TY3B TY3B protein 1008 616 4e-35 152 30.33 -lm_SuperContig_29_v2 40143 42272 YGR109w-b TY3B TY3B protein 1301 616 6e-39 165 26.47 -lm_SuperContig_29_v2 91762 92754 YGR109w-b TY3B TY3B protein 944 618 4e-23 113 30.24 -lm_SuperContig_29_v2 100993 102192 YGR109w-b TY3B TY3B protein 1008 616 8e-35 151 30.92 -lm_SuperContig_29_v2 133543 134535 YGR109w-b TY3B TY3B protein 943 616 4e-34 149 32.23 -lm_SuperContig_29_v2 167371 168564 YGR109w-b TY3B TY3B protein 1008 616 2e-35 151 30.83 -lm_SuperContig_29_v2 178464 179477 YGR109w-b TY3B TY3B protein 944 611 1e-21 107 29.03 -lm_SuperContig_29_v2 78139 78582 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 70 217 1e-27 105 39.19 -lm_SuperContig_29_v2 78662 78724 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 220 240 1e-27 39 57.14 -lm_SuperContig_29_v2 193630 193692 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 240 220 6e-27 39 57.14 -lm_SuperContig_29_v2 193772 194215 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 217 70 6e-27 105 39.19 -lm_SuperContig_29_v2 197024 197410 YHL028w WSC4 Cell wall integrity and stress response component 4 314 179 6e-22 106 47.79 -lm_SuperContig_29_v2 197024 197413 YHL028w WSC4 Cell wall integrity and stress response component 4 323 190 3e-23 111 47.01 -lm_SuperContig_29_v2 197024 197425 YHL028w WSC4 Cell wall integrity and stress response component 4 290 148 2e-23 111 49.65 -lm_SuperContig_29_v2 197024 197434 YHL028w WSC4 Cell wall integrity and stress response component 4 257 117 8e-21 103 42.55 -lm_SuperContig_29_v2 197024 197434 YHL028w WSC4 Cell wall integrity and stress response component 4 332 197 2e-22 108 42.03 -lm_SuperContig_29_v2 197024 197437 YHL028w WSC4 Cell wall integrity and stress response component 4 276 136 3e-25 117 47.52 -lm_SuperContig_29_v2 197024 197482 YHL028w WSC4 Cell wall integrity and stress response component 4 300 147 5e-22 107 41.29 -lm_SuperContig_29_v2 197027 197482 YHL028w WSC4 Cell wall integrity and stress response component 4 336 184 5e-22 107 39.22 -lm_SuperContig_29_v2 16081 17274 YIL082w-a TY3B TY3B protein 1034 642 1e-34 150 30.33 -lm_SuperContig_29_v2 40143 42272 YIL082w-a TY3B TY3B protein 1327 642 8e-39 165 26.47 -lm_SuperContig_29_v2 91762 92754 YIL082w-a TY3B TY3B protein 970 644 5e-23 112 30.24 -lm_SuperContig_29_v2 100993 102192 YIL082w-a TY3B TY3B protein 1034 642 3e-34 150 30.92 -lm_SuperContig_29_v2 133543 134535 YIL082w-a TY3B TY3B protein 969 642 1e-33 147 32.23 -lm_SuperContig_29_v2 167371 168564 YIL082w-a TY3B TY3B protein 1034 642 6e-35 149 30.83 -lm_SuperContig_29_v2 178464 179477 YIL082w-a TY3B TY3B protein 970 637 1e-21 106 29.03 -lm_SuperContig_29_v2 197021 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 300 165 6e-33 143 57.35 -lm_SuperContig_29_v2 197021 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 360 219 3e-25 118 52.08 -lm_SuperContig_29_v2 197024 197392 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 222 102 1e-26 122 56.91 -lm_SuperContig_29_v2 197024 197395 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 240 118 1e-31 139 59.68 -lm_SuperContig_29_v2 197024 197398 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 246 123 1e-31 139 60 -lm_SuperContig_29_v2 197024 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 267 132 1e-33 145 58.09 -lm_SuperContig_29_v2 197024 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 290 156 2e-33 144 57.78 -lm_SuperContig_29_v2 197024 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 303 174 3e-32 140 57.46 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 261 126 3e-33 144 58.39 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 276 141 6e-33 143 57.66 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 281 144 1e-32 142 55.8 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 285 147 6e-33 143 57.55 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 314 174 3e-31 137 55.32 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 350 201 1e-28 128 52 -lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 372 228 2e-24 115 48.28 -lm_SuperContig_29_v2 197027 197437 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 244 108 2e-31 138 57.97 -lm_SuperContig_29_v2 197030 197404 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 248 124 3e-32 140 59.2 -lm_SuperContig_29_v2 197036 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 378 246 7e-23 109 42.86 -lm_SuperContig_29_v2 197039 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 318 183 1e-31 139 57.35 -lm_SuperContig_29_v2 78112 78576 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 31 185 7e-29 105 33.55 -lm_SuperContig_29_v2 78662 78778 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 190 227 7e-29 43 48.72 -lm_SuperContig_29_v2 192985 193692 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 459 190 4e-43 94 27.68 -lm_SuperContig_29_v2 193778 194242 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 185 31 4e-43 105 33.55 -lm_SuperContig_29_v2 197024 197434 YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3 272 139 4e-22 107 45.65 -lm_SuperContig_29_v2 197042 197422 YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3 275 147 8e-21 103 45.8 -lm_SuperContig_29_v2 10747 11856 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 192757 193695 SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual 499 183 1e-35 89 22.84 -lm_SuperContig_29_v2 193787 194218 SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual 176 33 1e-35 85 31.25 -lm_SuperContig_29_v2 10747 11856 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 10747 11856 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 1e-36 157 31.18 -lm_SuperContig_29_v2 16081 17289 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 2e-39 166 28.15 -lm_SuperContig_29_v2 41079 42287 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 3e-42 176 28.89 -lm_SuperContig_29_v2 91693 92700 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 452 1e-37 161 32.94 -lm_SuperContig_29_v2 100993 102531 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 312 3e-44 183 27.86 -lm_SuperContig_29_v2 133341 133436 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 800 2e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 358 2e-46 184 28.54 -lm_SuperContig_29_v2 167371 168579 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 8e-43 175 29.38 -lm_SuperContig_29_v2 178395 179504 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 1e-37 160 30.91 -lm_SuperContig_29_v2 77950 78588 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 34 242 5e-29 109 30.99 -lm_SuperContig_29_v2 78662 78799 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 243 286 5e-29 39 41.3 -lm_SuperContig_29_v2 192844 193692 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 525 243 2e-50 113 28.03 -lm_SuperContig_29_v2 193766 194404 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 242 34 2e-50 109 30.99 -lm_SuperContig_29_v2 10747 11856 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 192760 193692 SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 551 242 7e-34 72 21.77 -lm_SuperContig_29_v2 193781 194482 SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 236 4 7e-34 95 23.93 -lm_SuperContig_29_v2 10747 11856 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 78133 78570 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 97 242 3e-30 115 39.04 -lm_SuperContig_29_v2 78662 78799 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 249 292 3e-30 37 42.55 -lm_SuperContig_29_v2 192874 193692 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 518 249 2e-55 124 27.37 -lm_SuperContig_29_v2 193784 194221 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 242 97 2e-55 115 39.04 -lm_SuperContig_29_v2 77950 78588 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 34 242 8e-30 114 30.99 -lm_SuperContig_29_v2 78662 78736 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 243 267 8e-30 37 52 -lm_SuperContig_29_v2 192844 193692 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 525 243 3e-53 118 30.8 -lm_SuperContig_29_v2 193766 194404 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 242 34 3e-53 114 30.99 -lm_SuperContig_29_v2 10747 11856 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 10747 11856 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-36 157 31.18 -lm_SuperContig_29_v2 16081 17289 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-39 166 28.15 -lm_SuperContig_29_v2 41079 42287 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 3e-42 176 28.89 -lm_SuperContig_29_v2 91693 92700 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 1e-37 161 32.94 -lm_SuperContig_29_v2 100993 102531 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 3e-44 183 27.86 -lm_SuperContig_29_v2 133341 133436 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 2e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 2e-46 184 28.54 -lm_SuperContig_29_v2 167371 168579 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 8e-43 175 29.38 -lm_SuperContig_29_v2 178395 179504 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-37 160 30.91 -lm_SuperContig_29_v2 10747 11856 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 10747 11856 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-36 157 31.18 -lm_SuperContig_29_v2 16081 17289 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-39 166 28.15 -lm_SuperContig_29_v2 41079 42287 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 3e-42 176 28.89 -lm_SuperContig_29_v2 91693 92700 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 1e-37 161 32.94 -lm_SuperContig_29_v2 100993 102531 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 3e-44 183 27.86 -lm_SuperContig_29_v2 133341 133436 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 2e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 2e-46 184 28.54 -lm_SuperContig_29_v2 167371 168579 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 8e-43 175 29.38 -lm_SuperContig_29_v2 178395 179504 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-37 160 30.91 -lm_SuperContig_29_v2 10747 11856 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 10747 11856 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -lm_SuperContig_29_v2 16081 17289 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -lm_SuperContig_29_v2 41079 42287 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -lm_SuperContig_29_v2 91693 92700 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -lm_SuperContig_29_v2 100993 102531 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -lm_SuperContig_29_v2 133341 133436 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -lm_SuperContig_29_v2 133471 134754 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -lm_SuperContig_29_v2 167371 168579 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -lm_SuperContig_29_v2 178395 179504 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -lm_SuperContig_29_v2 77980 78567 um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17 18 211 5e-25 114 31 -lm_SuperContig_29_v2 192772 193695 um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17 529 218 2e-42 82 20.7 -lm_SuperContig_29_v2 193787 194374 um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17 211 18 2e-42 114 31 -lm_SuperContig_29_v2 78115 78588 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 53 210 2e-53 183 55.06 -lm_SuperContig_29_v2 78662 78814 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 211 264 2e-53 47 44.44 -lm_SuperContig_29_v2 192760 193692 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 534 211 2e-104 220 36.92 -lm_SuperContig_29_v2 193766 194239 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 210 53 2e-104 183 55.06 -lm_SuperContig_29_v2 78112 78570 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 94 246 7e-23 104 35.95 -lm_SuperContig_29_v2 78659 78802 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 253 297 7e-23 24 25 -lm_SuperContig_29_v2 192760 193695 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 560 253 5e-40 84 19.43 -lm_SuperContig_29_v2 193784 194242 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 246 94 5e-40 104 35.95 -lm_SuperContig_29_v2 78019 78567 um01964 related to multidrug resistance protein, Contig um_contig_1.72 40 220 1e-24 113 33.7 -lm_SuperContig_29_v2 192901 193695 um01964 related to multidrug resistance protein, Contig um_contig_1.72 490 227 7e-43 85 24.16 -lm_SuperContig_29_v2 193787 194335 um01964 related to multidrug resistance protein, Contig um_contig_1.72 220 40 7e-43 113 33.7 -lm_SuperContig_29_v2 77890 78591 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 38 263 1e-32 115 32.07 -lm_SuperContig_29_v2 78659 78814 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 264 313 1e-32 46 36.54 -lm_SuperContig_29_v2 192760 193695 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 575 264 1e-65 158 30.6 -lm_SuperContig_29_v2 193763 194464 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 263 38 1e-65 115 32.07 -lm_SuperContig_29_v2 78136 78576 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 133 280 1e-21 91 30.41 -lm_SuperContig_29_v2 78650 78814 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 280 331 1e-21 33 29.09 -lm_SuperContig_29_v2 192754 193704 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 598 280 3e-45 114 25.93 -lm_SuperContig_29_v2 193778 194218 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 280 133 3e-45 91 30.41 -lm_SuperContig_29_v2 77938 78585 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 27 239 2e-24 93 30.73 -lm_SuperContig_29_v2 78650 78808 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 236 285 2e-24 40 33.96 -lm_SuperContig_29_v2 192757 193704 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 554 236 1e-48 124 25.7 -lm_SuperContig_29_v2 193769 194416 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 239 27 1e-48 93 30.73 -lm_SuperContig_29_v2 77938 78576 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 13 215 4e-45 167 39.91 -lm_SuperContig_29_v2 78650 78736 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 216 244 4e-45 36 55.17 -lm_SuperContig_29_v2 192826 193704 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 511 216 2e-98 216 37.04 -lm_SuperContig_29_v2 193778 194416 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 215 13 2e-98 167 39.91 -lm_SuperContig_29_v2 193006 193692 um05421 related to Multidrug resistance protein , Contig um_contig_1.192 496 272 6e-41 107 27.07 -lm_SuperContig_29_v2 193778 194107 um05421 related to Multidrug resistance protein , Contig um_contig_1.192 267 158 6e-41 83 35.45 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.map --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.map Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,341 +0,0 @@ -Afu3g02110.115 lm_SuperContig_29_v2 77989 78369 -Afu3g02110.116 lm_SuperContig_29_v2 194365 193985 -Afu3g01520.117 lm_SuperContig_29_v2 78109 78817 -Afu3g01520.118 lm_SuperContig_29_v2 194245 192760 -Afu3g02520.119 lm_SuperContig_29_v2 78010 78808 -Afu3g02520.120 lm_SuperContig_29_v2 194344 192766 -Afu3g02720.121 lm_SuperContig_29_v2 78109 78817 -Afu3g02720.122 lm_SuperContig_29_v2 194245 192754 -Afu6g03320.123 lm_SuperContig_29_v2 78061 78814 -Afu6g03320.124 lm_SuperContig_29_v2 194293 192760 -Afu6g02220.125 lm_SuperContig_29_v2 78007 78817 -Afu6g02220.126 lm_SuperContig_29_v2 194347 193288 -Afu8g00940.127 lm_SuperContig_29_v2 78133 78817 -Afu8g00940.128 lm_SuperContig_29_v2 194221 192760 -Afu4g02630.129 lm_SuperContig_29_v2 134343 133669 -Afu4g02630.130 lm_SuperContig_29_v2 168372 167776 -Afu4g02630.131 lm_SuperContig_29_v2 42080 41484 -Afu4g02630.132 lm_SuperContig_29_v2 102000 101404 -Afu4g02630.133 lm_SuperContig_29_v2 32272 31597 -Afu4g02630.134 lm_SuperContig_29_v2 17082 16462 -Afu4g02630.135 lm_SuperContig_29_v2 179264 178590 -Afu4g02630.136 lm_SuperContig_29_v2 11625 10942 -Afu4g02630.137 lm_SuperContig_29_v2 92562 91888 -Afu4g03920.138 lm_SuperContig_29_v2 78184 78814 -Afu4g03920.139 lm_SuperContig_29_v2 194170 192964 -Afu6g09110.140 lm_SuperContig_29_v2 78049 78775 -Afu6g09110.141 lm_SuperContig_29_v2 194305 192904 -Afu6g14640.142 lm_SuperContig_29_v2 78151 78814 -Afu6g14640.143 lm_SuperContig_29_v2 194203 192760 -Afu6g09710.144 lm_SuperContig_29_v2 78109 78814 -Afu6g09710.145 lm_SuperContig_29_v2 194245 192772 -Afu5g01540.146 lm_SuperContig_29_v2 78115 78817 -Afu5g01540.147 lm_SuperContig_29_v2 194239 192754 -Afu2g15140.148 lm_SuperContig_29_v2 194323 192868 -fg00095.149 lm_SuperContig_29_v2 194221 193303 -fg12051.150 lm_SuperContig_29_v2 194221 192877 -fg12074.151 lm_SuperContig_29_v2 77956 78814 -fg12074.152 lm_SuperContig_29_v2 194398 192883 -fg12335.153 lm_SuperContig_29_v2 78124 78718 -fg12335.154 lm_SuperContig_29_v2 194230 192769 -fg12717.155 lm_SuperContig_29_v2 194383 193222 -b13o8_150.156 lm_SuperContig_29_v2 194248 193036 -b18d24_100.157 lm_SuperContig_29_v2 78010 78814 -b18d24_100.158 lm_SuperContig_29_v2 194344 192916 -b5k2_230.159 lm_SuperContig_29_v2 78184 78814 -b5k2_230.160 lm_SuperContig_29_v2 194170 192760 -1nc550_030.161 lm_SuperContig_29_v2 194212 192832 -1nc570_120.162 lm_SuperContig_29_v2 77941 78736 -1nc570_120.163 lm_SuperContig_29_v2 194413 192760 -6nc360_090.164 lm_SuperContig_29_v2 194086 192817 -29e8_240.165 lm_SuperContig_29_v2 78112 78817 -29e8_240.166 lm_SuperContig_29_v2 194242 192769 -7nc450_010.167 lm_SuperContig_29_v2 194218 192940 -4nc446_010.168 lm_SuperContig_29_v2 194218 192865 -b11e5_230.169 lm_SuperContig_29_v2 194239 192904 -xnc126_050.170 lm_SuperContig_29_v2 77935 78817 -xnc126_050.171 lm_SuperContig_29_v2 194419 192757 -4nc135_070.172 lm_SuperContig_29_v2 78109 78817 -4nc135_070.173 lm_SuperContig_29_v2 194245 192751 -xnc164_090.174 lm_SuperContig_29_v2 78031 78588 -xnc164_090.175 lm_SuperContig_29_v2 194323 192802 -YBR293w.176 lm_SuperContig_29_v2 194107 192916 -YCL069w.177 lm_SuperContig_29_v2 193954 192985 -YDL037c.178 lm_SuperContig_29_v2 197422 197024 -YDL037c.179 lm_SuperContig_29_v2 197413 197027 -YDL037c.180 lm_SuperContig_29_v2 197437 197039 -YDL037c.181 lm_SuperContig_29_v2 197416 197021 -YGR109w-b.182 lm_SuperContig_29_v2 42272 40143 -YGR109w-b.183 lm_SuperContig_29_v2 17274 16081 -YGR109w-b.184 lm_SuperContig_29_v2 102192 100993 -YGR109w-b.185 lm_SuperContig_29_v2 168564 167371 -YGR109w-b.186 lm_SuperContig_29_v2 134535 133543 -YGR109w-b.187 lm_SuperContig_29_v2 92754 91762 -YGR109w-b.188 lm_SuperContig_29_v2 179477 178464 -YGR224w.189 lm_SuperContig_29_v2 78139 78724 -YGR224w.190 lm_SuperContig_29_v2 194215 193630 -YHL028w.191 lm_SuperContig_29_v2 197437 197024 -YHL028w.192 lm_SuperContig_29_v2 197413 197024 -YHL028w.193 lm_SuperContig_29_v2 197425 197024 -YHL028w.194 lm_SuperContig_29_v2 197434 197024 -YHL028w.195 lm_SuperContig_29_v2 197482 197024 -YHL028w.196 lm_SuperContig_29_v2 197482 197027 -YHL028w.197 lm_SuperContig_29_v2 197410 197024 -YHL028w.198 lm_SuperContig_29_v2 197434 197024 -YIL082w-a.199 lm_SuperContig_29_v2 42272 40143 -YIL082w-a.200 lm_SuperContig_29_v2 17274 16081 -YIL082w-a.201 lm_SuperContig_29_v2 102192 100993 -YIL082w-a.202 lm_SuperContig_29_v2 168564 167371 -YIL082w-a.203 lm_SuperContig_29_v2 134535 133543 -YIL082w-a.204 lm_SuperContig_29_v2 92754 91762 -YIL082w-a.205 lm_SuperContig_29_v2 179477 178464 -YJR151c.206 lm_SuperContig_29_v2 197425 197024 -YJR151c.207 lm_SuperContig_29_v2 197425 197024 -YJR151c.208 lm_SuperContig_29_v2 197434 197024 -YJR151c.209 lm_SuperContig_29_v2 197425 197021 -YJR151c.210 lm_SuperContig_29_v2 197434 197024 -YJR151c.211 lm_SuperContig_29_v2 197434 197024 -YJR151c.212 lm_SuperContig_29_v2 197434 197024 -YJR151c.213 lm_SuperContig_29_v2 197425 197024 -YJR151c.214 lm_SuperContig_29_v2 197404 197030 -YJR151c.215 lm_SuperContig_29_v2 197398 197024 -YJR151c.216 lm_SuperContig_29_v2 197395 197024 -YJR151c.217 lm_SuperContig_29_v2 197434 197039 -YJR151c.218 lm_SuperContig_29_v2 197437 197027 -YJR151c.219 lm_SuperContig_29_v2 197434 197024 -YJR151c.220 lm_SuperContig_29_v2 197434 197024 -YJR151c.221 lm_SuperContig_29_v2 197392 197024 -YJR151c.222 lm_SuperContig_29_v2 197425 197021 -YJR151c.223 lm_SuperContig_29_v2 197434 197024 -YJR151c.224 lm_SuperContig_29_v2 197434 197036 -YKR105c.225 lm_SuperContig_29_v2 78112 78778 -YKR105c.226 lm_SuperContig_29_v2 194242 192985 -YNL283c.227 lm_SuperContig_29_v2 197434 197024 -YNL283c.228 lm_SuperContig_29_v2 197422 197042 -SPAC167.08.229 lm_SuperContig_29_v2 134754 133341 -SPAC167.08.230 lm_SuperContig_29_v2 102531 100993 -SPAC167.08.231 lm_SuperContig_29_v2 42287 41079 -SPAC167.08.232 lm_SuperContig_29_v2 168579 167371 -SPAC167.08.233 lm_SuperContig_29_v2 17289 16081 -SPAC167.08.234 lm_SuperContig_29_v2 92700 91693 -SPAC167.08.235 lm_SuperContig_29_v2 179504 178395 -SPAC167.08.236 lm_SuperContig_29_v2 11856 10747 -SPBC12C2.13c.237 lm_SuperContig_29_v2 194218 192757 -SPAPB15E9.03c.238 lm_SuperContig_29_v2 134754 133341 -SPAPB15E9.03c.239 lm_SuperContig_29_v2 102531 100993 -SPAPB15E9.03c.240 lm_SuperContig_29_v2 42287 41079 -SPAPB15E9.03c.241 lm_SuperContig_29_v2 168579 167371 -SPAPB15E9.03c.242 lm_SuperContig_29_v2 17289 16081 -SPAPB15E9.03c.243 lm_SuperContig_29_v2 92700 91693 -SPAPB15E9.03c.244 lm_SuperContig_29_v2 179504 178395 -SPAPB15E9.03c.245 lm_SuperContig_29_v2 11856 10747 -SPBC1289.17.246 lm_SuperContig_29_v2 134754 133341 -SPBC1289.17.247 lm_SuperContig_29_v2 102531 100993 -SPBC1289.17.248 lm_SuperContig_29_v2 42287 41079 -SPBC1289.17.249 lm_SuperContig_29_v2 168579 167371 -SPBC1289.17.250 lm_SuperContig_29_v2 17289 16081 -SPBC1289.17.251 lm_SuperContig_29_v2 92700 91693 -SPBC1289.17.252 lm_SuperContig_29_v2 179504 178395 -SPBC1289.17.253 lm_SuperContig_29_v2 11856 10747 -SPAC3H1.06c.254 lm_SuperContig_29_v2 77950 78799 -SPAC3H1.06c.255 lm_SuperContig_29_v2 194404 192844 -SPCC1020.14.256 lm_SuperContig_29_v2 134754 133341 -SPCC1020.14.257 lm_SuperContig_29_v2 102531 100993 -SPCC1020.14.258 lm_SuperContig_29_v2 42287 41079 -SPCC1020.14.259 lm_SuperContig_29_v2 168579 167371 -SPCC1020.14.260 lm_SuperContig_29_v2 17289 16081 -SPCC1020.14.261 lm_SuperContig_29_v2 92700 91693 -SPCC1020.14.262 lm_SuperContig_29_v2 179504 178395 -SPCC1020.14.263 lm_SuperContig_29_v2 11856 10747 -SPBC3E7.06c.264 lm_SuperContig_29_v2 194482 192760 -SPAC26A3.13c.265 lm_SuperContig_29_v2 134754 133341 -SPAC26A3.13c.266 lm_SuperContig_29_v2 102531 100993 -SPAC26A3.13c.267 lm_SuperContig_29_v2 42287 41079 -SPAC26A3.13c.268 lm_SuperContig_29_v2 168579 167371 -SPAC26A3.13c.269 lm_SuperContig_29_v2 17289 16081 -SPAC26A3.13c.270 lm_SuperContig_29_v2 92700 91693 -SPAC26A3.13c.271 lm_SuperContig_29_v2 179504 178395 -SPAC26A3.13c.272 lm_SuperContig_29_v2 11856 10747 -SPBC16A3.17c.273 lm_SuperContig_29_v2 78133 78799 -SPBC16A3.17c.274 lm_SuperContig_29_v2 194221 192874 -SPAC1399.02.275 lm_SuperContig_29_v2 77950 78736 -SPAC1399.02.276 lm_SuperContig_29_v2 194404 192844 -SPAC2E1P3.03c.277 lm_SuperContig_29_v2 134754 133341 -SPAC2E1P3.03c.278 lm_SuperContig_29_v2 102531 100993 -SPAC2E1P3.03c.279 lm_SuperContig_29_v2 42287 41079 -SPAC2E1P3.03c.280 lm_SuperContig_29_v2 168579 167371 -SPAC2E1P3.03c.281 lm_SuperContig_29_v2 17289 16081 -SPAC2E1P3.03c.282 lm_SuperContig_29_v2 92700 91693 -SPAC2E1P3.03c.283 lm_SuperContig_29_v2 179504 178395 -SPAC2E1P3.03c.284 lm_SuperContig_29_v2 11856 10747 -SPAC19D5.09c.285 lm_SuperContig_29_v2 134754 133341 -SPAC19D5.09c.286 lm_SuperContig_29_v2 102531 100993 -SPAC19D5.09c.287 lm_SuperContig_29_v2 42287 41079 -SPAC19D5.09c.288 lm_SuperContig_29_v2 168579 167371 -SPAC19D5.09c.289 lm_SuperContig_29_v2 17289 16081 -SPAC19D5.09c.290 lm_SuperContig_29_v2 92700 91693 -SPAC19D5.09c.291 lm_SuperContig_29_v2 179504 178395 -SPAC19D5.09c.292 lm_SuperContig_29_v2 11856 10747 -SPAC27E2.08.293 lm_SuperContig_29_v2 134754 133341 -SPAC27E2.08.294 lm_SuperContig_29_v2 102531 100993 -SPAC27E2.08.295 lm_SuperContig_29_v2 42287 41079 -SPAC27E2.08.296 lm_SuperContig_29_v2 168579 167371 -SPAC27E2.08.297 lm_SuperContig_29_v2 17289 16081 -SPAC27E2.08.298 lm_SuperContig_29_v2 92700 91693 -SPAC27E2.08.299 lm_SuperContig_29_v2 179504 178395 -SPAC27E2.08.300 lm_SuperContig_29_v2 11856 10747 -SPAC13D1.01c.301 lm_SuperContig_29_v2 134754 133341 -SPAC13D1.01c.302 lm_SuperContig_29_v2 102531 100993 -SPAC13D1.01c.303 lm_SuperContig_29_v2 42287 41079 -SPAC13D1.01c.304 lm_SuperContig_29_v2 168579 167371 -SPAC13D1.01c.305 lm_SuperContig_29_v2 17289 16081 -SPAC13D1.01c.306 lm_SuperContig_29_v2 92700 91693 -SPAC13D1.01c.307 lm_SuperContig_29_v2 179504 178395 -SPAC13D1.01c.308 lm_SuperContig_29_v2 11856 10747 -SPBC9B6.02c.309 lm_SuperContig_29_v2 134754 133341 -SPBC9B6.02c.310 lm_SuperContig_29_v2 102531 100993 -SPBC9B6.02c.311 lm_SuperContig_29_v2 42287 41079 -SPBC9B6.02c.312 lm_SuperContig_29_v2 168579 167371 -SPBC9B6.02c.313 lm_SuperContig_29_v2 17289 16081 -SPBC9B6.02c.314 lm_SuperContig_29_v2 92700 91693 -SPBC9B6.02c.315 lm_SuperContig_29_v2 179504 178395 -SPBC9B6.02c.316 lm_SuperContig_29_v2 11856 10747 -SPAC9.04.317 lm_SuperContig_29_v2 134754 133341 -SPAC9.04.318 lm_SuperContig_29_v2 102531 100993 -SPAC9.04.319 lm_SuperContig_29_v2 42287 41079 -SPAC9.04.320 lm_SuperContig_29_v2 168579 167371 -SPAC9.04.321 lm_SuperContig_29_v2 17289 16081 -SPAC9.04.322 lm_SuperContig_29_v2 92700 91693 -SPAC9.04.323 lm_SuperContig_29_v2 179504 178395 -SPAC9.04.324 lm_SuperContig_29_v2 11856 10747 -um00679.325 lm_SuperContig_29_v2 77980 78567 -um00679.326 lm_SuperContig_29_v2 194374 192772 -um00842.327 lm_SuperContig_29_v2 78115 78814 -um00842.328 lm_SuperContig_29_v2 194239 192760 -um01882.329 lm_SuperContig_29_v2 78112 78802 -um01882.330 lm_SuperContig_29_v2 194242 192760 -um01964.331 lm_SuperContig_29_v2 78019 78567 -um01964.332 lm_SuperContig_29_v2 194335 192901 -um02062.333 lm_SuperContig_29_v2 77890 78814 -um02062.334 lm_SuperContig_29_v2 194464 192760 -um02598.335 lm_SuperContig_29_v2 78136 78814 -um02598.336 lm_SuperContig_29_v2 194218 192754 -um03115.337 lm_SuperContig_29_v2 77938 78808 -um03115.338 lm_SuperContig_29_v2 194416 192757 -um05414.339 lm_SuperContig_29_v2 77938 78736 -um05414.340 lm_SuperContig_29_v2 194416 192826 -um05421.341 lm_SuperContig_29_v2 194107 193006 -mito_010.1 lm_SuperContig_30_v2 35498 37823 -mito_010.2 lm_SuperContig_30_v2 27615 29673 -mito_010.3 lm_SuperContig_30_v2 23817 24089 -mito_020.4 lm_SuperContig_30_v2 27615 29418 -mito_020.5 lm_SuperContig_30_v2 95085 94306 -mito_020.6 lm_SuperContig_30_v2 23817 24089 -mito_030.7 lm_SuperContig_30_v2 23817 27509 -mito_030.8 lm_SuperContig_30_v2 62656 61805 -mito_030.9 lm_SuperContig_30_v2 146223 147503 -mito_030.10 lm_SuperContig_30_v2 109925 109092 -mito_030.11 lm_SuperContig_30_v2 117965 119308 -mito_030.12 lm_SuperContig_30_v2 83615 82749 -mito_030.13 lm_SuperContig_30_v2 35963 37213 -mito_030.14 lm_SuperContig_30_v2 87770 86928 -mito_030.15 lm_SuperContig_30_v2 116645 117925 -mito_030.16 lm_SuperContig_30_v2 81706 80861 -mito_030.17 lm_SuperContig_30_v2 150994 152199 -mito_030.18 lm_SuperContig_30_v2 56582 55780 -mito_030.19 lm_SuperContig_30_v2 18181 19317 -mito_030.20 lm_SuperContig_30_v2 91238 90399 -mito_030.21 lm_SuperContig_30_v2 141039 141858 -mito_030.22 lm_SuperContig_30_v2 64676 63837 -mito_030.23 lm_SuperContig_30_v2 115228 116103 -mito_030.24 lm_SuperContig_30_v2 149559 150444 -mito_030.25 lm_SuperContig_30_v2 22437 23375 -mito_030.26 lm_SuperContig_30_v2 32527 33390 -mito_040.27 lm_SuperContig_30_v2 21984 22220 -mito_050.28 lm_SuperContig_30_v2 21984 23387 -mito_050.29 lm_SuperContig_30_v2 62650 61793 -mito_050.30 lm_SuperContig_30_v2 18466 19329 -mito_050.31 lm_SuperContig_30_v2 81703 80849 -mito_050.32 lm_SuperContig_30_v2 36323 37234 -mito_050.33 lm_SuperContig_30_v2 83594 82737 -mito_050.34 lm_SuperContig_30_v2 149583 150450 -mito_050.35 lm_SuperContig_30_v2 64748 63768 -mito_050.36 lm_SuperContig_30_v2 118442 119320 -mito_050.37 lm_SuperContig_30_v2 87767 86916 -mito_050.38 lm_SuperContig_30_v2 26661 27530 -mito_050.39 lm_SuperContig_30_v2 109925 109071 -mito_050.40 lm_SuperContig_30_v2 115249 116115 -mito_050.41 lm_SuperContig_30_v2 91259 90387 -mito_050.42 lm_SuperContig_30_v2 32542 33390 -mito_050.43 lm_SuperContig_30_v2 141021 141879 -mito_050.44 lm_SuperContig_30_v2 117050 117943 -mito_050.45 lm_SuperContig_30_v2 146610 147515 -mito_050.46 lm_SuperContig_30_v2 151234 152220 -mito_060.47 lm_SuperContig_30_v2 53696 53343 -mito_080.48 lm_SuperContig_30_v2 5079 5582 -mito_080.49 lm_SuperContig_30_v2 59799 53703 -mito_110.50 lm_SuperContig_30_v2 65165 64707 -mito_150.51 lm_SuperContig_30_v2 110387 108494 -mito_150.52 lm_SuperContig_30_v2 103711 103508 -mito_170.53 lm_SuperContig_30_v2 17614 20481 -mito_180.54 lm_SuperContig_30_v2 17614 19341 -mito_180.55 lm_SuperContig_30_v2 62653 61781 -mito_180.56 lm_SuperContig_30_v2 32542 33390 -mito_180.57 lm_SuperContig_30_v2 83615 82716 -mito_180.58 lm_SuperContig_30_v2 36329 37252 -mito_180.59 lm_SuperContig_30_v2 109979 109059 -mito_180.60 lm_SuperContig_30_v2 141030 141897 -mito_180.61 lm_SuperContig_30_v2 81706 80825 -mito_180.62 lm_SuperContig_30_v2 149580 150465 -mito_180.63 lm_SuperContig_30_v2 64718 63756 -mito_180.64 lm_SuperContig_30_v2 115189 116127 -mito_180.65 lm_SuperContig_30_v2 87770 86895 -mito_180.66 lm_SuperContig_30_v2 22509 23405 -mito_180.67 lm_SuperContig_30_v2 91256 90384 -mito_180.68 lm_SuperContig_30_v2 118439 119344 -mito_180.69 lm_SuperContig_30_v2 56585 55774 -mito_180.70 lm_SuperContig_30_v2 117050 117955 -mito_180.71 lm_SuperContig_30_v2 26640 27542 -mito_180.72 lm_SuperContig_30_v2 151309 152232 -mito_180.73 lm_SuperContig_30_v2 146610 147527 -mito_180.74 lm_SuperContig_30_v2 42209 42879 -mito_180.75 lm_SuperContig_30_v2 125743 126138 -mito_190.76 lm_SuperContig_30_v2 44197 47305 -mito_210.77 lm_SuperContig_30_v2 102604 102101 -mito_210.78 lm_SuperContig_30_v2 94202 89139 -mito_220.79 lm_SuperContig_30_v2 14626 15192 -mito_220.80 lm_SuperContig_30_v2 15860 16315 -mito_220.81 lm_SuperContig_30_v2 9733 9936 -mito_220.82 lm_SuperContig_30_v2 6405 6605 -mito_230.83 lm_SuperContig_30_v2 9733 9936 -mito_230.84 lm_SuperContig_30_v2 6405 6605 -mito_240.85 lm_SuperContig_30_v2 9733 9927 -mito_240.86 lm_SuperContig_30_v2 6405 6605 -mito_155.87 lm_SuperContig_30_v2 18442 19341 -mito_155.88 lm_SuperContig_30_v2 110081 109056 -mito_155.89 lm_SuperContig_30_v2 36323 37249 -mito_155.90 lm_SuperContig_30_v2 62650 61781 -mito_155.91 lm_SuperContig_30_v2 141021 141891 -mito_155.92 lm_SuperContig_30_v2 81703 80828 -mito_155.93 lm_SuperContig_30_v2 149583 150462 -mito_155.94 lm_SuperContig_30_v2 83594 82716 -mito_155.95 lm_SuperContig_30_v2 116981 117955 -mito_155.96 lm_SuperContig_30_v2 87767 86895 -mito_155.97 lm_SuperContig_30_v2 146610 147533 -mito_155.98 lm_SuperContig_30_v2 64655 63756 -mito_155.99 lm_SuperContig_30_v2 151258 152232 -mito_155.100 lm_SuperContig_30_v2 91256 90381 -mito_155.101 lm_SuperContig_30_v2 32494 33504 -mito_155.102 lm_SuperContig_30_v2 115198 116127 -mito_155.103 lm_SuperContig_30_v2 26607 27542 -mito_155.104 lm_SuperContig_30_v2 118442 119341 -mito_155.105 lm_SuperContig_30_v2 22509 23387 -mito_155.106 lm_SuperContig_30_v2 125740 126240 -mito_195.107 lm_SuperContig_30_v2 44996 45911 -mito_195.108 lm_SuperContig_30_v2 46058 46769 -SPMIT.05.109 lm_SuperContig_30_v2 14662 15189 -SPMIT.05.110 lm_SuperContig_30_v2 15941 16303 -SPMIT.04.111 lm_SuperContig_30_v2 65204 64752 -SPMIT.03.112 lm_SuperContig_30_v2 95262 94345 -SPMIT.01.113 lm_SuperContig_30_v2 102580 102098 -SPMIT.01.114 lm_SuperContig_30_v2 94202 93876 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.path --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.path Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,456 +0,0 @@ -1 lm_SuperContig_30_v2 35498 35914 mito_010 NADH dehydrogenase (ubiquinone) chain 5 307 445 1e-62 244 82.73 -1 lm_SuperContig_30_v2 37314 37823 mito_010 NADH dehydrogenase (ubiquinone) chain 5 494 663 8e-67 258 67.65 -2 lm_SuperContig_30_v2 27615 28001 mito_010 NADH dehydrogenase (ubiquinone) chain 5 109 237 1e-53 214 77.52 -2 lm_SuperContig_30_v2 29503 29673 mito_010 NADH dehydrogenase (ubiquinone) chain 5 254 310 3e-21 107 92.98 -3 lm_SuperContig_30_v2 23817 24089 mito_010 NADH dehydrogenase (ubiquinone) chain 5 1 91 7e-25 119 63.74 -4 lm_SuperContig_30_v2 27615 28001 mito_020 predicted ND5 intron 2 protein 109 237 1e-53 214 77.52 -4 lm_SuperContig_30_v2 28681 29418 mito_020 predicted ND5 intron 2 protein 303 540 4e-37 159 41.2 -5 lm_SuperContig_30_v2 94306 95085 mito_020 predicted ND5 intron 2 protein 544 279 2e-22 110 28.46 -6 lm_SuperContig_30_v2 23817 24089 mito_020 predicted ND5 intron 2 protein 1 91 7e-25 119 63.74 -7 lm_SuperContig_30_v2 23817 24089 mito_030 predicted ND5 intron 1 protein 1 91 7e-25 119 63.74 -7 lm_SuperContig_30_v2 26190 27509 mito_030 predicted ND5 intron 1 protein 84 525 0 666 76.52 -8 lm_SuperContig_30_v2 61805 62656 mito_030 predicted ND5 intron 1 protein 528 241 3e-55 219 38.89 -9 lm_SuperContig_30_v2 146223 147503 mito_030 predicted ND5 intron 1 protein 114 528 2e-64 250 37.61 -10 lm_SuperContig_30_v2 109092 109925 mito_030 predicted ND5 intron 1 protein 525 243 2e-49 200 38.16 -11 lm_SuperContig_30_v2 117965 119308 mito_030 predicted ND5 intron 1 protein 87 525 1e-63 248 35.79 -12 lm_SuperContig_30_v2 82749 83615 mito_030 predicted ND5 intron 1 protein 525 236 3e-47 193 35.27 -13 lm_SuperContig_30_v2 35963 37213 mito_030 predicted ND5 intron 1 protein 114 525 4e-62 242 38.08 -14 lm_SuperContig_30_v2 86928 87770 mito_030 predicted ND5 intron 1 protein 525 242 3e-47 193 36.14 -15 lm_SuperContig_30_v2 116645 117925 mito_030 predicted ND5 intron 1 protein 121 526 6e-60 235 37.12 -16 lm_SuperContig_30_v2 80861 81706 mito_030 predicted ND5 intron 1 protein 525 242 5e-44 182 35.66 -17 lm_SuperContig_30_v2 150994 152199 mito_030 predicted ND5 intron 1 protein 121 525 4e-58 229 36.3 -18 lm_SuperContig_30_v2 56292 56582 mito_030 predicted ND5 intron 1 protein 351 255 1e-34 74 38.78 -18 lm_SuperContig_30_v2 55780 56187 mito_030 predicted ND5 intron 1 protein 492 357 1e-34 96 36.96 -19 lm_SuperContig_30_v2 18181 19317 mito_030 predicted ND5 intron 1 protein 167 528 3e-57 226 37.76 -20 lm_SuperContig_30_v2 90399 91238 mito_030 predicted ND5 intron 1 protein 528 249 1e-37 161 32.52 -21 lm_SuperContig_30_v2 141039 141308 mito_030 predicted ND5 intron 1 protein 250 342 8e-47 58 34.41 -21 lm_SuperContig_30_v2 141292 141858 mito_030 predicted ND5 intron 1 protein 337 525 8e-47 155 42.11 -22 lm_SuperContig_30_v2 63837 64676 mito_030 predicted ND5 intron 1 protein 511 232 1e-35 155 35.21 -23 lm_SuperContig_30_v2 115228 116103 mito_030 predicted ND5 intron 1 protein 236 528 6e-48 195 35.93 -24 lm_SuperContig_30_v2 149559 149744 mito_030 predicted ND5 intron 1 protein 233 296 6e-40 41 35.94 -24 lm_SuperContig_30_v2 149749 150444 mito_030 predicted ND5 intron 1 protein 299 530 6e-40 149 37.02 -25 lm_SuperContig_30_v2 22437 23375 mito_030 predicted ND5 intron 1 protein 219 528 1e-43 181 32.59 -26 lm_SuperContig_30_v2 32527 33390 mito_030 predicted ND5 intron 1 protein 236 518 6e-40 169 36.15 -27 lm_SuperContig_30_v2 21984 22220 mito_040 NADH dehydrogenase (ubiquinone) chain 4L 1 79 3e-30 136 84.81 -28 lm_SuperContig_30_v2 21984 22229 mito_050 predicted ND4L intron protein 1 82 8e-31 138 82.93 -28 lm_SuperContig_30_v2 22509 23387 mito_050 predicted ND4L intron protein 145 438 7e-81 305 49 -29 lm_SuperContig_30_v2 61793 62650 mito_050 predicted ND4L intron protein 438 145 3e-49 200 40.33 -30 lm_SuperContig_30_v2 18466 19329 mito_050 predicted ND4L intron protein 145 438 6e-54 215 40.53 -31 lm_SuperContig_30_v2 80849 81703 mito_050 predicted ND4L intron protein 435 145 1e-45 188 39.6 -32 lm_SuperContig_30_v2 36323 37234 mito_050 predicted ND4L intron protein 145 438 4e-49 199 40.39 -33 lm_SuperContig_30_v2 82737 83594 mito_050 predicted ND4L intron protein 435 145 1e-45 188 37.46 -34 lm_SuperContig_30_v2 149583 149747 mito_050 predicted ND4L intron protein 145 199 3e-39 58 47.27 -34 lm_SuperContig_30_v2 149743 150450 mito_050 predicted ND4L intron protein 199 438 3e-39 130 35.34 -35 lm_SuperContig_30_v2 63768 64748 mito_050 predicted ND4L intron protein 438 111 4e-45 186 37.09 -36 lm_SuperContig_30_v2 118442 119320 mito_050 predicted ND4L intron protein 145 435 3e-44 183 38.64 -37 lm_SuperContig_30_v2 86916 87767 mito_050 predicted ND4L intron protein 435 145 4e-45 186 36.49 -38 lm_SuperContig_30_v2 26661 27530 mito_050 predicted ND4L intron protein 145 438 1e-43 181 35.67 -39 lm_SuperContig_30_v2 109071 109925 mito_050 predicted ND4L intron protein 438 145 7e-42 175 35.67 -40 lm_SuperContig_30_v2 115249 116115 mito_050 predicted ND4L intron protein 145 438 1e-43 181 38.41 -41 lm_SuperContig_30_v2 90387 91259 mito_050 predicted ND4L intron protein 438 144 2e-39 167 33.33 -42 lm_SuperContig_30_v2 32542 33390 mito_050 predicted ND4L intron protein 145 424 6e-43 179 38.91 -43 lm_SuperContig_30_v2 141021 141260 mito_050 predicted ND4L intron protein 146 228 6e-38 52 40.96 -43 lm_SuperContig_30_v2 141295 141879 mito_050 predicted ND4L intron protein 241 438 6e-38 131 39.51 -44 lm_SuperContig_30_v2 117050 117943 mito_050 predicted ND4L intron protein 145 438 1e-42 178 37.62 -45 lm_SuperContig_30_v2 146610 147515 mito_050 predicted ND4L intron protein 149 438 4e-37 159 34.18 -46 lm_SuperContig_30_v2 151234 152220 mito_050 predicted ND4L intron protein 118 438 2e-35 154 34.72 -47 lm_SuperContig_30_v2 53343 53696 mito_060 probable NADH dehydrogenase (ubiquinone) chain 3 117 1 2e-26 121 50 -48 lm_SuperContig_30_v2 5079 5582 mito_080 NADH dehydrogenase (ubiquinone) chain 2 403 582 7e-41 172 49.73 -49 lm_SuperContig_30_v2 59011 59799 mito_080 NADH dehydrogenase (ubiquinone) chain 2 271 1 1e-68 264 52.71 -49 lm_SuperContig_30_v2 55010 55561 mito_080 NADH dehydrogenase (ubiquinone) chain 2 423 242 1e-47 191 57.22 -49 lm_SuperContig_30_v2 53703 54143 mito_080 NADH dehydrogenase (ubiquinone) chain 2 582 425 3e-30 134 46.91 -50 lm_SuperContig_30_v2 64707 65165 mito_110 cytochrome-c oxidase chain III 227 74 2e-55 220 68.18 -51 lm_SuperContig_30_v2 110007 110387 mito_150 H+-transporting ATP synthase protein 6 134 6 2e-31 140 54.96 -51 lm_SuperContig_30_v2 108494 108691 mito_150 H+-transporting ATP synthase protein 6 179 114 3e-23 113 77.27 -52 lm_SuperContig_30_v2 103508 103711 mito_150 H+-transporting ATP synthase protein 6 261 194 7e-26 122 85.29 -53 lm_SuperContig_30_v2 17614 18054 mito_170 probable NADH dehydrogenase (ubiquinone) chain 4 83 229 3e-56 223 70.75 -53 lm_SuperContig_30_v2 19465 20481 mito_170 probable NADH dehydrogenase (ubiquinone) chain 4 195 536 3e-130 469 67.54 -54 lm_SuperContig_30_v2 17614 19341 mito_180 predicted ND4 intron protein 83 666 0 664 57.81 -55 lm_SuperContig_30_v2 61781 62653 mito_180 predicted ND4 intron protein 666 371 3e-63 246 42.62 -56 lm_SuperContig_30_v2 32542 33390 mito_180 predicted ND4 intron protein 372 648 6e-64 248 44.14 -57 lm_SuperContig_30_v2 82716 83615 mito_180 predicted ND4 intron protein 666 365 1e-60 237 41.45 -58 lm_SuperContig_30_v2 36329 37252 mito_180 predicted ND4 intron protein 374 668 2e-62 243 43.91 -59 lm_SuperContig_30_v2 109059 109979 mito_180 predicted ND4 intron protein 666 354 3e-58 229 37.7 -60 lm_SuperContig_30_v2 141030 141308 mito_180 predicted ND4 intron protein 376 469 3e-54 65 38.3 -60 lm_SuperContig_30_v2 141292 141897 mito_180 predicted ND4 intron protein 464 668 3e-54 173 43.9 -61 lm_SuperContig_30_v2 80825 81706 mito_180 predicted ND4 intron protein 667 371 1e-57 228 41.28 -62 lm_SuperContig_30_v2 149580 149747 mito_180 predicted ND4 intron protein 371 426 7e-54 59 44.64 -62 lm_SuperContig_30_v2 149743 150465 mito_180 predicted ND4 intron protein 425 667 7e-54 178 39.18 -63 lm_SuperContig_30_v2 63756 64718 mito_180 predicted ND4 intron protein 666 347 2e-57 227 42.25 -64 lm_SuperContig_30_v2 115189 116127 mito_180 predicted ND4 intron protein 352 666 8e-59 231 37.85 -65 lm_SuperContig_30_v2 86895 87770 mito_180 predicted ND4 intron protein 666 371 4e-57 226 41.47 -66 lm_SuperContig_30_v2 22509 23405 mito_180 predicted ND4 intron protein 372 668 3e-57 226 39 -67 lm_SuperContig_30_v2 90384 91256 mito_180 predicted ND4 intron protein 663 372 4e-43 179 32.55 -68 lm_SuperContig_30_v2 118439 119344 mito_180 predicted ND4 intron protein 371 667 3e-54 216 41.56 -69 lm_SuperContig_30_v2 56307 56585 mito_180 predicted ND4 intron protein 473 383 9e-27 64 43.01 -69 lm_SuperContig_30_v2 55774 56199 mito_180 predicted ND4 intron protein 624 480 9e-27 79 32.41 -70 lm_SuperContig_30_v2 117050 117955 mito_180 predicted ND4 intron protein 372 666 9e-54 215 41.5 -71 lm_SuperContig_30_v2 26640 27542 mito_180 predicted ND4 intron protein 365 666 9e-53 211 40.46 -72 lm_SuperContig_30_v2 151309 152232 mito_180 predicted ND4 intron protein 369 666 3e-50 203 40.76 -73 lm_SuperContig_30_v2 146610 147527 mito_180 predicted ND4 intron protein 376 666 6e-48 195 39.23 -74 lm_SuperContig_30_v2 42209 42388 mito_180 predicted ND4 intron protein 319 380 2e-21 26 30.16 -74 lm_SuperContig_30_v2 42457 42879 mito_180 predicted ND4 intron protein 384 528 2e-21 101 37.24 -75 lm_SuperContig_30_v2 125743 126138 mito_180 predicted ND4 intron protein 384 515 4e-23 113 41.67 -76 lm_SuperContig_30_v2 44197 44541 mito_190 NADH dehydrogenase (ubiquinone) chain 1 98 212 3e-43 180 76.52 -76 lm_SuperContig_30_v2 46832 47305 mito_190 NADH dehydrogenase (ubiquinone) chain 1 213 370 5e-44 182 59.01 -77 lm_SuperContig_30_v2 102101 102604 mito_210 cytochrome-c oxidase chain I 169 2 4e-74 282 80.36 -78 lm_SuperContig_30_v2 93858 94202 mito_210 cytochrome-c oxidase chain I 364 250 6e-51 205 87.83 -78 lm_SuperContig_30_v2 89713 89913 mito_210 cytochrome-c oxidase chain I 441 375 6e-24 116 79.1 -78 lm_SuperContig_30_v2 89139 89414 mito_210 cytochrome-c oxidase chain I 533 442 1e-22 111 58.7 -79 lm_SuperContig_30_v2 14626 15192 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 194 384 8e-78 295 73.82 -80 lm_SuperContig_30_v2 15860 16315 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 228 384 3e-37 160 56.25 -81 lm_SuperContig_30_v2 9733 9936 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 68 136 2e-27 127 89.86 -82 lm_SuperContig_30_v2 6405 6605 mito_220 ubiquinol--cytochrome-c reductase cytochrome b 1 67 2e-23 114 76.12 -83 lm_SuperContig_30_v2 9733 9936 mito_230 related to cob intron2 maturase/endonuclease 68 136 2e-27 127 89.86 -84 lm_SuperContig_30_v2 6405 6605 mito_230 related to cob intron2 maturase/endonuclease 1 67 2e-23 114 76.12 -85 lm_SuperContig_30_v2 9733 9927 mito_240 related to cob intron1 maturase 68 132 6e-27 126 90.77 -86 lm_SuperContig_30_v2 6405 6605 mito_240 related to cob intron1 maturase 1 67 2e-23 114 76.12 -87 lm_SuperContig_30_v2 18442 19341 mito_155 predicted ATP6 intron maturase 56 357 3e-68 263 45.07 -88 lm_SuperContig_30_v2 109056 110081 mito_155 predicted ATP6 intron maturase 358 11 4e-91 338 51.85 -89 lm_SuperContig_30_v2 36323 37249 mito_155 predicted ATP6 intron maturase 64 358 2e-63 247 45.02 -90 lm_SuperContig_30_v2 61781 62650 mito_155 predicted ATP6 intron maturase 357 64 2e-58 230 41.75 -91 lm_SuperContig_30_v2 141021 141311 mito_155 predicted ATP6 intron maturase 65 161 2e-51 79 42.86 -91 lm_SuperContig_30_v2 141292 141891 mito_155 predicted ATP6 intron maturase 155 357 2e-51 150 40 -92 lm_SuperContig_30_v2 80828 81703 mito_155 predicted ATP6 intron maturase 357 64 3e-51 206 39.6 -93 lm_SuperContig_30_v2 149583 149747 mito_155 predicted ATP6 intron maturase 64 117 6e-49 55 45.45 -93 lm_SuperContig_30_v2 149746 150462 mito_155 predicted ATP6 intron maturase 117 357 6e-49 165 38.93 -94 lm_SuperContig_30_v2 82716 83594 mito_155 predicted ATP6 intron maturase 357 64 1e-50 204 38.8 -95 lm_SuperContig_30_v2 116981 117955 mito_155 predicted ATP6 intron maturase 36 357 4e-53 213 37.01 -96 lm_SuperContig_30_v2 86895 87767 mito_155 predicted ATP6 intron maturase 357 64 7e-50 202 37.92 -97 lm_SuperContig_30_v2 146610 147533 mito_155 predicted ATP6 intron maturase 68 359 2e-52 210 42.22 -98 lm_SuperContig_30_v2 63756 64655 mito_155 predicted ATP6 intron maturase 357 60 1e-47 194 38.64 -99 lm_SuperContig_30_v2 151258 152232 mito_155 predicted ATP6 intron maturase 42 357 2e-52 210 39.34 -100 lm_SuperContig_30_v2 90381 91256 mito_155 predicted ATP6 intron maturase 355 64 8e-32 142 31 -101 lm_SuperContig_30_v2 32494 33504 mito_155 predicted ATP6 intron maturase 46 360 4e-52 209 37.64 -102 lm_SuperContig_30_v2 115198 116127 mito_155 predicted ATP6 intron maturase 47 357 1e-50 204 37.78 -103 lm_SuperContig_30_v2 26607 27542 mito_155 predicted ATP6 intron maturase 46 357 7e-50 202 37.34 -104 lm_SuperContig_30_v2 118442 119341 mito_155 predicted ATP6 intron maturase 64 357 7e-42 175 35.5 -105 lm_SuperContig_30_v2 22509 23387 mito_155 predicted ATP6 intron maturase 64 353 2e-37 161 31.19 -106 lm_SuperContig_30_v2 125740 126240 mito_155 predicted ATP6 intron maturase 75 237 3e-30 136 46.11 -107 lm_SuperContig_30_v2 44996 45490 mito_195 predicted ND1 intron protein 39 206 3e-48 196 57.74 -107 lm_SuperContig_30_v2 45636 45911 mito_195 predicted ND1 intron protein 209 300 2e-21 107 58.7 -108 lm_SuperContig_30_v2 46058 46228 mito_195 predicted ND1 intron protein 44 100 1e-70 58 51.72 -108 lm_SuperContig_30_v2 46230 46769 mito_195 predicted ND1 intron protein 101 304 1e-70 235 58.54 -109 lm_SuperContig_30_v2 14662 15189 SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual 206 381 1e-42 178 48.86 -110 lm_SuperContig_30_v2 15941 16303 SPMIT.05 |cob||cytochrome b|Schizosaccharomyces pombe|chr mitochondrial|||Manual 260 378 1e-22 111 48.76 -111 lm_SuperContig_30_v2 64752 65204 SPMIT.04 |cox3||cytochrome c oxidase 3|Schizosaccharomyces pombe|chr mitochondrial|||Manual 215 65 2e-34 150 50.98 -112 lm_SuperContig_30_v2 94345 95262 SPMIT.03 |||hypothetical protein|Schizosaccharomyces pombe|chr mitochondrial||Partial|Manual 312 3 1e-94 350 57.68 -113 lm_SuperContig_30_v2 102098 102580 SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual 171 10 3e-48 196 54.94 -114 lm_SuperContig_30_v2 93876 94202 SPMIT.01 |cox1||cytochrome c oxidase 1|Schizosaccharomyces pombe|chr mitochondrial|||Manual 360 251 3e-30 136 58.56 -115 lm_SuperContig_29_v2 77989 78369 Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 3 126 2e-22 105 40.94 -116 lm_SuperContig_29_v2 193985 194365 Afu3g02110 | MFS efflux transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 126 3 1e-21 105 40.94 -117 lm_SuperContig_29_v2 78109 78582 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 20 177 7e-59 207 58.86 -117 lm_SuperContig_29_v2 78662 78817 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 180 231 7e-59 42 30.77 -118 lm_SuperContig_29_v2 193772 194245 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 177 20 2e-128 207 58.86 -118 lm_SuperContig_29_v2 192760 193692 Afu3g01520 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 485 180 2e-128 275 41.8 -119 lm_SuperContig_29_v2 78010 78567 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 21 208 5e-23 100 29.79 -119 lm_SuperContig_29_v2 78662 78808 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 216 261 5e-23 28 26.53 -120 lm_SuperContig_29_v2 193787 194344 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 208 21 3e-40 100 29.79 -120 lm_SuperContig_29_v2 192766 193692 Afu3g02520 | MSF multidrug transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 535 216 3e-40 88 22.53 -121 lm_SuperContig_29_v2 78109 78588 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 45 204 1e-39 144 43.75 -121 lm_SuperContig_29_v2 78662 78817 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 205 258 1e-39 40 45.61 -122 lm_SuperContig_29_v2 193766 194245 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 204 45 2e-83 144 43.75 -122 lm_SuperContig_29_v2 192754 193692 Afu3g02720 | MFS transporter, putative | Aspergillus fumigatus | chr_3 | AAHF01000010 | 100 521 205 2e-83 188 33.33 -123 lm_SuperContig_29_v2 78061 78573 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 15 189 3e-22 87 29.71 -123 lm_SuperContig_29_v2 78662 78814 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 195 242 3e-22 39 39.22 -124 lm_SuperContig_29_v2 193781 194293 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 189 15 1e-49 87 29.71 -124 lm_SuperContig_29_v2 192760 193692 Afu6g03320 | MFS drug transporter, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 506 195 1e-49 133 27.85 -125 lm_SuperContig_29_v2 78007 78576 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 48 237 2e-59 198 47.37 -125 lm_SuperContig_29_v2 78662 78817 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 242 293 2e-59 52 46.15 -126 lm_SuperContig_29_v2 193778 194347 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 237 48 1e-79 198 47.37 -126 lm_SuperContig_29_v2 193288 193692 Afu6g02220 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000012 | 101 375 242 1e-79 122 43.7 -127 lm_SuperContig_29_v2 78133 78576 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 77 224 2e-44 159 51.35 -127 lm_SuperContig_29_v2 78662 78817 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 229 282 2e-44 41 41.07 -128 lm_SuperContig_29_v2 193778 194221 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 224 77 3e-91 159 51.35 -128 lm_SuperContig_29_v2 192760 193692 Afu8g00940 | MFS drug transporter, putative | Aspergillus fumigatus | chr_8 | AAHF01000014 | 102 541 229 3e-91 200 35.65 -129 lm_SuperContig_29_v2 133669 134343 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 226 2 3e-37 159 37.78 -130 lm_SuperContig_29_v2 167776 168372 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 200 2 9e-34 145 38.69 -131 lm_SuperContig_29_v2 41484 42080 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 200 2 8e-32 142 38.69 -132 lm_SuperContig_29_v2 101404 102000 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 200 2 3e-31 140 38.69 -133 lm_SuperContig_29_v2 31868 32272 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 136 4 6e-25 95 38.52 -133 lm_SuperContig_29_v2 31597 31836 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 147 6e-25 46 33.73 -134 lm_SuperContig_29_v2 16462 17082 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 208 2 4e-30 135 37.2 -135 lm_SuperContig_29_v2 178590 179264 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 4 1e-29 133 35.96 -136 lm_SuperContig_29_v2 10942 11625 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 1 2e-29 132 35.06 -137 lm_SuperContig_29_v2 91888 92562 Afu4g02630 | reverse transcriptase; protease; endonuclease | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 229 4 3e-27 126 35.53 -138 lm_SuperContig_29_v2 78184 78585 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 53 186 2e-25 96 35.07 -138 lm_SuperContig_29_v2 78644 78814 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 186 239 2e-25 41 40.35 -139 lm_SuperContig_29_v2 193769 194170 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 186 53 3e-59 96 35.07 -139 lm_SuperContig_29_v2 192964 193710 Afu4g03920 | MFS drug transporter, putative | Aspergillus fumigatus | chr_4 | AAHF01000016 | 104 430 186 3e-59 156 35.74 -140 lm_SuperContig_29_v2 78049 78567 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 19 191 3e-23 101 27.75 -140 lm_SuperContig_29_v2 78659 78775 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 198 236 3e-23 28 28.21 -141 lm_SuperContig_29_v2 193787 194305 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 191 19 9e-43 101 27.75 -141 lm_SuperContig_29_v2 192904 193695 Afu6g09110 | MSF multidrug transporter (Fnx1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 459 198 9e-43 96 26.12 -142 lm_SuperContig_29_v2 78151 78576 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 93 235 3e-31 124 41.96 -142 lm_SuperContig_29_v2 78662 78814 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 242 293 3e-31 32 30.77 -143 lm_SuperContig_29_v2 193778 194203 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 235 93 6e-83 124 41.96 -143 lm_SuperContig_29_v2 192760 193692 Afu6g14640 | MFS transporter (Bcmfs1), putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 552 242 6e-83 207 32.69 -144 lm_SuperContig_29_v2 78109 78576 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 34 189 3e-49 169 50 -144 lm_SuperContig_29_v2 78650 78814 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 190 245 3e-49 48 35.71 -145 lm_SuperContig_29_v2 193778 194245 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 189 34 2e-97 169 50 -145 lm_SuperContig_29_v2 192772 193704 Afu6g09710 | MFS toxin efflux pump, putative | Aspergillus fumigatus | chr_6 | AAHF01000006 | 108 501 190 2e-97 210 32.27 -146 lm_SuperContig_29_v2 78115 78576 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 51 204 6e-62 204 58.44 -146 lm_SuperContig_29_v2 78662 78817 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 209 260 6e-62 55 40.38 -147 lm_SuperContig_29_v2 193778 194239 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 204 51 1e-132 204 58.44 -147 lm_SuperContig_29_v2 192754 193692 Afu5g01540 | MFS aflatoxin efflux pump, putative | Aspergillus fumigatus | chr_5 | AAHF01000011 | 53 520 209 1e-132 293 43.77 -148 lm_SuperContig_29_v2 193784 194323 Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92 195 16 1e-31 89 25 -148 lm_SuperContig_29_v2 192868 193695 Afu2g15140 | MSF drug transporter, putative | Aspergillus fumigatus | chr_2 | AAHF01000001 | 92 482 201 1e-31 70 21.48 -149 lm_SuperContig_29_v2 193793 194221 fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5 169 27 6e-29 97 32.87 -149 lm_SuperContig_29_v2 193303 193707 fg00095 related to tetracycline efflux protein (otrb), Contig fg_contig_1.5 308 174 6e-29 54 28.06 -150 lm_SuperContig_29_v2 193784 194221 fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168 205 60 7e-40 78 27.4 -150 lm_SuperContig_29_v2 192877 193695 fg12051 related to DHA14-like major facilitator efflux transporter (MFS transporter), Contig fg_contig_1.168 483 215 7e-40 109 24.18 -151 lm_SuperContig_29_v2 77956 78576 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 2 220 7e-35 126 34.25 -151 lm_SuperContig_29_v2 78650 78814 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 221 272 7e-35 42 34.55 -152 lm_SuperContig_29_v2 193778 194398 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 220 2 7e-62 126 34.25 -152 lm_SuperContig_29_v2 192883 193704 fg12074 related to DHA14-like major facilitator efflux transporter, Contig fg_contig_1.35 490 221 7e-62 135 29.2 -153 lm_SuperContig_29_v2 78124 78576 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 62 212 4e-45 166 52.32 -153 lm_SuperContig_29_v2 78662 78718 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 217 236 4e-45 36 65 -154 lm_SuperContig_29_v2 193778 194230 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 212 62 1e-92 166 52.32 -154 lm_SuperContig_29_v2 192769 193692 fg12335 probable aflatoxin efflux pump AFLT, Contig fg_contig_1.231 537 217 1e-92 197 32.61 -155 lm_SuperContig_29_v2 193778 194383 fg12717 related to putative multidrug transporter, Contig fg_contig_1.37 219 15 2e-26 76 25.85 -155 lm_SuperContig_29_v2 193222 193707 fg12717 related to putative multidrug transporter, Contig fg_contig_1.37 402 218 2e-26 66 25 -156 lm_SuperContig_29_v2 193784 194248 b13o8_150 conserved hypothetical protein 232 73 3e-31 85 28.12 -156 lm_SuperContig_29_v2 193036 193695 b13o8_150 conserved hypothetical protein 460 238 3e-31 73 23.35 -157 lm_SuperContig_29_v2 78010 78585 b18d24_100 related to tetracycline efflux protein (otrb) 9 199 2e-27 99 28.12 -157 lm_SuperContig_29_v2 78644 78814 b18d24_100 related to tetracycline efflux protein (otrb) 197 250 2e-27 43 42.11 -158 lm_SuperContig_29_v2 193769 194344 b18d24_100 related to tetracycline efflux protein (otrb) 199 9 4e-60 99 28.12 -158 lm_SuperContig_29_v2 192916 193710 b18d24_100 related to tetracycline efflux protein (otrb) 457 197 4e-60 155 33.96 -159 lm_SuperContig_29_v2 78184 78576 b5k2_230 related to major facilitator (MFS1) transporter 211 341 4e-42 141 50.38 -159 lm_SuperContig_29_v2 78662 78814 b5k2_230 related to major facilitator (MFS1) transporter 346 396 4e-42 51 49.06 -160 lm_SuperContig_29_v2 193778 194170 b5k2_230 related to major facilitator (MFS1) transporter 341 211 7e-99 141 50.38 -160 lm_SuperContig_29_v2 192760 193692 b5k2_230 related to major facilitator (MFS1) transporter 657 346 7e-99 243 38.1 -161 lm_SuperContig_29_v2 193781 194212 1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 228 85 1e-40 84 30.56 -161 lm_SuperContig_29_v2 192832 193704 1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 522 229 1e-40 106 23.99 -162 lm_SuperContig_29_v2 77941 78576 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 28 241 1e-30 111 28.97 -162 lm_SuperContig_29_v2 78662 78736 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 246 270 1e-30 42 56 -163 lm_SuperContig_29_v2 193778 194413 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 241 28 5e-62 111 28.97 -163 lm_SuperContig_29_v2 192760 193692 1nc570_120 related to DHA14-like major facilitator efflux transporter (MFS transporter) 559 246 5e-62 149 28.3 -164 lm_SuperContig_29_v2 193778 194086 6nc360_090 related to DHA14-like major facilitator 188 86 8e-44 69 38.83 -164 lm_SuperContig_29_v2 192817 193695 6nc360_090 related to DHA14-like major facilitator 491 194 8e-44 132 28.9 -165 lm_SuperContig_29_v2 78112 78576 29e8_240 probable aflatoxin efflux pump AFLT 62 216 1e-56 190 55.48 -165 lm_SuperContig_29_v2 78662 78817 29e8_240 probable aflatoxin efflux pump AFLT 221 272 1e-56 50 40.38 -166 lm_SuperContig_29_v2 193778 194242 29e8_240 probable aflatoxin efflux pump AFLT 216 62 2e-117 190 55.48 -166 lm_SuperContig_29_v2 192769 193692 29e8_240 probable aflatoxin efflux pump AFLT 535 221 2e-117 256 41.14 -167 lm_SuperContig_29_v2 193787 194218 7nc450_010 related to multidrug resistance protein 221 78 3e-24 57 20.83 -167 lm_SuperContig_29_v2 192940 193695 7nc450_010 related to multidrug resistance protein 484 228 3e-24 79 25 -168 lm_SuperContig_29_v2 193781 194218 4nc446_010 related to putative multidrug transporter 253 106 3e-48 82 29.73 -168 lm_SuperContig_29_v2 192865 193692 4nc446_010 related to putative multidrug transporter 530 259 3e-48 134 28.26 -169 lm_SuperContig_29_v2 193766 194239 b11e5_230 related to multidrug resistance protein fnx1 254 97 1e-40 97 29.75 -169 lm_SuperContig_29_v2 192904 193704 b11e5_230 related to multidrug resistance protein fnx1 518 253 1e-40 93 25.27 -170 lm_SuperContig_29_v2 77935 78576 xnc126_050 probable DHA14-like major facilitator; ABC transporter 38 241 7e-60 190 46.26 -170 lm_SuperContig_29_v2 78662 78817 xnc126_050 probable DHA14-like major facilitator; ABC transporter 246 298 7e-60 62 43.4 -171 lm_SuperContig_29_v2 193778 194419 xnc126_050 probable DHA14-like major facilitator; ABC transporter 241 38 2e-130 190 46.26 -171 lm_SuperContig_29_v2 192757 193692 xnc126_050 probable DHA14-like major facilitator; ABC transporter 559 246 2e-130 299 45.08 -172 lm_SuperContig_29_v2 78109 78576 4nc135_070 related to aflatoxin efflux pump AFLT 17 172 2e-53 184 53.85 -172 lm_SuperContig_29_v2 78662 78817 4nc135_070 related to aflatoxin efflux pump AFLT 177 238 2e-53 46 38.71 -173 lm_SuperContig_29_v2 193778 194245 4nc135_070 related to aflatoxin efflux pump AFLT 172 17 4e-99 184 53.85 -173 lm_SuperContig_29_v2 192751 193692 4nc135_070 related to aflatoxin efflux pump AFLT 494 177 4e-99 201 34.46 -174 lm_SuperContig_29_v2 78031 78588 xnc164_090 related to multidrug resistance protein 19 209 3e-21 101 30.89 -175 lm_SuperContig_29_v2 193766 194323 xnc164_090 related to multidrug resistance protein 209 19 1e-42 101 30.89 -175 lm_SuperContig_29_v2 192802 193692 xnc164_090 related to multidrug resistance protein 509 210 1e-42 95 26.77 -176 lm_SuperContig_29_v2 193766 194107 YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane 117 6 3e-23 57 27.19 -176 lm_SuperContig_29_v2 192916 193704 YBR293w VBA2 Permease of basic amino acids in the vacuolar membrane 384 116 3e-23 74 23.53 -177 lm_SuperContig_29_v2 193778 193954 YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane 61 3 7e-28 52 38.98 -177 lm_SuperContig_29_v2 192985 193692 YCL069w VBA3 Permease of basic amino acids in the vacuolar membrane 335 66 7e-28 95 28.04 -178 lm_SuperContig_29_v2 197024 197422 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 298 166 5e-24 113 45.52 -179 lm_SuperContig_29_v2 197027 197413 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 292 164 2e-23 111 46.56 -180 lm_SuperContig_29_v2 197039 197437 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 310 170 2e-22 108 46.1 -181 lm_SuperContig_29_v2 197021 197416 YDL037c BSC1 Transcript encoded by this ORF shows a high level of stop codon bypass EC:3.2.1.3 282 151 3e-22 107 39.39 -182 lm_SuperContig_29_v2 40143 42272 YGR109w-b TY3B TY3B protein 1301 616 6e-39 165 26.47 -183 lm_SuperContig_29_v2 16081 17274 YGR109w-b TY3B TY3B protein 1008 616 4e-35 152 30.33 -184 lm_SuperContig_29_v2 100993 102192 YGR109w-b TY3B TY3B protein 1008 616 8e-35 151 30.92 -185 lm_SuperContig_29_v2 167371 168564 YGR109w-b TY3B TY3B protein 1008 616 2e-35 151 30.83 -186 lm_SuperContig_29_v2 133543 134535 YGR109w-b TY3B TY3B protein 943 616 4e-34 149 32.23 -187 lm_SuperContig_29_v2 91762 92754 YGR109w-b TY3B TY3B protein 944 618 4e-23 113 30.24 -188 lm_SuperContig_29_v2 178464 179477 YGR109w-b TY3B TY3B protein 944 611 1e-21 107 29.03 -189 lm_SuperContig_29_v2 78139 78582 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 70 217 1e-27 105 39.19 -189 lm_SuperContig_29_v2 78662 78724 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 220 240 1e-27 39 57.14 -190 lm_SuperContig_29_v2 193772 194215 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 217 70 6e-27 105 39.19 -190 lm_SuperContig_29_v2 193630 193692 YGR224w AZR1 Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs 240 220 6e-27 39 57.14 -191 lm_SuperContig_29_v2 197024 197437 YHL028w WSC4 Cell wall integrity and stress response component 4 276 136 3e-25 117 47.52 -192 lm_SuperContig_29_v2 197024 197413 YHL028w WSC4 Cell wall integrity and stress response component 4 323 190 3e-23 111 47.01 -193 lm_SuperContig_29_v2 197024 197425 YHL028w WSC4 Cell wall integrity and stress response component 4 290 148 2e-23 111 49.65 -194 lm_SuperContig_29_v2 197024 197434 YHL028w WSC4 Cell wall integrity and stress response component 4 332 197 2e-22 108 42.03 -195 lm_SuperContig_29_v2 197024 197482 YHL028w WSC4 Cell wall integrity and stress response component 4 300 147 5e-22 107 41.29 -196 lm_SuperContig_29_v2 197027 197482 YHL028w WSC4 Cell wall integrity and stress response component 4 336 184 5e-22 107 39.22 -197 lm_SuperContig_29_v2 197024 197410 YHL028w WSC4 Cell wall integrity and stress response component 4 314 179 6e-22 106 47.79 -198 lm_SuperContig_29_v2 197024 197434 YHL028w WSC4 Cell wall integrity and stress response component 4 257 117 8e-21 103 42.55 -199 lm_SuperContig_29_v2 40143 42272 YIL082w-a TY3B TY3B protein 1327 642 8e-39 165 26.47 -200 lm_SuperContig_29_v2 16081 17274 YIL082w-a TY3B TY3B protein 1034 642 1e-34 150 30.33 -201 lm_SuperContig_29_v2 100993 102192 YIL082w-a TY3B TY3B protein 1034 642 3e-34 150 30.92 -202 lm_SuperContig_29_v2 167371 168564 YIL082w-a TY3B TY3B protein 1034 642 6e-35 149 30.83 -203 lm_SuperContig_29_v2 133543 134535 YIL082w-a TY3B TY3B protein 969 642 1e-33 147 32.23 -204 lm_SuperContig_29_v2 91762 92754 YIL082w-a TY3B TY3B protein 970 644 5e-23 112 30.24 -205 lm_SuperContig_29_v2 178464 179477 YIL082w-a TY3B TY3B protein 970 637 1e-21 106 29.03 -206 lm_SuperContig_29_v2 197024 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 267 132 1e-33 145 58.09 -207 lm_SuperContig_29_v2 197024 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 290 156 2e-33 144 57.78 -208 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 261 126 3e-33 144 58.39 -209 lm_SuperContig_29_v2 197021 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 300 165 6e-33 143 57.35 -210 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 285 147 6e-33 143 57.55 -211 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 276 141 6e-33 143 57.66 -212 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 281 144 1e-32 142 55.8 -213 lm_SuperContig_29_v2 197024 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 303 174 3e-32 140 57.46 -214 lm_SuperContig_29_v2 197030 197404 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 248 124 3e-32 140 59.2 -215 lm_SuperContig_29_v2 197024 197398 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 246 123 1e-31 139 60 -216 lm_SuperContig_29_v2 197024 197395 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 240 118 1e-31 139 59.68 -217 lm_SuperContig_29_v2 197039 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 318 183 1e-31 139 57.35 -218 lm_SuperContig_29_v2 197027 197437 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 244 108 2e-31 138 57.97 -219 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 314 174 3e-31 137 55.32 -220 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 350 201 1e-28 128 52 -221 lm_SuperContig_29_v2 197024 197392 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 222 102 1e-26 122 56.91 -222 lm_SuperContig_29_v2 197021 197425 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 360 219 3e-25 118 52.08 -223 lm_SuperContig_29_v2 197024 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 372 228 2e-24 115 48.28 -224 lm_SuperContig_29_v2 197036 197434 YJR151c DAN4 Cell wall mannoprotein, expressed under anaerobic conditions, completely repressed during aerobic growth 378 246 7e-23 109 42.86 -225 lm_SuperContig_29_v2 78112 78576 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 31 185 7e-29 105 33.55 -225 lm_SuperContig_29_v2 78662 78778 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 190 227 7e-29 43 48.72 -226 lm_SuperContig_29_v2 193778 194242 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 185 31 4e-43 105 33.55 -226 lm_SuperContig_29_v2 192985 193692 YKR105c Putative member of family of basic amino acid transporters localised to vacuolar membrane 459 190 4e-43 94 27.68 -227 lm_SuperContig_29_v2 197024 197434 YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3 272 139 4e-22 107 45.65 -228 lm_SuperContig_29_v2 197042 197422 YNL283c WSC2 Glucoamylase III (alpha-1,4-glucan-glucosidase) EC:3.2.1.3 275 147 8e-21 103 45.8 -229 lm_SuperContig_29_v2 133471 134754 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -229 lm_SuperContig_29_v2 133341 133436 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -230 lm_SuperContig_29_v2 100993 102531 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -231 lm_SuperContig_29_v2 41079 42287 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -232 lm_SuperContig_29_v2 167371 168579 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -233 lm_SuperContig_29_v2 16081 17289 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -234 lm_SuperContig_29_v2 91693 92700 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -235 lm_SuperContig_29_v2 178395 179504 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -236 lm_SuperContig_29_v2 10747 11856 SPAC167.08 |Tf2-2|SPAC1705.01c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -237 lm_SuperContig_29_v2 193787 194218 SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual 176 33 1e-35 85 31.25 -237 lm_SuperContig_29_v2 192757 193695 SPBC12C2.13c |fnx1|SPBC21D10.04c|MFS multidrug efflux transporter|Schizosaccharomyces pombe|chr 2|||Manual 499 183 1e-35 89 22.84 -238 lm_SuperContig_29_v2 133471 134754 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -238 lm_SuperContig_29_v2 133341 133436 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -239 lm_SuperContig_29_v2 100993 102531 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -240 lm_SuperContig_29_v2 41079 42287 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -241 lm_SuperContig_29_v2 167371 168579 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -242 lm_SuperContig_29_v2 16081 17289 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -243 lm_SuperContig_29_v2 91693 92700 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -244 lm_SuperContig_29_v2 178395 179504 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -245 lm_SuperContig_29_v2 10747 11856 SPAPB15E9.03c |Tf2-5||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -246 lm_SuperContig_29_v2 133471 134754 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 358 2e-46 184 28.54 -246 lm_SuperContig_29_v2 133341 133436 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 800 2e-46 27 46.88 -247 lm_SuperContig_29_v2 100993 102531 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 312 3e-44 183 27.86 -248 lm_SuperContig_29_v2 41079 42287 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 3e-42 176 28.89 -249 lm_SuperContig_29_v2 167371 168579 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 8e-43 175 29.38 -250 lm_SuperContig_29_v2 16081 17289 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 2e-39 166 28.15 -251 lm_SuperContig_29_v2 91693 92700 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 452 1e-37 161 32.94 -252 lm_SuperContig_29_v2 178395 179504 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 1e-37 160 30.91 -253 lm_SuperContig_29_v2 10747 11856 SPBC1289.17 |Tf2-11|SPBC8E4.11c|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 1e-36 157 31.18 -254 lm_SuperContig_29_v2 77950 78588 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 34 242 5e-29 109 30.99 -254 lm_SuperContig_29_v2 78662 78799 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 243 286 5e-29 39 41.3 -255 lm_SuperContig_29_v2 193766 194404 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 242 34 2e-50 109 30.99 -255 lm_SuperContig_29_v2 192844 193692 SPAC3H1.06c |||membrane transporter |Schizosaccharomyces pombe|chr 1|||Manual 525 243 2e-50 113 28.03 -256 lm_SuperContig_29_v2 133471 134754 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 358 4e-46 183 28.31 -256 lm_SuperContig_29_v2 133341 133436 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 800 4e-46 27 46.88 -257 lm_SuperContig_29_v2 100993 102531 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 312 7e-44 182 27.67 -258 lm_SuperContig_29_v2 41079 42287 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 427 7e-42 175 28.64 -259 lm_SuperContig_29_v2 167371 168579 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 427 2e-42 174 29.14 -260 lm_SuperContig_29_v2 16081 17289 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 831 427 4e-39 165 27.9 -261 lm_SuperContig_29_v2 91693 92700 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 452 3e-37 159 32.64 -262 lm_SuperContig_29_v2 178395 179504 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 418 3e-37 158 30.65 -263 lm_SuperContig_29_v2 10747 11856 SPCC1020.14 |Tf2-12||retrotransposable element|Schizosaccharomyces pombe|chr 3|||Manual 786 418 3e-36 155 30.91 -264 lm_SuperContig_29_v2 193781 194482 SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 236 4 7e-34 95 23.93 -264 lm_SuperContig_29_v2 192760 193692 SPBC3E7.06c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 551 242 7e-34 72 21.77 -265 lm_SuperContig_29_v2 133471 134754 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -265 lm_SuperContig_29_v2 133341 133436 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -266 lm_SuperContig_29_v2 100993 102531 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -267 lm_SuperContig_29_v2 41079 42287 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -268 lm_SuperContig_29_v2 167371 168579 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -269 lm_SuperContig_29_v2 16081 17289 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -270 lm_SuperContig_29_v2 91693 92700 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -271 lm_SuperContig_29_v2 178395 179504 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -272 lm_SuperContig_29_v2 10747 11856 SPAC26A3.13c |Tf2-4||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -273 lm_SuperContig_29_v2 78133 78570 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 97 242 3e-30 115 39.04 -273 lm_SuperContig_29_v2 78662 78799 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 249 292 3e-30 37 42.55 -274 lm_SuperContig_29_v2 193784 194221 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 242 97 2e-55 115 39.04 -274 lm_SuperContig_29_v2 192874 193692 SPBC16A3.17c |||membrane transporter|Schizosaccharomyces pombe|chr 2|||Manual 518 249 2e-55 124 27.37 -275 lm_SuperContig_29_v2 77950 78588 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 34 242 8e-30 114 30.99 -275 lm_SuperContig_29_v2 78662 78736 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 243 267 8e-30 37 52 -276 lm_SuperContig_29_v2 193766 194404 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 242 34 3e-53 114 30.99 -276 lm_SuperContig_29_v2 192844 193692 SPAC1399.02 |||membrane transporter|Schizosaccharomyces pombe|chr 1|||Manual 525 243 3e-53 118 30.8 -277 lm_SuperContig_29_v2 133471 134754 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -277 lm_SuperContig_29_v2 133341 133436 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -278 lm_SuperContig_29_v2 100993 102531 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -279 lm_SuperContig_29_v2 41079 42287 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -280 lm_SuperContig_29_v2 167371 168579 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -281 lm_SuperContig_29_v2 16081 17289 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -282 lm_SuperContig_29_v2 91693 92700 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -283 lm_SuperContig_29_v2 178395 179504 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -284 lm_SuperContig_29_v2 10747 11856 SPAC2E1P3.03c |Tf2-3||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -285 lm_SuperContig_29_v2 133471 134754 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 2e-46 184 28.54 -285 lm_SuperContig_29_v2 133341 133436 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 2e-46 27 46.88 -286 lm_SuperContig_29_v2 100993 102531 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 3e-44 183 27.86 -287 lm_SuperContig_29_v2 41079 42287 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 3e-42 176 28.89 -288 lm_SuperContig_29_v2 167371 168579 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 8e-43 175 29.38 -289 lm_SuperContig_29_v2 16081 17289 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-39 166 28.15 -290 lm_SuperContig_29_v2 91693 92700 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 1e-37 161 32.94 -291 lm_SuperContig_29_v2 178395 179504 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-37 160 30.91 -292 lm_SuperContig_29_v2 10747 11856 SPAC19D5.09c |Tf2-8|SPAC13D1.02c|retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-36 157 31.18 -293 lm_SuperContig_29_v2 133471 134754 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -293 lm_SuperContig_29_v2 133341 133436 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -294 lm_SuperContig_29_v2 100993 102531 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -295 lm_SuperContig_29_v2 41079 42287 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -296 lm_SuperContig_29_v2 167371 168579 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -297 lm_SuperContig_29_v2 16081 17289 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -298 lm_SuperContig_29_v2 91693 92700 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -299 lm_SuperContig_29_v2 178395 179504 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -300 lm_SuperContig_29_v2 10747 11856 SPAC27E2.08 |Tf2-6||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -301 lm_SuperContig_29_v2 133471 134754 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 2e-46 184 28.54 -301 lm_SuperContig_29_v2 133341 133436 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 2e-46 27 46.88 -302 lm_SuperContig_29_v2 100993 102531 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 3e-44 183 27.86 -303 lm_SuperContig_29_v2 41079 42287 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 3e-42 176 28.89 -304 lm_SuperContig_29_v2 167371 168579 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 8e-43 175 29.38 -305 lm_SuperContig_29_v2 16081 17289 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-39 166 28.15 -306 lm_SuperContig_29_v2 91693 92700 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 1e-37 161 32.94 -307 lm_SuperContig_29_v2 178395 179504 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-37 160 30.91 -308 lm_SuperContig_29_v2 10747 11856 SPAC13D1.01c |Tf2-7||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 1e-36 157 31.18 -309 lm_SuperContig_29_v2 133471 134754 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 358 4e-46 183 28.31 -309 lm_SuperContig_29_v2 133341 133436 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 800 4e-46 27 46.88 -310 lm_SuperContig_29_v2 100993 102531 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 312 7e-44 182 27.67 -311 lm_SuperContig_29_v2 41079 42287 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 7e-42 175 28.64 -312 lm_SuperContig_29_v2 167371 168579 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 2e-42 174 29.14 -313 lm_SuperContig_29_v2 16081 17289 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 831 427 4e-39 165 27.9 -314 lm_SuperContig_29_v2 91693 92700 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 452 3e-37 159 32.64 -315 lm_SuperContig_29_v2 178395 179504 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 3e-37 158 30.65 -316 lm_SuperContig_29_v2 10747 11856 SPBC9B6.02c |Tf2-9|SPBC9B6.02|retrotransposable element|Schizosaccharomyces pombe|chr 2|||Manual 786 418 3e-36 155 30.91 -317 lm_SuperContig_29_v2 133471 134754 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 358 4e-46 183 28.31 -317 lm_SuperContig_29_v2 133341 133436 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 800 4e-46 27 46.88 -318 lm_SuperContig_29_v2 100993 102531 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 312 7e-44 182 27.67 -319 lm_SuperContig_29_v2 41079 42287 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 7e-42 175 28.64 -320 lm_SuperContig_29_v2 167371 168579 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 2e-42 174 29.14 -321 lm_SuperContig_29_v2 16081 17289 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 831 427 4e-39 165 27.9 -322 lm_SuperContig_29_v2 91693 92700 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 452 3e-37 159 32.64 -323 lm_SuperContig_29_v2 178395 179504 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-37 158 30.65 -324 lm_SuperContig_29_v2 10747 11856 SPAC9.04 |Tf2-1||retrotransposable element|Schizosaccharomyces pombe|chr 1|||Manual 786 418 3e-36 155 30.91 -325 lm_SuperContig_29_v2 77980 78567 um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17 18 211 5e-25 114 31 -326 lm_SuperContig_29_v2 193787 194374 um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17 211 18 2e-42 114 31 -326 lm_SuperContig_29_v2 192772 193695 um00679 related to VBA1 - Vacuolar Basic Amino acid transporter, Contig um_contig_1.17 529 218 2e-42 82 20.7 -327 lm_SuperContig_29_v2 78115 78588 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 53 210 2e-53 183 55.06 -327 lm_SuperContig_29_v2 78662 78814 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 211 264 2e-53 47 44.44 -328 lm_SuperContig_29_v2 193766 194239 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 210 53 2e-104 183 55.06 -328 lm_SuperContig_29_v2 192760 193692 um00842 probable aflatoxin efflux pump AFLT, Contig um_contig_1.27 534 211 2e-104 220 36.92 -329 lm_SuperContig_29_v2 78112 78570 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 94 246 7e-23 104 35.95 -329 lm_SuperContig_29_v2 78659 78802 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 253 297 7e-23 24 25 -330 lm_SuperContig_29_v2 193784 194242 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 246 94 5e-40 104 35.95 -330 lm_SuperContig_29_v2 192760 193695 um01882 related to multidrug resistance proteins, Contig um_contig_1.70 560 253 5e-40 84 19.43 -331 lm_SuperContig_29_v2 78019 78567 um01964 related to multidrug resistance protein, Contig um_contig_1.72 40 220 1e-24 113 33.7 -332 lm_SuperContig_29_v2 193787 194335 um01964 related to multidrug resistance protein, Contig um_contig_1.72 220 40 7e-43 113 33.7 -332 lm_SuperContig_29_v2 192901 193695 um01964 related to multidrug resistance protein, Contig um_contig_1.72 490 227 7e-43 85 24.16 -333 lm_SuperContig_29_v2 77890 78591 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 38 263 1e-32 115 32.07 -333 lm_SuperContig_29_v2 78659 78814 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 264 313 1e-32 46 36.54 -334 lm_SuperContig_29_v2 193763 194464 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 263 38 1e-65 115 32.07 -334 lm_SuperContig_29_v2 192760 193695 um02062 related to multidrug resistance proteins, Contig um_contig_1.75 575 264 1e-65 158 30.6 -335 lm_SuperContig_29_v2 78136 78576 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 133 280 1e-21 91 30.41 -335 lm_SuperContig_29_v2 78650 78814 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 280 331 1e-21 33 29.09 -336 lm_SuperContig_29_v2 193778 194218 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 280 133 3e-45 91 30.41 -336 lm_SuperContig_29_v2 192754 193704 um02598 related to mfs1 - putative multidrug transporter, Contig um_contig_1.86 598 280 3e-45 114 25.93 -337 lm_SuperContig_29_v2 77938 78585 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 27 239 2e-24 93 30.73 -337 lm_SuperContig_29_v2 78650 78808 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 236 285 2e-24 40 33.96 -338 lm_SuperContig_29_v2 193769 194416 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 239 27 1e-48 93 30.73 -338 lm_SuperContig_29_v2 192757 193704 um03115 related to Sge1 - drug resistance protein, Contig um_contig_1.105 554 236 1e-48 124 25.7 -339 lm_SuperContig_29_v2 77938 78576 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 13 215 4e-45 167 39.91 -339 lm_SuperContig_29_v2 78650 78736 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 216 244 4e-45 36 55.17 -340 lm_SuperContig_29_v2 193778 194416 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 215 13 2e-98 167 39.91 -340 lm_SuperContig_29_v2 192826 193704 um05414 probable aflatoxin efflux pump AFLT, Contig um_contig_1.192 511 216 2e-98 216 37.04 -341 lm_SuperContig_29_v2 193778 194107 um05421 related to Multidrug resistance protein , Contig um_contig_1.192 267 158 6e-41 83 35.45 -341 lm_SuperContig_29_v2 193006 193692 um05421 related to Multidrug resistance protein , Contig um_contig_1.192 496 272 6e-41 107 27.07 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.tab --- a/commons/pyRepetUnit/components/blastx2GFF/tests/datas/lm_supctg_v2_29_30_vs_BlastBank.align.match.tab Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,342 +0,0 @@ -query.name query.start query.end query.length query.length.% match.length.% subject.name subject.start subject.end subject.length subject.length.% E.value Score Identity path -lm_SuperContig_30_v2 35498 37823 927 0.00598594 1.29469 mito_010 307 663 309 0.431564 8e-67 424 74.4336 1 -lm_SuperContig_30_v2 27615 29673 558 0.00360318 0.77933 mito_010 109 310 186 0.259777 1e-53 244 82.2577 2 -lm_SuperContig_30_v2 23817 24089 273 0.00176285 0.381285 mito_010 1 91 91 0.127095 7e-25 119 63.74 3 -lm_SuperContig_30_v2 27615 29418 1125 0.00726449 2.06044 mito_020 109 540 367 0.672161 1e-53 329 53.6941 4 -lm_SuperContig_30_v2 94306 95085 780 0.00503671 1.42857 mito_020 544 279 266 0.487179 2e-22 110 28.46 5 -lm_SuperContig_30_v2 23817 24089 273 0.00176285 0.5 mito_020 1 91 91 0.166667 7e-25 119 63.74 6 -lm_SuperContig_30_v2 23817 27509 1593 0.0102865 2.98315 mito_030 1 525 525 0.983146 0 680 74.3298 7 -lm_SuperContig_30_v2 61805 62656 852 0.00550164 1.59551 mito_030 528 241 288 0.539326 3e-55 219 38.89 8 -lm_SuperContig_30_v2 146223 147503 1281 0.00827183 2.39888 mito_030 114 528 415 0.777154 2e-64 250 37.61 9 -lm_SuperContig_30_v2 109092 109925 834 0.00538541 1.5618 mito_030 525 243 283 0.529963 2e-49 200 38.16 10 -lm_SuperContig_30_v2 117965 119308 1344 0.00867864 2.51685 mito_030 87 525 439 0.822097 1e-63 248 35.79 11 -lm_SuperContig_30_v2 82749 83615 867 0.0055985 1.6236 mito_030 525 236 290 0.543071 3e-47 193 35.27 12 -lm_SuperContig_30_v2 35963 37213 1251 0.00807811 2.3427 mito_030 114 525 412 0.771536 4e-62 242 38.08 13 -lm_SuperContig_30_v2 86928 87770 843 0.00544352 1.57865 mito_030 525 242 284 0.531835 3e-47 193 36.14 14 -lm_SuperContig_30_v2 116645 117925 1281 0.00827183 2.39888 mito_030 121 526 406 0.7603 6e-60 235 37.12 15 -lm_SuperContig_30_v2 80861 81706 846 0.00546289 1.58427 mito_030 525 242 284 0.531835 5e-44 182 35.66 16 -lm_SuperContig_30_v2 150994 152199 1206 0.00778753 2.25843 mito_030 121 525 405 0.758427 4e-58 229 36.3 17 -lm_SuperContig_30_v2 55780 56582 699 0.00451367 1.30899 mito_030 492 255 233 0.43633 1e-34 118 37.7177 18 -lm_SuperContig_30_v2 18181 19317 1137 0.00734197 2.12921 mito_030 167 528 362 0.677903 3e-57 226 37.76 19 -lm_SuperContig_30_v2 90399 91238 840 0.00542415 1.57303 mito_030 528 249 280 0.524345 1e-37 161 32.52 20 -lm_SuperContig_30_v2 141039 141858 820 0.005295 1.53558 mito_030 250 525 276 0.516854 8e-47 212 39.6261 21 -lm_SuperContig_30_v2 63837 64676 840 0.00542415 1.57303 mito_030 511 232 280 0.524345 1e-35 155 35.21 22 -lm_SuperContig_30_v2 115228 116103 876 0.00565661 1.64045 mito_030 236 528 293 0.548689 6e-48 195 35.93 23 -lm_SuperContig_30_v2 149559 150444 882 0.00569536 1.65169 mito_030 233 530 296 0.554307 6e-40 189 36.7922 24 -lm_SuperContig_30_v2 22437 23375 939 0.00606342 1.75843 mito_030 219 528 310 0.580524 1e-43 181 32.59 25 -lm_SuperContig_30_v2 32527 33390 864 0.00557912 1.61798 mito_030 236 518 283 0.529963 6e-40 169 36.15 26 -lm_SuperContig_30_v2 21984 22220 237 0.00153038 2.63333 mito_040 1 79 79 0.877778 3e-30 136 84.81 27 -lm_SuperContig_30_v2 21984 23387 1125 0.00726449 2.48344 mito_050 1 438 376 0.830022 7e-81 419 56.4194 28 -lm_SuperContig_30_v2 61793 62650 858 0.00554038 1.89404 mito_050 438 145 294 0.649007 3e-49 200 40.33 29 -lm_SuperContig_30_v2 18466 19329 864 0.00557912 1.90728 mito_050 145 438 294 0.649007 6e-54 215 40.53 30 -lm_SuperContig_30_v2 80849 81703 855 0.00552101 1.88742 mito_050 435 145 291 0.642384 1e-45 188 39.6 31 -lm_SuperContig_30_v2 36323 37234 912 0.00588908 2.01325 mito_050 145 438 294 0.649007 4e-49 199 40.39 32 -lm_SuperContig_30_v2 82737 83594 858 0.00554038 1.89404 mito_050 435 145 291 0.642384 1e-45 188 37.46 33 -lm_SuperContig_30_v2 149583 150450 868 0.00560495 1.91611 mito_050 145 438 294 0.649007 3e-39 188 37.5948 34 -lm_SuperContig_30_v2 63768 64748 981 0.00633463 2.16556 mito_050 438 111 328 0.724062 4e-45 186 37.09 35 -lm_SuperContig_30_v2 118442 119320 879 0.00567598 1.9404 mito_050 145 435 291 0.642384 3e-44 183 38.64 36 -lm_SuperContig_30_v2 86916 87767 852 0.00550164 1.88079 mito_050 435 145 291 0.642384 4e-45 186 36.49 37 -lm_SuperContig_30_v2 26661 27530 870 0.00561787 1.92053 mito_050 145 438 294 0.649007 1e-43 181 35.67 38 -lm_SuperContig_30_v2 109071 109925 855 0.00552101 1.88742 mito_050 438 145 294 0.649007 7e-42 175 35.67 39 -lm_SuperContig_30_v2 115249 116115 867 0.0055985 1.91391 mito_050 145 438 294 0.649007 1e-43 181 38.41 40 -lm_SuperContig_30_v2 90387 91259 873 0.00563724 1.92715 mito_050 438 144 295 0.651214 2e-39 167 33.33 41 -lm_SuperContig_30_v2 32542 33390 849 0.00548226 1.87417 mito_050 145 424 280 0.618102 6e-43 179 38.91 42 -lm_SuperContig_30_v2 141021 141879 825 0.00532729 1.82119 mito_050 146 438 281 0.620309 6e-38 179 39.9318 43 -lm_SuperContig_30_v2 117050 117943 894 0.00577284 1.97351 mito_050 145 438 294 0.649007 1e-42 178 37.62 44 -lm_SuperContig_30_v2 146610 147515 906 0.00585033 2 mito_050 149 438 290 0.640177 4e-37 159 34.18 45 -lm_SuperContig_30_v2 151234 152220 987 0.00637338 2.17881 mito_050 118 438 321 0.708609 2e-35 154 34.72 46 -lm_SuperContig_30_v2 53343 53696 354 0.00228589 2.39189 mito_060 117 1 117 0.790541 2e-26 121 50 47 -lm_SuperContig_30_v2 5079 5582 504 0.00325449 0.863014 mito_080 403 582 180 0.308219 7e-41 172 49.73 48 -lm_SuperContig_30_v2 53703 59799 1782 0.0115069 3.05137 mito_080 582 1 581 0.994863 1e-68 218 52.6717 49 -lm_SuperContig_30_v2 64707 65165 459 0.00296391 1.7 mito_110 227 74 154 0.57037 2e-55 220 68.18 50 -lm_SuperContig_30_v2 108494 110387 579 0.00373879 2.20992 mito_150 179 6 174 0.664122 2e-31 150 62.5893 51 -lm_SuperContig_30_v2 103508 103711 204 0.00131729 0.778626 mito_150 261 194 68 0.259542 7e-26 122 85.29 52 -lm_SuperContig_30_v2 17614 20481 1458 0.00941477 2.68015 mito_170 83 536 454 0.834559 3e-130 620 68.5109 53 -lm_SuperContig_30_v2 17614 19341 1728 0.0111582 2.58296 mito_180 83 666 584 0.872945 0 664 57.81 54 -lm_SuperContig_30_v2 61781 62653 873 0.00563724 1.30493 mito_180 666 371 296 0.442451 3e-63 246 42.62 55 -lm_SuperContig_30_v2 32542 33390 849 0.00548226 1.26906 mito_180 372 648 277 0.414051 6e-64 248 44.14 56 -lm_SuperContig_30_v2 82716 83615 900 0.00581159 1.34529 mito_180 666 365 302 0.45142 1e-60 237 41.45 57 -lm_SuperContig_30_v2 36329 37252 924 0.00596656 1.38117 mito_180 374 668 295 0.440957 2e-62 243 43.91 58 -lm_SuperContig_30_v2 109059 109979 921 0.00594719 1.37668 mito_180 666 354 313 0.467862 3e-58 229 37.7 59 -lm_SuperContig_30_v2 141030 141897 868 0.00560495 1.29746 mito_180 376 668 293 0.437967 3e-54 237 42.1346 60 -lm_SuperContig_30_v2 80825 81706 882 0.00569536 1.31839 mito_180 667 371 297 0.443946 1e-57 228 41.28 61 -lm_SuperContig_30_v2 149580 150465 886 0.00572119 1.32436 mito_180 371 667 297 0.443946 7e-54 237 40.2095 62 -lm_SuperContig_30_v2 63756 64718 963 0.0062184 1.43946 mito_180 666 347 320 0.478326 2e-57 227 42.25 63 -lm_SuperContig_30_v2 115189 116127 939 0.00606342 1.40359 mito_180 352 666 315 0.470852 8e-59 231 37.85 64 -lm_SuperContig_30_v2 86895 87770 876 0.00565661 1.30942 mito_180 666 371 296 0.442451 4e-57 226 41.47 65 -lm_SuperContig_30_v2 22509 23405 897 0.00579222 1.34081 mito_180 372 668 297 0.443946 3e-57 226 39 66 -lm_SuperContig_30_v2 90384 91256 873 0.00563724 1.30493 mito_180 663 372 292 0.436472 4e-43 179 32.55 67 -lm_SuperContig_30_v2 118439 119344 906 0.00585033 1.35426 mito_180 371 667 297 0.443946 3e-54 216 41.56 68 -lm_SuperContig_30_v2 55774 56585 705 0.00455241 1.05381 mito_180 624 383 236 0.352765 9e-27 90 36.6049 69 -lm_SuperContig_30_v2 117050 117955 906 0.00585033 1.35426 mito_180 372 666 295 0.440957 9e-54 215 41.5 70 -lm_SuperContig_30_v2 26640 27542 903 0.00583096 1.34978 mito_180 365 666 302 0.45142 9e-53 211 40.46 71 -lm_SuperContig_30_v2 151309 152232 924 0.00596656 1.38117 mito_180 369 666 298 0.445441 3e-50 203 40.76 72 -lm_SuperContig_30_v2 146610 147527 918 0.00592782 1.3722 mito_180 376 666 291 0.434978 6e-48 195 39.23 73 -lm_SuperContig_30_v2 42209 42879 603 0.00389376 0.901345 mito_180 319 528 207 0.309417 2e-21 123 35.1266 74 -lm_SuperContig_30_v2 125743 126138 396 0.0025571 0.591928 mito_180 384 515 132 0.197309 4e-23 113 41.67 75 -lm_SuperContig_30_v2 44197 47305 819 0.00528855 2.20161 mito_190 98 370 273 0.733871 5e-44 248 66.386 76 -lm_SuperContig_30_v2 102101 102604 504 0.00325449 0.903226 mito_210 169 2 168 0.301075 4e-74 282 80.36 77 -lm_SuperContig_30_v2 89139 94202 822 0.00530792 1.47312 mito_210 533 250 274 0.491039 6e-51 151 75.9144 78 -lm_SuperContig_30_v2 14626 15192 567 0.0036613 1.46512 mito_220 194 384 191 0.49354 8e-78 295 73.82 79 -lm_SuperContig_30_v2 15860 16315 456 0.00294454 1.17829 mito_220 228 384 157 0.405685 3e-37 160 56.25 80 -lm_SuperContig_30_v2 9733 9936 204 0.00131729 0.527132 mito_220 68 136 69 0.178295 2e-27 127 89.86 81 -lm_SuperContig_30_v2 6405 6605 201 0.00129792 0.51938 mito_220 1 67 67 0.173127 2e-23 114 76.12 82 -lm_SuperContig_30_v2 9733 9936 204 0.00131729 0.425887 mito_230 68 136 69 0.14405 2e-27 127 89.86 83 -lm_SuperContig_30_v2 6405 6605 201 0.00129792 0.419624 mito_230 1 67 67 0.139875 2e-23 114 76.12 84 -lm_SuperContig_30_v2 9733 9927 195 0.00125918 0.434298 mito_240 68 132 65 0.144766 6e-27 126 90.77 85 -lm_SuperContig_30_v2 6405 6605 201 0.00129792 0.447661 mito_240 1 67 67 0.14922 2e-23 114 76.12 86 -lm_SuperContig_30_v2 18442 19341 900 0.00581159 2.47934 mito_155 56 357 302 0.831956 3e-68 263 45.07 87 -lm_SuperContig_30_v2 109056 110081 1026 0.00662521 2.82645 mito_155 358 11 348 0.958678 4e-91 338 51.85 88 -lm_SuperContig_30_v2 36323 37249 927 0.00598594 2.55372 mito_155 64 358 295 0.812672 2e-63 247 45.02 89 -lm_SuperContig_30_v2 61781 62650 870 0.00561787 2.39669 mito_155 357 64 294 0.809917 2e-58 230 41.75 90 -lm_SuperContig_30_v2 141021 141891 871 0.00562433 2.39945 mito_155 65 357 293 0.807163 2e-51 228 40.9341 91 -lm_SuperContig_30_v2 80828 81703 876 0.00565661 2.41322 mito_155 357 64 294 0.809917 3e-51 206 39.6 92 -lm_SuperContig_30_v2 149583 150462 880 0.00568244 2.42424 mito_155 64 357 294 0.809917 6e-49 220 40.1497 93 -lm_SuperContig_30_v2 82716 83594 879 0.00567598 2.42149 mito_155 357 64 294 0.809917 1e-50 204 38.8 94 -lm_SuperContig_30_v2 116981 117955 975 0.00629589 2.68595 mito_155 36 357 322 0.887052 4e-53 213 37.01 95 -lm_SuperContig_30_v2 86895 87767 873 0.00563724 2.40496 mito_155 357 64 294 0.809917 7e-50 202 37.92 96 -lm_SuperContig_30_v2 146610 147533 924 0.00596656 2.54545 mito_155 68 359 292 0.804408 2e-52 210 42.22 97 -lm_SuperContig_30_v2 63756 64655 900 0.00581159 2.47934 mito_155 357 60 298 0.820937 1e-47 194 38.64 98 -lm_SuperContig_30_v2 151258 152232 975 0.00629589 2.68595 mito_155 42 357 316 0.870523 2e-52 210 39.34 99 -lm_SuperContig_30_v2 90381 91256 876 0.00565661 2.41322 mito_155 355 64 292 0.804408 8e-32 142 31 100 -lm_SuperContig_30_v2 32494 33504 1011 0.00652835 2.78512 mito_155 46 360 315 0.867769 4e-52 209 37.64 101 -lm_SuperContig_30_v2 115198 116127 930 0.00600531 2.56198 mito_155 47 357 311 0.856749 1e-50 204 37.78 102 -lm_SuperContig_30_v2 26607 27542 936 0.00604405 2.57851 mito_155 46 357 312 0.859504 7e-50 202 37.34 103 -lm_SuperContig_30_v2 118442 119341 900 0.00581159 2.47934 mito_155 64 357 294 0.809917 7e-42 175 35.5 104 -lm_SuperContig_30_v2 22509 23387 879 0.00567598 2.42149 mito_155 64 353 290 0.798898 2e-37 161 31.19 105 -lm_SuperContig_30_v2 125740 126240 501 0.00323512 1.38017 mito_155 75 237 163 0.449036 3e-30 136 46.11 106 -lm_SuperContig_30_v2 44996 45911 771 0.00497859 2.52787 mito_195 39 300 260 0.852459 3e-48 295 58.0837 107 -lm_SuperContig_30_v2 46058 46769 711 0.00459115 2.33115 mito_195 44 304 261 0.855738 1e-70 293 56.8997 108 -lm_SuperContig_30_v2 14662 15189 528 0.00340947 1.36434 SPMIT.05 206 381 176 0.45478 1e-42 178 48.86 109 -lm_SuperContig_30_v2 15941 16303 363 0.00234401 0.937984 SPMIT.05 260 378 119 0.307494 1e-22 111 48.76 110 -lm_SuperContig_30_v2 64752 65204 453 0.00292517 1.65934 SPMIT.04 215 65 151 0.553114 2e-34 150 50.98 111 -lm_SuperContig_30_v2 94345 95262 918 0.00592782 2.84211 SPMIT.03 312 3 310 0.959752 1e-94 350 57.68 112 -lm_SuperContig_30_v2 102098 102580 483 0.00311889 0.899441 SPMIT.01 171 10 162 0.301676 3e-48 196 54.94 113 -lm_SuperContig_30_v2 93876 94202 327 0.00211154 0.608939 SPMIT.01 360 251 110 0.204842 3e-30 136 58.56 114 -lm_SuperContig_29_v2 77989 78369 381 0.00189609 1.99476 Afu3g02110 3 126 124 0.649215 2e-22 105 40.94 115 -lm_SuperContig_29_v2 193985 194365 381 0.00189609 1.99476 Afu3g02110 126 3 124 0.649215 1e-21 105 40.94 116 -lm_SuperContig_29_v2 78109 78817 630 0.00313526 1.14964 Afu3g01520 20 231 210 0.383212 7e-59 244 51.9044 117 -lm_SuperContig_29_v2 192760 194245 1407 0.00700209 2.56752 Afu3g01520 485 20 464 0.846715 2e-128 384 47.5473 118 -lm_SuperContig_29_v2 78010 78808 705 0.00350851 1.20926 Afu3g02520 21 261 234 0.401372 5e-23 122 29.1103 119 -lm_SuperContig_29_v2 192766 194344 1485 0.00739027 2.54717 Afu3g02520 535 21 508 0.871355 3e-40 83 25.258 120 -lm_SuperContig_29_v2 78109 78817 636 0.00316512 1.10035 Afu3g02720 45 258 214 0.370242 1e-39 180 44.2062 121 -lm_SuperContig_29_v2 192754 194245 1419 0.00706181 2.45502 Afu3g02720 521 45 477 0.82526 2e-83 234 36.8547 122 -lm_SuperContig_29_v2 78061 78814 666 0.00331442 1.19784 Afu6g03320 15 242 223 0.401079 3e-22 121 31.8947 123 -lm_SuperContig_29_v2 192760 194293 1446 0.00719618 2.60072 Afu6g03320 506 15 487 0.875899 1e-49 119 28.5099 124 -lm_SuperContig_29_v2 78007 78817 726 0.00361302 1.13972 Afu6g02220 48 293 242 0.379906 2e-59 245 47.1079 125 -lm_SuperContig_29_v2 193288 194347 975 0.00485219 1.53061 Afu6g02220 375 48 324 0.508634 1e-79 251 45.8455 126 -lm_SuperContig_29_v2 78133 78817 600 0.00298597 1.02389 Afu8g00940 77 282 202 0.34471 2e-44 195 48.6772 127 -lm_SuperContig_29_v2 192760 194221 1377 0.00685279 2.34983 Afu8g00940 541 77 461 0.786689 3e-91 263 40.7123 128 -lm_SuperContig_29_v2 133669 134343 675 0.00335921 1.80481 Afu4g02630 226 2 225 0.601604 3e-37 159 37.78 129 -lm_SuperContig_29_v2 167776 168372 597 0.00297104 1.59626 Afu4g02630 200 2 199 0.532086 9e-34 145 38.69 130 -lm_SuperContig_29_v2 41484 42080 597 0.00297104 1.59626 Afu4g02630 200 2 199 0.532086 8e-32 142 38.69 131 -lm_SuperContig_29_v2 101404 102000 597 0.00297104 1.59626 Afu4g02630 200 2 199 0.532086 3e-31 140 38.69 132 -lm_SuperContig_29_v2 31597 32272 645 0.00320991 1.7246 Afu4g02630 229 4 216 0.57754 6e-25 96 36.7377 133 -lm_SuperContig_29_v2 16462 17082 621 0.00309047 1.66043 Afu4g02630 208 2 207 0.553476 4e-30 135 37.2 134 -lm_SuperContig_29_v2 178590 179264 675 0.00335921 1.80481 Afu4g02630 229 4 226 0.604278 1e-29 133 35.96 135 -lm_SuperContig_29_v2 10942 11625 684 0.003404 1.82888 Afu4g02630 229 1 229 0.612299 2e-29 132 35.06 136 -lm_SuperContig_29_v2 91888 92562 675 0.00335921 1.80481 Afu4g02630 229 4 226 0.604278 3e-27 126 35.53 137 -lm_SuperContig_29_v2 78184 78814 573 0.0028516 1.06903 Afu4g03920 53 239 187 0.348881 2e-25 134 36.6457 138 -lm_SuperContig_29_v2 192964 194170 1149 0.00571812 2.14366 Afu4g03920 430 53 378 0.705224 3e-59 173 35.5056 139 -lm_SuperContig_29_v2 78049 78775 636 0.00316512 1.16912 Afu6g09110 19 236 212 0.389706 3e-23 124 27.8346 140 -lm_SuperContig_29_v2 192904 194305 1311 0.00652434 2.40993 Afu6g09110 459 19 435 0.799632 9e-43 105 26.7653 141 -lm_SuperContig_29_v2 78151 78814 579 0.00288146 0.969849 Afu6g14640 93 293 195 0.326633 3e-31 151 39.0031 142 -lm_SuperContig_29_v2 192760 194203 1359 0.00676321 2.27638 Afu6g14640 552 93 454 0.760469 6e-83 236 35.5958 143 -lm_SuperContig_29_v2 78109 78814 633 0.00315019 1.16575 Afu6g09710 34 245 212 0.390424 3e-49 213 46.2751 144 -lm_SuperContig_29_v2 192772 194245 1401 0.00697223 2.58011 Afu6g09710 501 34 468 0.861878 2e-97 282 38.1927 145 -lm_SuperContig_29_v2 78115 78817 618 0.00307554 1.09381 Afu5g01540 51 260 206 0.364602 6e-62 254 53.8812 146 -lm_SuperContig_29_v2 192754 194239 1401 0.00697223 2.47965 Afu5g01540 520 51 466 0.824779 1e-132 399 48.6076 147 -lm_SuperContig_29_v2 192868 194323 1368 0.006808 2.44286 Afu2g15140 482 16 462 0.825 1e-31 63 22.8695 148 -lm_SuperContig_29_v2 193303 194221 834 0.00415049 1.86161 fg00095 308 27 278 0.620536 6e-29 91 30.5342 149 -lm_SuperContig_29_v2 192877 194221 1257 0.0062556 2.19755 fg12051 483 60 415 0.725524 7e-40 99 25.302 150 -lm_SuperContig_29_v2 77956 78814 786 0.00391162 1.29917 fg12074 2 272 271 0.447934 7e-35 164 34.313 151 -lm_SuperContig_29_v2 192883 194398 1443 0.00718125 2.38512 fg12074 490 2 489 0.808264 7e-62 161 31.3733 152 -lm_SuperContig_29_v2 78124 78718 510 0.00253807 0.882353 fg12335 62 236 171 0.295848 4e-45 197 53.7372 153 -lm_SuperContig_29_v2 192769 194230 1377 0.00685279 2.38235 fg12335 537 62 472 0.816609 1e-92 266 39.0941 154 -lm_SuperContig_29_v2 193222 194383 1092 0.00543446 1.81697 fg12717 402 15 388 0.645591 2e-26 65 25.4717 155 -lm_SuperContig_29_v2 193036 194248 1125 0.00559869 1.9198 b13o8_150 460 73 383 0.653584 3e-31 78 25.3216 156 -lm_SuperContig_29_v2 78010 78814 747 0.00371753 1.28571 b18d24_100 9 250 242 0.416523 2e-27 139 31.3225 157 -lm_SuperContig_29_v2 192916 194344 1371 0.00682293 2.35972 b18d24_100 457 9 449 0.772806 4e-60 160 31.5064 158 -lm_SuperContig_29_v2 78184 78814 546 0.00271723 0.767932 b5k2_230 211 396 182 0.255977 4e-42 187 50.0101 159 -lm_SuperContig_29_v2 192760 194170 1326 0.00659898 1.86498 b5k2_230 657 211 443 0.623066 7e-99 291 41.7395 160 -lm_SuperContig_29_v2 192832 194212 1305 0.00649448 2.13934 1nc550_030 522 85 438 0.718033 1e-40 99 26.1649 161 -lm_SuperContig_29_v2 77941 78736 711 0.00353837 1.13942 1nc570_120 28 270 239 0.383013 1e-30 148 31.8213 162 -lm_SuperContig_29_v2 192760 194413 1569 0.0078083 2.51442 1nc570_120 559 28 528 0.846154 5e-62 151 28.5716 163 -lm_SuperContig_29_v2 192817 194086 1188 0.00591221 1.8193 6nc360_090 491 86 401 0.614089 8e-44 117 31.4828 164 -lm_SuperContig_29_v2 78112 78817 621 0.00309047 0.885877 29e8_240 62 272 207 0.295292 1e-56 235 51.6868 165 -lm_SuperContig_29_v2 192769 194242 1389 0.00691251 1.98146 29e8_240 535 62 470 0.670471 2e-117 349 45.9406 166 -lm_SuperContig_29_v2 192940 194218 1188 0.00591221 2.05536 7nc450_010 484 78 401 0.693772 3e-24 52 23.4836 167 -lm_SuperContig_29_v2 192865 194218 1266 0.00630039 1.15196 4nc446_010 530 106 420 0.382166 3e-48 127 28.7686 168 -lm_SuperContig_29_v2 192904 194239 1275 0.00634518 2.12146 b11e5_230 518 97 422 0.702163 1e-40 102 26.9355 169 -lm_SuperContig_29_v2 77935 78817 798 0.00397133 1.34343 xnc126_050 38 298 257 0.43266 7e-60 247 45.7009 170 -lm_SuperContig_29_v2 192757 194419 1578 0.00785309 2.65657 xnc126_050 559 38 518 0.872054 2e-130 380 45.5601 171 -lm_SuperContig_29_v2 78109 78817 624 0.0031054 1.16636 4nc135_070 17 238 218 0.407477 2e-53 225 50.065 172 -lm_SuperContig_29_v2 192751 194245 1410 0.00701702 2.63551 4nc135_070 494 17 474 0.885981 4e-99 286 40.8958 173 -lm_SuperContig_29_v2 78031 78588 558 0.00277695 0.980668 xnc164_090 19 209 191 0.335677 3e-21 101 30.89 174 -lm_SuperContig_29_v2 192802 194323 1449 0.00721111 2.54657 xnc164_090 509 19 491 0.862917 1e-42 95 28.3566 175 -lm_SuperContig_29_v2 192916 194107 1131 0.00562855 2.38608 YBR293w 384 6 379 0.799578 3e-23 53 24.6367 176 -lm_SuperContig_29_v2 192985 193954 885 0.0044043 1.93231 YCL069w 335 3 329 0.718341 7e-28 82 30.228 177 -lm_SuperContig_29_v2 197024 197422 399 0.00198567 1.21646 YDL037c 298 166 133 0.405488 5e-24 113 45.52 178 -lm_SuperContig_29_v2 197027 197413 387 0.00192595 1.17988 YDL037c 292 164 129 0.393293 2e-23 111 46.56 179 -lm_SuperContig_29_v2 197039 197437 399 0.00198567 1.21646 YDL037c 310 170 141 0.429878 2e-22 108 46.1 180 -lm_SuperContig_29_v2 197021 197416 396 0.00197074 1.20732 YDL037c 282 151 132 0.402439 3e-22 107 39.39 181 -lm_SuperContig_29_v2 40143 42272 2130 0.0106002 1.37686 YGR109w-b 1301 616 686 0.443439 6e-39 165 26.47 182 -lm_SuperContig_29_v2 16081 17274 1194 0.00594207 0.771816 YGR109w-b 1008 616 393 0.25404 4e-35 152 30.33 183 -lm_SuperContig_29_v2 100993 102192 1200 0.00597193 0.775695 YGR109w-b 1008 616 393 0.25404 8e-35 151 30.92 184 -lm_SuperContig_29_v2 167371 168564 1194 0.00594207 0.771816 YGR109w-b 1008 616 393 0.25404 2e-35 151 30.83 185 -lm_SuperContig_29_v2 133543 134535 993 0.00494177 0.641888 YGR109w-b 943 616 328 0.212023 4e-34 149 32.23 186 -lm_SuperContig_29_v2 91762 92754 993 0.00494177 0.641888 YGR109w-b 944 618 327 0.211377 4e-23 113 30.24 187 -lm_SuperContig_29_v2 178464 179477 1014 0.00504628 0.655462 YGR109w-b 944 611 334 0.215902 1e-21 107 29.03 188 -lm_SuperContig_29_v2 78139 78724 507 0.00252314 0.82708 YGR224w 70 240 169 0.275693 1e-27 139 41.4205 189 -lm_SuperContig_29_v2 193630 194215 507 0.00252314 0.82708 YGR224w 240 70 169 0.275693 6e-27 106 41.4205 190 -lm_SuperContig_29_v2 197024 197437 414 0.00206032 0.684298 YHL028w 276 136 141 0.233058 3e-25 117 47.52 191 -lm_SuperContig_29_v2 197024 197413 390 0.00194088 0.644628 YHL028w 323 190 134 0.221488 3e-23 111 47.01 192 -lm_SuperContig_29_v2 197024 197425 402 0.0020006 0.664463 YHL028w 290 148 143 0.236364 2e-23 111 49.65 193 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.679339 YHL028w 332 197 136 0.224793 2e-22 108 42.03 194 -lm_SuperContig_29_v2 197024 197482 459 0.00228426 0.758678 YHL028w 300 147 154 0.254545 5e-22 107 41.29 195 -lm_SuperContig_29_v2 197027 197482 456 0.00226933 0.753719 YHL028w 336 184 153 0.252893 5e-22 107 39.22 196 -lm_SuperContig_29_v2 197024 197410 387 0.00192595 0.639669 YHL028w 314 179 136 0.224793 6e-22 106 47.79 197 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.679339 YHL028w 257 117 141 0.233058 8e-21 103 42.55 198 -lm_SuperContig_29_v2 40143 42272 2130 0.0106002 1.4219 YIL082w-a 1327 642 686 0.457944 8e-39 165 26.47 199 -lm_SuperContig_29_v2 16081 17274 1194 0.00594207 0.797063 YIL082w-a 1034 642 393 0.26235 1e-34 150 30.33 200 -lm_SuperContig_29_v2 100993 102192 1200 0.00597193 0.801068 YIL082w-a 1034 642 393 0.26235 3e-34 150 30.92 201 -lm_SuperContig_29_v2 167371 168564 1194 0.00594207 0.797063 YIL082w-a 1034 642 393 0.26235 6e-35 149 30.83 202 -lm_SuperContig_29_v2 133543 134535 993 0.00494177 0.662884 YIL082w-a 969 642 328 0.218959 1e-33 147 32.23 203 -lm_SuperContig_29_v2 91762 92754 993 0.00494177 0.662884 YIL082w-a 970 644 327 0.218291 5e-23 112 30.24 204 -lm_SuperContig_29_v2 178464 179477 1014 0.00504628 0.676903 YIL082w-a 970 637 334 0.222964 1e-21 106 29.03 205 -lm_SuperContig_29_v2 197024 197425 402 0.0020006 0.346253 YJR151c 267 132 136 0.11714 1e-33 145 58.09 206 -lm_SuperContig_29_v2 197024 197425 402 0.0020006 0.346253 YJR151c 290 156 135 0.116279 2e-33 144 57.78 207 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 261 126 136 0.11714 3e-33 144 58.39 208 -lm_SuperContig_29_v2 197021 197425 405 0.00201553 0.348837 YJR151c 300 165 136 0.11714 6e-33 143 57.35 209 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 285 147 139 0.119724 6e-33 143 57.55 210 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 276 141 136 0.11714 6e-33 143 57.66 211 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 281 144 138 0.118863 1e-32 142 55.8 212 -lm_SuperContig_29_v2 197024 197425 402 0.0020006 0.346253 YJR151c 303 174 130 0.111972 3e-32 140 57.46 213 -lm_SuperContig_29_v2 197030 197404 375 0.00186623 0.322997 YJR151c 248 124 125 0.107666 3e-32 140 59.2 214 -lm_SuperContig_29_v2 197024 197398 375 0.00186623 0.322997 YJR151c 246 123 124 0.106804 1e-31 139 60 215 -lm_SuperContig_29_v2 197024 197395 372 0.0018513 0.320413 YJR151c 240 118 123 0.105943 1e-31 139 59.68 216 -lm_SuperContig_29_v2 197039 197434 396 0.00197074 0.341085 YJR151c 318 183 136 0.11714 1e-31 139 57.35 217 -lm_SuperContig_29_v2 197027 197437 411 0.00204539 0.354005 YJR151c 244 108 137 0.118002 2e-31 138 57.97 218 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 314 174 141 0.121447 3e-31 137 55.32 219 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 350 201 150 0.129199 1e-28 128 52 220 -lm_SuperContig_29_v2 197024 197392 369 0.00183637 0.317829 YJR151c 222 102 121 0.10422 1e-26 122 56.91 221 -lm_SuperContig_29_v2 197021 197425 405 0.00201553 0.348837 YJR151c 360 219 142 0.122308 3e-25 118 52.08 222 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.354005 YJR151c 372 228 145 0.124892 2e-24 115 48.28 223 -lm_SuperContig_29_v2 197036 197434 399 0.00198567 0.343669 YJR151c 378 246 133 0.114556 7e-23 109 42.86 224 -lm_SuperContig_29_v2 78112 78778 582 0.00289639 1 YKR105c 31 227 193 0.331615 7e-29 143 36.5996 225 -lm_SuperContig_29_v2 192985 194242 1173 0.00583756 2.01546 YKR105c 459 31 425 0.730241 4e-43 115 30.007 226 -lm_SuperContig_29_v2 197024 197434 411 0.00204539 0.817097 YNL283c 272 139 134 0.266402 4e-22 107 45.65 227 -lm_SuperContig_29_v2 197042 197422 381 0.00189609 0.757455 YNL283c 275 147 129 0.256461 8e-21 103 45.8 228 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC167.08 831 358 461 0.345836 4e-46 116 29.6018 229 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC167.08 831 312 520 0.390098 7e-44 182 27.67 230 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC167.08 831 427 405 0.303826 7e-42 175 28.64 231 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC167.08 831 427 405 0.303826 2e-42 174 29.14 232 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC167.08 831 427 405 0.303826 4e-39 165 27.9 233 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC167.08 786 452 335 0.251313 3e-37 159 32.64 234 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC167.08 786 418 369 0.276819 3e-37 158 30.65 235 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC167.08 786 418 369 0.276819 3e-36 155 30.91 236 -lm_SuperContig_29_v2 192757 194218 1371 0.00682293 2.58192 SPBC12C2.13c 499 33 461 0.868173 1e-35 78 25.49 237 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAPB15E9.03c 831 358 461 0.345836 4e-46 116 29.6018 238 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAPB15E9.03c 831 312 520 0.390098 7e-44 182 27.67 239 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAPB15E9.03c 831 427 405 0.303826 7e-42 175 28.64 240 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAPB15E9.03c 831 427 405 0.303826 2e-42 174 29.14 241 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAPB15E9.03c 831 427 405 0.303826 4e-39 165 27.9 242 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAPB15E9.03c 786 452 335 0.251313 3e-37 159 32.64 243 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAPB15E9.03c 786 418 369 0.276819 3e-37 158 30.65 244 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAPB15E9.03c 786 418 369 0.276819 3e-36 155 30.91 245 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPBC1289.17 831 358 461 0.345836 2e-46 117 29.8158 246 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPBC1289.17 831 312 520 0.390098 3e-44 183 27.86 247 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPBC1289.17 831 427 405 0.303826 3e-42 176 28.89 248 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPBC1289.17 831 427 405 0.303826 8e-43 175 29.38 249 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPBC1289.17 831 427 405 0.303826 2e-39 166 28.15 250 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPBC1289.17 786 452 335 0.251313 1e-37 161 32.94 251 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPBC1289.17 786 418 369 0.276819 1e-37 160 30.91 252 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPBC1289.17 786 418 369 0.276819 1e-36 157 31.18 253 -lm_SuperContig_29_v2 77950 78799 777 0.00386683 1.31919 SPAC3H1.06c 34 286 253 0.429542 5e-29 144 32.8211 254 -lm_SuperContig_29_v2 192844 194404 1488 0.0074052 2.52632 SPAC3H1.06c 525 34 492 0.835314 2e-50 119 29.3011 255 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPCC1020.14 831 358 461 0.345836 4e-46 116 29.6018 256 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPCC1020.14 831 312 520 0.390098 7e-44 182 27.67 257 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPCC1020.14 831 427 405 0.303826 7e-42 175 28.64 258 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPCC1020.14 831 427 405 0.303826 2e-42 174 29.14 259 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPCC1020.14 831 427 405 0.303826 4e-39 165 27.9 260 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPCC1020.14 786 452 335 0.251313 3e-37 159 32.64 261 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPCC1020.14 786 418 369 0.276819 3e-37 158 30.65 262 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPCC1020.14 786 418 369 0.276819 3e-36 155 30.91 263 -lm_SuperContig_29_v2 192760 194482 1635 0.00813676 2.83362 SPBC3E7.06c 551 4 543 0.941075 7e-34 54 22.6974 264 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC26A3.13c 831 358 461 0.345836 4e-46 116 29.6018 265 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC26A3.13c 831 312 520 0.390098 7e-44 182 27.67 266 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC26A3.13c 831 427 405 0.303826 7e-42 175 28.64 267 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC26A3.13c 831 427 405 0.303826 2e-42 174 29.14 268 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC26A3.13c 831 427 405 0.303826 4e-39 165 27.9 269 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC26A3.13c 786 452 335 0.251313 3e-37 159 32.64 270 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC26A3.13c 786 418 369 0.276819 3e-37 158 30.65 271 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC26A3.13c 786 418 369 0.276819 3e-36 155 30.91 272 -lm_SuperContig_29_v2 78133 78799 576 0.00286653 0.961603 SPBC16A3.17c 97 292 190 0.317195 3e-30 147 39.8809 273 -lm_SuperContig_29_v2 192874 194221 1257 0.0062556 2.0985 SPBC16A3.17c 518 97 416 0.694491 2e-55 151 31.4364 274 -lm_SuperContig_29_v2 77950 78736 714 0.0035533 1.21222 SPAC1399.02 34 267 234 0.397284 8e-30 147 33.1969 275 -lm_SuperContig_29_v2 192844 194404 1488 0.0074052 2.52632 SPAC1399.02 525 34 492 0.835314 3e-53 129 30.8816 276 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC2E1P3.03c 831 358 461 0.345836 4e-46 116 29.6018 277 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC2E1P3.03c 831 312 520 0.390098 7e-44 182 27.67 278 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC2E1P3.03c 831 427 405 0.303826 7e-42 175 28.64 279 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC2E1P3.03c 831 427 405 0.303826 2e-42 174 29.14 280 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC2E1P3.03c 831 427 405 0.303826 4e-39 165 27.9 281 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC2E1P3.03c 786 452 335 0.251313 3e-37 159 32.64 282 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC2E1P3.03c 786 418 369 0.276819 3e-37 158 30.65 283 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC2E1P3.03c 786 418 369 0.276819 3e-36 155 30.91 284 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC19D5.09c 831 358 461 0.345836 2e-46 117 29.8158 285 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC19D5.09c 831 312 520 0.390098 3e-44 183 27.86 286 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC19D5.09c 831 427 405 0.303826 3e-42 176 28.89 287 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC19D5.09c 831 427 405 0.303826 8e-43 175 29.38 288 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC19D5.09c 831 427 405 0.303826 2e-39 166 28.15 289 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC19D5.09c 786 452 335 0.251313 1e-37 161 32.94 290 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC19D5.09c 786 418 369 0.276819 1e-37 160 30.91 291 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC19D5.09c 786 418 369 0.276819 1e-36 157 31.18 292 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC27E2.08 831 358 461 0.345836 4e-46 116 29.6018 293 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC27E2.08 831 312 520 0.390098 7e-44 182 27.67 294 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC27E2.08 831 427 405 0.303826 7e-42 175 28.64 295 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC27E2.08 831 427 405 0.303826 2e-42 174 29.14 296 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC27E2.08 831 427 405 0.303826 4e-39 165 27.9 297 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC27E2.08 786 452 335 0.251313 3e-37 159 32.64 298 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC27E2.08 786 418 369 0.276819 3e-37 158 30.65 299 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC27E2.08 786 418 369 0.276819 3e-36 155 30.91 300 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC13D1.01c 831 358 461 0.345836 2e-46 117 29.8158 301 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC13D1.01c 831 312 520 0.390098 3e-44 183 27.86 302 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC13D1.01c 831 427 405 0.303826 3e-42 176 28.89 303 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC13D1.01c 831 427 405 0.303826 8e-43 175 29.38 304 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC13D1.01c 831 427 405 0.303826 2e-39 166 28.15 305 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC13D1.01c 786 452 335 0.251313 1e-37 161 32.94 306 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC13D1.01c 786 418 369 0.276819 1e-37 160 30.91 307 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC13D1.01c 786 418 369 0.276819 1e-36 157 31.18 308 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPBC9B6.02c 831 358 461 0.345836 4e-46 116 29.6018 309 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPBC9B6.02c 831 312 520 0.390098 7e-44 182 27.67 310 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPBC9B6.02c 831 427 405 0.303826 7e-42 175 28.64 311 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPBC9B6.02c 831 427 405 0.303826 2e-42 174 29.14 312 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPBC9B6.02c 831 427 405 0.303826 4e-39 165 27.9 313 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPBC9B6.02c 786 452 335 0.251313 3e-37 159 32.64 314 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPBC9B6.02c 786 418 369 0.276819 3e-37 158 30.65 315 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPBC9B6.02c 786 418 369 0.276819 3e-36 155 30.91 316 -lm_SuperContig_29_v2 133341 134754 1380 0.00686772 1.03526 SPAC9.04 831 358 461 0.345836 4e-46 116 29.6018 317 -lm_SuperContig_29_v2 100993 102531 1539 0.007659 1.15454 SPAC9.04 831 312 520 0.390098 7e-44 182 27.67 318 -lm_SuperContig_29_v2 41079 42287 1209 0.00601672 0.906977 SPAC9.04 831 427 405 0.303826 7e-42 175 28.64 319 -lm_SuperContig_29_v2 167371 168579 1209 0.00601672 0.906977 SPAC9.04 831 427 405 0.303826 2e-42 174 29.14 320 -lm_SuperContig_29_v2 16081 17289 1209 0.00601672 0.906977 SPAC9.04 831 427 405 0.303826 4e-39 165 27.9 321 -lm_SuperContig_29_v2 91693 92700 1008 0.00501642 0.756189 SPAC9.04 786 452 335 0.251313 3e-37 159 32.64 322 -lm_SuperContig_29_v2 178395 179504 1110 0.00552404 0.832708 SPAC9.04 786 418 369 0.276819 3e-37 158 30.65 323 -lm_SuperContig_29_v2 10747 11856 1110 0.00552404 0.832708 SPAC9.04 786 418 369 0.276819 3e-36 155 30.91 324 -lm_SuperContig_29_v2 77980 78567 588 0.00292625 1.01379 um00679 18 211 194 0.334483 5e-25 114 31 325 -lm_SuperContig_29_v2 192772 194374 1512 0.00752463 2.6069 um00679 529 18 506 0.872414 2e-42 90 24.7056 326 -lm_SuperContig_29_v2 78115 78814 627 0.00312033 1.07179 um00842 53 264 212 0.362393 2e-53 226 52.4685 327 -lm_SuperContig_29_v2 192760 194239 1407 0.00700209 2.40513 um00842 534 53 482 0.823932 2e-104 305 43.0311 328 -lm_SuperContig_29_v2 78112 78802 603 0.0030009 1.005 um01882 94 297 198 0.33 7e-23 123 33.3351 329 -lm_SuperContig_29_v2 192760 194242 1395 0.00694237 2.325 um01882 560 94 461 0.768333 5e-40 91 24.8656 330 -lm_SuperContig_29_v2 78019 78567 549 0.00273216 0.90894 um01964 40 220 181 0.299669 1e-24 113 33.7 331 -lm_SuperContig_29_v2 192901 194335 1344 0.00668856 2.22517 um01964 490 40 445 0.736755 7e-43 104 28.0569 332 -lm_SuperContig_29_v2 77890 78814 858 0.00426993 1.33645 um02062 38 313 276 0.429907 1e-32 158 32.8827 333 -lm_SuperContig_29_v2 192760 194464 1638 0.00815169 2.5514 um02062 575 38 538 0.838006 1e-65 161 31.23 334 -lm_SuperContig_29_v2 78136 78814 606 0.00301583 0.795276 um02598 133 331 199 0.261155 1e-21 120 30.0506 335 -lm_SuperContig_29_v2 192754 194218 1392 0.00692744 1.82677 um02598 598 133 466 0.611549 3e-45 109 27.3493 336 -lm_SuperContig_29_v2 77938 78808 807 0.00401612 1.30161 um03115 27 285 259 0.417742 2e-24 130 31.3664 337 -lm_SuperContig_29_v2 192757 194416 1596 0.00794267 2.57419 um03115 554 27 528 0.851613 1e-48 108 27.7423 338 -lm_SuperContig_29_v2 77938 78736 726 0.00361302 1.24528 um05414 13 244 232 0.397942 4e-45 199 41.7387 339 -lm_SuperContig_29_v2 192826 194416 1518 0.00755449 2.60377 um05414 511 13 499 0.855918 2e-98 279 38.2481 340 -lm_SuperContig_29_v2 193006 194107 1017 0.00506121 1.44255 um05421 496 158 335 0.475177 6e-41 118 29.7892 341 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/ConvMapChr2Chunk.py --- a/commons/pyRepetUnit/convCoord/ConvMapChr2Chunk.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -from copy import deepcopy -from commons.core.sql.TableMapAdaptator import TableMapAdaptator -from commons.core.coord.Map import Map -import os - -class ConvMapChr2Chunk(object): - - def __init__(self, db, table, chunk_table, outtable): - self._tablename = table - self._chunk_table = chunk_table - self._db = db - self._outtable = outtable - - def convert(self): - """ - Convert a 'set' table format. - """ - temp_file=str(os.getpid()) + ".on_chunk" - fout=open(temp_file,'w') - - str_mask = "SELECT * FROM "+\ - self._chunk_table + " WHERE chr='%s' AND ("+\ - "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\ - " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\ - " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));" - - iTMA = TableMapAdaptator(self._db, self._tablename) - chr_list = iTMA.getSeqNameList() - - for chr in chr_list: - mlist = iTMA.getMapListFromChr(chr) - for m in mlist: - sql_cmd = str_mask%(m.seqname,m.getMin(),m.getMax(),m.getMin(),m.getMax()) - self._db.execute(sql_cmd) - res = self._db.fetchall() - for i in res: - chunk = Map(i[0],i[1],int(i[2]),int(i[3])) - - new_m = deepcopy(m) - new_m.seqname = chunk.name - - if (m.start > chunk.start and m.start < chunk.end): - new_m.start = m.start - chunk.start + 1 - if (m.end > chunk.start and m.end < chunk.end): - new_m.end = m.end - chunk.start + 1 - - if m.isOnDirectStrand(): - if m.start <= chunk.start: - new_m.start = 1 - if m.end >= chunk.end: - new_m.end = chunk.end - chunk.start + 1 - else: - if m.end <= chunk.start: - new_m.end = 1 - if m.start >= chunk.end: - new_m.start = chunk.end - chunk.start + 1 - - new_m.write(fout) - - fout.close() - - self._db.createTable(self._outtable, "map", temp_file) - - os.remove(temp_file) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/ConvPathChr2Chunk.py --- a/commons/pyRepetUnit/convCoord/ConvPathChr2Chunk.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -from copy import deepcopy -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.coord.PathUtils import PathUtils -from commons.core.coord.Map import Map -from commons.core.coord.Path import Path -import os - -class ConvPathChr2Chunk(object): - - def __init__(self, db, table, chunk_table, outtable): - self._tablename = table - self._chunk_table = chunk_table - self._db = db - self._outtable = outtable - - def convert(self): - """ - Convert a 'path' table format. - """ - temp_file = str(os.getpid()) + ".on_chunk" - fout = open(temp_file,'w') - - str_mask = "SELECT * FROM "+\ - self._chunk_table + " WHERE chr='%s' AND ("+\ - "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\ - " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\ - " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));" - - iTPA = TablePathAdaptator(self._db, self._tablename) - path_num_list = iTPA.getIdList() - - for path_num in path_num_list: - slist = iTPA.getPathListFromId(path_num) - for r in slist: - r_min, r_max = PathUtils.getQueryMinMaxFromPathList([r]) - sql_cmd = str_mask%(r.range_query.seqname,r_min,r_max,r_min,r_max) - self._db.execute(sql_cmd) - res = self._db.fetchall() - for i in res: - chunk = Map(i[0],i[1],int(i[2]),int(i[3])) - - new_r = Path() - new_r = deepcopy(r) - new_r.range_query.seqname = chunk.name - - if (r.range_query.start > chunk.start and r.range_query.start < chunk.end): - new_r.range_query.start = r.range_query.start - chunk.start + 1 - if (r.range_query.end > chunk.start and r.range_query.end < chunk.end): - new_r.range_query.end = r.range_query.end - chunk.start + 1 - - if r.range_query.isOnDirectStrand(): - if r.range_query.start <= chunk.start: - new_r.range_query.start = 1 - if r.range_query.end >= chunk.end: - new_r.range_query.end = chunk.end - chunk.start + 1 - else: - if r.range_query.end <= chunk.start: - new_r.range_query.end = 1 - if r.range_query.start >= chunk.end: - new_r.range_query.start = chunk.end - chunk.start + 1 - - new_r.write(fout) - - fout.close() - - self._db.createTable(self._outtable, "path", temp_file) - - os.remove(temp_file) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/ConvSetChr2Chunk.py --- a/commons/pyRepetUnit/convCoord/ConvSetChr2Chunk.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -from copy import deepcopy -from commons.core.sql.TableSetAdaptator import TableSetAdaptator -from commons.core.coord.Map import Map -from commons.core.coord.Set import Set -import os - -class ConvSetChr2Chunk(object): - - def __init__(self, db, table, chunk_table, outtable): - self._tablename = table - self._chunk_table = chunk_table - self._db = db - self._outtable = outtable - - def convert(self): - """ - Convert a 'set' table format. - """ - temp_file = str(os.getpid()) + ".on_chunk" - fout = open(temp_file,'w') - - str_mask = "SELECT * FROM "+\ - self._chunk_table + " WHERE chr='%s' AND ("+\ - "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\ - " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\ - " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));" - - iTSA = TableSetAdaptator(self._db, self._tablename) - path_num_list = iTSA.getIdList() - - for path_num in path_num_list: - slist = iTSA.getSetListFromId(path_num) - for r in slist: - sql_cmd = str_mask%(r.seqname,r.getMin(),r.getMax(),r.getMin(),r.getMax()) - self._db.execute(sql_cmd) - res = self._db.fetchall() - for i in res: - chunk = Map(i[0],i[1],int(i[2]),int(i[3])) - - new_r = Set() - new_r = deepcopy(r) - new_r.seqname = chunk.name - - if (r.start > chunk.start and r.start < chunk.end): - new_r.start = r.start - chunk.start + 1 - if (r.end > chunk.start and r.end < chunk.end): - new_r.end = r.end - chunk.start + 1 - - if r.isOnDirectStrand(): - if r.start <= chunk.start: - new_r.start = 1 - if r.end >= chunk.end: - new_r.end = chunk.end - chunk.start + 1 - else: - if r.end <= chunk.start: - new_r.end = 1 - if r.start >= chunk.end: - new_r.start = chunk.end - chunk.start + 1 - - new_r.write(fout) - - fout.close() - - self._db.createTable(self._outtable, "set", temp_file) - - os.remove(temp_file) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/PathChunkConnector.py --- a/commons/pyRepetUnit/convCoord/PathChunkConnector.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,134 +0,0 @@ -from pyRepet.coord.Map import Map -import commons.core.sql.TablePathAdaptator - - -## Connect overlapping chunks in a single fragment -# -class PathChunkConnector( object): - - def __init__(self, mapFileName, db, table, verbose): - - self._verbose = verbose - self._chunk = self._getChunkDictFromMapFileForConnectPathChunks( mapFileName ) - self._tablePathAdaptator = commons.core.sql.TablePathAdaptator.TablePathAdaptator( db, table ) - - def run (self): - for num_chunk in xrange(1,len(self._chunk.keys())): - chunkName = "chunk"+str(num_chunk) - if self._verbose > 1: - print chunkName - next_chunkName="chunk"+str(num_chunk+1) - - if next_chunkName not in self._chunk.keys(): - break - - start=self._chunk[chunkName][2] - end=self._chunk[next_chunkName][1] - - if self._chunk[chunkName][0] == self._chunk[next_chunkName][0]: - lpath=self._tablePathAdaptator.getPathListIncludedInQueryCoord(self._chunk[chunkName][0],start,end) - - if self._verbose > 1: - print "----------" - - lpath.sort() - chg_path_id={} - pathnum_to_ins=[] - pathnum_to_del=[] - - self._createDirectAndReversePaths(lpath) - - self._mergeDirectPaths(chg_path_id, pathnum_to_ins, pathnum_to_del) - - if self._verbose > 1: - print "..........." - - self._mergeReversePaths(chg_path_id, pathnum_to_ins, pathnum_to_del) - - if self._verbose > 1: - print "..........." - print pathnum_to_del - - self._tablePathAdaptator.deleteFromIdList(pathnum_to_del) - - if self._verbose > 1: - print pathnum_to_ins - - self._tablePathAdaptator.deleteFromIdList(pathnum_to_ins) - - self._insertDirectPaths(chg_path_id, pathnum_to_ins) - - self._insertReversePaths(chg_path_id, pathnum_to_ins) - - - def _createDirectAndReversePaths(self, lpath): - self._dpath = [] - self._rpath = [] - for i in lpath: - if i.range_query.isOnDirectStrand() and i.range_subject.isOnDirectStrand(): - self._dpath.append(i) - else: - self._rpath.append(i) - - def _insertDirectPaths (self, chg_path_id, pathnum_to_ins): - self._insertPaths(chg_path_id, pathnum_to_ins, self._dpath) - - def _insertReversePaths (self, chg_path_id, pathnum_to_ins): - self._insertPaths(chg_path_id, pathnum_to_ins, self._rpath) - - def _insertPaths(self, chg_path_id, pathnum_to_ins, paths2Insert): - for i in paths2Insert: - if chg_path_id.has_key(i.id): - i.id = chg_path_id[i.id] - - if self._verbose > 1: - i.show() - - if i.id in pathnum_to_ins: - self._tablePathAdaptator.insert(i) - if self._verbose > 1: - print "--> inserted!" - - if self._verbose > 1: - print "==========" - - def _mergeDirectPaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del): - self._mergePaths(chg_path_id, pathnum_to_ins, pathnum_to_del, self._dpath) - - def _mergeReversePaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del): - self._mergePaths(chg_path_id, pathnum_to_ins, pathnum_to_del, self._rpath) - - def _mergePaths(self, chg_path_id, pathnum_to_ins, pathnum_to_del, dpath): - x = 0 - while x < len(dpath) - 1: - x = x + 1 - if self._verbose > 1: - print "++++" - dpath[x - 1].show() - dpath[x].show() - - if dpath[x - 1].canMerge(dpath[x]): - chg_path_id[dpath[x].id] = dpath[x - 1].id - if dpath[x - 1].id not in pathnum_to_ins: - pathnum_to_ins.append(dpath[x - 1].id) - - if dpath[x].id not in pathnum_to_del: - pathnum_to_del.append(dpath[x].id) - - dpath[x - 1].merge(dpath[x]) - del dpath[x] - x = x - 1 - if self._verbose > 1: - print "--> merged" - - def _getChunkDictFromMapFileForConnectPathChunks(self, mapFileName): - mapDict = {} - mapFile = open(mapFileName) - mapInstance = Map() - while True: - if not mapInstance.read(mapFile): - break - mapDict[mapInstance.name] = (mapInstance.seqname, mapInstance.start, mapInstance.end) - - mapFile.close() - return mapDict diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/TestConvCoordWithOverlapps.py --- a/commons/pyRepetUnit/convCoord/test/TestConvCoordWithOverlapps.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,169 +0,0 @@ -import unittest -import os -import time -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbMySql import DbMySql - - -class Test_ConvCoordWithOverlaps( unittest.TestCase ): - pass - -# def setUp(self): -# self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) -# self._mapFile = "map_file.map" -# _MockMapFile( self._mapFile ) -# self._resultFile = "dummyObsFile_%s" % ( self._uniqId ) -# self._refFileToCompare = "dummyExpFile_%s" % ( self._uniqId ) -# self._configFileName = "dummyConfigFile_%s" % ( self._uniqId ) -# configF = open(self._configFileName, "w" ) -# configF.write( "[repet_env]\n" ) -# configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) -# configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) -# configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) -# configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) -# configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) -# configF.close() -# self._db = DbMySql( cfgFileName = self._configFileName ) -# -# def tearDown(self): -# os.remove( self._mapFile ) -# os.remove( self._resultFile ) -# os.remove( self._refFileToCompare ) -# self._db.close() -# self._uniqId = None -# -# -# def test_run_TwoHitsOverlapOnFirstAndSecondChunks( self ): -# file2Process = "two_hits_overlap_on_first_and_second_chunk.align" -# linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", -# "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n" ] -# _MockAlignFile( file2Process, linesToProcess ) -# -# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) -# convCoord.run() -# -# refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "97.78" + "\n"] -# _MockAlignFile( self._refFileToCompare, refLine ) -# -# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) -# os.remove( file2Process ) -# -# -# def test_run_ThreeHitsOverlapOnFirstAndSecondChunks( self ): -# file2Process = "three_hits_overlap_on_first_and_second_chunk.align" -# linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", -# "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n" -# "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj2" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] -# _MockAlignFile( file2Process, linesToProcess ) -# -# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) -# convCoord.run() -# -# refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "8e-58" + "\t" + "224" + "\t" + "97.78" + "\n"] -# _MockAlignFile( self._refFileToCompare, refLine ) -# -# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) -# os.remove( file2Process ) -# -# -# def test_run_HitsOnDifferentStrandsAndDifferentSubjects( self ): -# file2Process = "hits_on_different_strands_and_different_subjects.align" -# linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", -# "chunk2" + "\t" + "5575" + "\t" + "5544" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", -# "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] -# _MockAlignFile( file2Process, linesToProcess ) -# -# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) -# convCoord.run() -# -# refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", -# "dmel_chr4" + "\t" + "95544" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", -# "dmel_chr4" + "\t" + "95540" + "\t" + "95573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] -# _MockAlignFile( self._refFileToCompare, refLine ) -# -# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) -# os.remove( file2Process ) -# -# -# def test_run_TwoHitsOnChunksOnlyAndOnOverlap( self ): -# file2Process = "two_hits_on_chunks_only_and_on_overlap.align" -# linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", -# "chunk3" + "\t" + "1000" + "\t" +" 5000" + "\t" + "sbj2" + "\t" + "125454" + "\t" + "125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] -# _MockAlignFile( file2Process, linesToProcess ) -# -# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) -# convCoord.run() -# -# refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000"+ "\t" + "sbj2"+ "\t" + "125454"+ "\t" + "133465"+ "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"] -# _MockAlignFile( self._refFileToCompare, refLine ) -# -# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) -# os.remove( file2Process ) -# -# -# def test_run_TwoHitsOnChunks_And_OnOverlap_OnReverseStrand_ForSubject( self ): -# file2Process = "two_hits_on_chunks_and_on_overlap_on_reverse_strand_for_subject.align" -# linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", -# "chunk3" + "\t" + "1000" + "\t" + "5000" + "\t" + "sbj2" + "\t" + "125750" + "\t" + "125454" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] -# _MockAlignFile( file2Process, linesToProcess ) -# -# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) -# convCoord.run() -# -# refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000" + "\t" + "sbj2"+ "\t" + "133465" + "\t" + "125454" + "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"] -# _MockAlignFile( self._refFileToCompare, refLine ) -# -# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) -# os.remove( file2Process ) -# -# -# def test_run_ThreeHitsAllByAllWithTwoHitsWithinAChunkOverlap( self ): -# file2Process = "dummyAlignFile_%s" % ( self._uniqId ) -# linesToProcess = [ "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n", -# "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n", -# "chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ] -# _MockAlignFile( file2Process, linesToProcess ) -# -# mapFileName = "dummyMapFile_%s" % ( self._uniqId ) -# mapF = open( mapFileName, "w" ) -# mapF.write( "chunk1\tdmel_chr4\t1\t200\n" ) -# mapF.write( "chunk2\tdmel_chr4\t191\t390\n" ) -# mapF.close() -# -# convCoord = ConvCoord( file2Process, "qs", mapFileName, self._resultFile, "", 0, self._db ) -# convCoord.run() -# -# refLine = [ "dmel_chr4"+"\t"+"192"+"\t"+"197"+"\t"+"dmel_chr4"+"\t"+"241"+"\t"+"246"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ] -# _MockAlignFile( self._refFileToCompare, refLine ) -# -# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) -# os.remove( file2Process ) -# os.remove( mapFileName ) -# -# -#class _MockAlignFile: -# -# def __init__(self, fileName, lines): -# alignF = open(fileName, "w"); -# for line in lines: -# alignF.write(line) -# alignF.close -# -# -#class _MockMapFile: -# -# def __init__ (self, fileName): -# mapF = open(fileName, "w") -# line1 = "chunk1" + '\t' + "dmel_chr4" + '\t' + "1" + '\t'+ "100000" + "\n" -# line2 = "chunk2" + '\t' + "dmel_chr4" + '\t' + "90001" + '\t'+ "190000" + "\n" -# line3 = "chunk3" + '\t' + "dmel_chr4" + '\t' + "180001" + '\t' + "280000" + "\n" -# mapF.write(line1) -# mapF.write(line2) -# mapF.write(line3) -# mapF.close - - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_ConvCoordWithOverlaps ) ) -if __name__ == "__main__": - unittest.TextTestRunner(verbosity=2).run( test_suite ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/Test_ConvMapChr2Chunk.py --- a/commons/pyRepetUnit/convCoord/test/Test_ConvMapChr2Chunk.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -from commons.core.sql.DbFactory import DbFactory -from commons.core.utils.FileUtils import FileUtils -from commons.pyRepetUnit.convCoord.ConvMapChr2Chunk import ConvMapChr2Chunk -import unittest -import os - -class Test_ConvMapChr2Chunk(unittest.TestCase): - - def setUp(self): - self._mapfilename="dummy.map" - self._maptablename="dummy_map" - - self._chunkmapfilename="chunk.map" - self._chunkmaptable="test_chunk_map" - - self._resfilename="dummy_res.map" - - map4convData="chunk1\tchr1\t1\t100\n" - map4convData+="chunk2\tchr1\t90\t200\n" - map4convData+="chunk3\tchr1\t190\t300\n" - - map4conv=open(self._chunkmapfilename,"w") - map4conv.write(map4convData) - map4conv.close() - - self._db = DbFactory.createInstance() - self._db.createTable(self._chunkmaptable, "map", self._chunkmapfilename, True) - - map2convData="reg1\tchr1\t10\t80\n" - map2convData+="reg1\tchr1\t90\t110\n" - map2convData+="reg2\tchr1\t150\t160\n" - - map2convData+="reg3\tchr1\t70\t210\n" - map2convData+="reg4\tchr1\t85\t100\n" - map2convData+="reg5\tchr1\t85\t110\n" - - map2convData+="reg6\tchr1\t80\t10\n" - map2convData+="reg6\tchr1\t110\t90\n" - map2convData+="reg7\tchr1\t160\t150\n" - map2convData+="reg8\tchr1\t190\t300\n" - - map2convData+="reg9\tchr1\t210\t70\n" - map2convData+="reg10\tchr1\t100\t85\n" - map2convData+="reg11\tchr1\t110\t85\n" - map2convData+="reg12\tchr1\t300\t190\n" - - map2conv=open(self._mapfilename,"w") - map2conv.write(map2convData) - map2conv.close() - - self._db.createTable(self._maptablename, "map", self._mapfilename, True) - - mapResData="reg1\tchunk1\t10\t80\n" - mapResData+="reg1\tchunk1\t90\t100\n" - mapResData+="reg1\tchunk2\t1\t21\n" - mapResData+="reg2\tchunk2\t61\t71\n" - - mapResData+="reg3\tchunk1\t70\t100\n" - mapResData+="reg3\tchunk2\t1\t111\n" - mapResData+="reg3\tchunk3\t1\t21\n" - - mapResData+="reg4\tchunk1\t85\t100\n" - mapResData+="reg4\tchunk2\t1\t11\n" - mapResData+="reg5\tchunk1\t85\t100\n" - mapResData+="reg5\tchunk2\t1\t21\n" - - mapResData+="reg6\tchunk1\t80\t10\n" - mapResData+="reg6\tchunk1\t100\t90\n" - mapResData+="reg6\tchunk2\t21\t1\n" - mapResData+="reg7\tchunk2\t71\t61\n" - mapResData+="reg8\tchunk2\t101\t111\n" - mapResData+="reg8\tchunk3\t1\t111\n" - - mapResData+="reg9\tchunk1\t100\t70\n" - mapResData+="reg9\tchunk2\t111\t1\n" - mapResData+="reg9\tchunk3\t21\t1\n" - - mapResData+="reg10\tchunk1\t100\t85\n" - mapResData+="reg10\tchunk2\t11\t1\n" - mapResData+="reg11\tchunk1\t100\t85\n" - mapResData+="reg11\tchunk2\t21\t1\n" - mapResData+="reg12\tchunk2\t111\t101\n" - mapResData+="reg12\tchunk3\t111\t1\n" - - mapRes=open(self._resfilename,"w") - mapRes.write(mapResData) - mapRes.close() - - def tearDown(self): - self._db.dropTable(self._chunkmaptable) - self._db.dropTable(self._maptablename) - self._db.close() - os.remove(self._resfilename) - os.remove(self._mapfilename) - os.remove(self._chunkmapfilename) - - def test_convert(self): - conv = ConvMapChr2Chunk(self._db,self._maptablename, self._chunkmaptable, self._maptablename+"_onchk") - conv.convert() - obsFileName = "dummy_map.onchk" - self._db.exportDataToFile("dummy_map_onchk", obsFileName) - self._db.dropTable("dummy_map_onchk") - self.assertTrue(FileUtils.are2FilesIdentical(self._resfilename, obsFileName)) - os.remove(obsFileName) - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_ConvMapChr2Chunk ) ) -if __name__ == '__main__': - unittest.TextTestRunner(verbosity=2).run( test_suite ) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/Test_ConvPathChr2Chunk.py --- a/commons/pyRepetUnit/convCoord/test/Test_ConvPathChr2Chunk.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbFactory import DbFactory -from commons.pyRepetUnit.convCoord.ConvPathChr2Chunk import ConvPathChr2Chunk -import unittest -import os - -class Test_ConvPathChr2Chunk(unittest.TestCase): - - def setUp(self): - self._pathfilename="dummy.path" - self._pathtablename="dummy_path" - - self._chunkmapfilename="chunk.map" - self._chunkmaptable="test_chunk_map" - - self._resfilename="dummy_res.path" - - map4convData="chunk1\tchr1\t1\t100\n" - map4convData+="chunk2\tchr1\t90\t200\n" - map4convData+="chunk3\tchr1\t190\t300\n" - - map4conv=open(self._chunkmapfilename,"w") - map4conv.write(map4convData) - map4conv.close() - - self._db = DbFactory.createInstance() - self._db.createTable(self._chunkmaptable, "map", self._chunkmapfilename, True) - - path2convData="1\tchr1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="1\tchr1\t90\t110\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="2\tchr1\t150\t160\tsub1\t10\t50\t0.01\t1000\t99\n" - - path2convData+="3\tchr1\t70\t210\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="4\tchr1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="5\tchr1\t85\t110\tsub1\t10\t50\t0.01\t1000\t99\n" - - path2convData+="6\tchr1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="6\tchr1\t90\t110\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="7\tchr1\t150\t160\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="8\tchr1\t190\t300\tsub1\t10\t50\t0.01\t1000\t99\n" - - path2convData+="9\tchr1\t70\t210\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="10\tchr1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="11\tchr1\t85\t110\tsub1\t10\t50\t0.01\t1000\t99\n" - path2convData+="12\tchr1\t190\t300\tsub1\t10\t50\t0.01\t1000\t99\n" - - path2conv=open(self._pathfilename,"w") - path2conv.write(path2convData) - path2conv.close() - - self._db.createTable(self._pathtablename, "path", self._pathfilename) - - pathResData="1\tchunk1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="1\tchunk1\t90\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="1\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="2\tchunk2\t61\t71\tsub1\t10\t50\t0.01\t1000\t99\n" - - pathResData+="3\tchunk1\t70\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="3\tchunk2\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="3\tchunk3\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n" - - pathResData+="4\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="4\tchunk2\t1\t11\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="5\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="5\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n" - - pathResData+="6\tchunk1\t10\t80\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="6\tchunk1\t90\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="6\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="7\tchunk2\t61\t71\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="8\tchunk2\t101\t111\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="8\tchunk3\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n" - - pathResData+="9\tchunk1\t70\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="9\tchunk2\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="9\tchunk3\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n" - - pathResData+="10\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="10\tchunk2\t1\t11\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="11\tchunk1\t85\t100\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="11\tchunk2\t1\t21\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="12\tchunk2\t101\t111\tsub1\t10\t50\t0.01\t1000\t99\n" - pathResData+="12\tchunk3\t1\t111\tsub1\t10\t50\t0.01\t1000\t99\n" - - pathRes=open(self._resfilename,"w") - pathRes.write(pathResData) - pathRes.close() - - def tearDown(self): - self._db.dropTable(self._chunkmaptable) - self._db.dropTable(self._pathtablename) - self._db.close() - os.remove(self._resfilename) - os.remove(self._pathfilename) - os.remove(self._chunkmapfilename) - - def test_convert(self): - conv=ConvPathChr2Chunk(self._db,self._pathtablename, self._chunkmaptable, self._pathtablename+"_onchk") - conv.convert() - expPath = self._resfilename - obsPath = "dummy_path.onchk" - self._db.exportDataToFile("dummy_path_onchk", obsPath) - self._db.dropTable("dummy_path_onchk") - self.assertTrue(FileUtils.are2FilesIdentical(expPath, obsPath)) - os.remove(obsPath) - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_ConvPathChr2Chunk ) ) -if __name__ == '__main__': - unittest.TextTestRunner(verbosity=2).run( test_suite ) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/Test_ConvSetChr2Chunk.py --- a/commons/pyRepetUnit/convCoord/test/Test_ConvSetChr2Chunk.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -from commons.core.sql.DbFactory import DbFactory -from commons.core.utils.FileUtils import FileUtils -from commons.pyRepetUnit.convCoord.ConvSetChr2Chunk import ConvSetChr2Chunk -import unittest -import os - -class Test_ConvSetChr2Chunk(unittest.TestCase): - - def setUp(self): - self._setfilename="dummy.set" - self._settablename="dummy_set" - - self._chunkmapfilename="chunk.map" - self._chunkmaptable="test_chunk_map" - - self._resfilename="dummy_res.set" - - map4convData="chunk1\tchr1\t1\t100\n" - map4convData+="chunk2\tchr1\t90\t200\n" - map4convData+="chunk3\tchr1\t190\t300\n" - - map4conv=open(self._chunkmapfilename,"w") - map4conv.write(map4convData) - map4conv.close() - - self._db = DbFactory.createInstance() - self._db.createTable(self._chunkmaptable, "map", self._chunkmapfilename, True) - - set2convData="1\treg1\tchr1\t10\t80\n" - set2convData+="1\treg1\tchr1\t90\t110\n" - set2convData+="2\treg2\tchr1\t150\t160\n" - - set2convData+="3\treg3\tchr1\t70\t210\n" - set2convData+="4\treg4\tchr1\t85\t100\n" - set2convData+="5\treg5\tchr1\t85\t110\n" - - set2convData+="6\treg6\tchr1\t80\t10\n" - set2convData+="6\treg6\tchr1\t110\t90\n" - set2convData+="7\treg7\tchr1\t160\t150\n" - set2convData+="8\treg8\tchr1\t190\t300\n" - - set2convData+="9\treg9\tchr1\t210\t70\n" - set2convData+="10\treg10\tchr1\t100\t85\n" - set2convData+="11\treg11\tchr1\t110\t85\n" - set2convData+="12\treg12\tchr1\t300\t190\n" - - set2conv=open(self._setfilename,"w") - set2conv.write(set2convData) - set2conv.close() - - self._db.createTable(self._settablename, "set", self._setfilename, True) - - setResData="1\treg1\tchunk1\t10\t80\n" - setResData+="1\treg1\tchunk1\t90\t100\n" - setResData+="1\treg1\tchunk2\t1\t21\n" - setResData+="2\treg2\tchunk2\t61\t71\n" - - setResData+="3\treg3\tchunk1\t70\t100\n" - setResData+="3\treg3\tchunk2\t1\t111\n" - setResData+="3\treg3\tchunk3\t1\t21\n" - - setResData+="4\treg4\tchunk1\t85\t100\n" - setResData+="4\treg4\tchunk2\t1\t11\n" - setResData+="5\treg5\tchunk1\t85\t100\n" - setResData+="5\treg5\tchunk2\t1\t21\n" - - setResData+="6\treg6\tchunk1\t80\t10\n" - setResData+="6\treg6\tchunk1\t100\t90\n" - setResData+="6\treg6\tchunk2\t21\t1\n" - setResData+="7\treg7\tchunk2\t71\t61\n" - setResData+="8\treg8\tchunk2\t101\t111\n" - setResData+="8\treg8\tchunk3\t1\t111\n" - - setResData+="9\treg9\tchunk1\t100\t70\n" - setResData+="9\treg9\tchunk2\t111\t1\n" - setResData+="9\treg9\tchunk3\t21\t1\n" - - setResData+="10\treg10\tchunk1\t100\t85\n" - setResData+="10\treg10\tchunk2\t11\t1\n" - setResData+="11\treg11\tchunk1\t100\t85\n" - setResData+="11\treg11\tchunk2\t21\t1\n" - setResData+="12\treg12\tchunk2\t111\t101\n" - setResData+="12\treg12\tchunk3\t111\t1\n" - - setRes=open(self._resfilename,"w") - setRes.write(setResData) - setRes.close() - - def tearDown(self): - self._db.dropTable(self._chunkmaptable) - self._db.dropTable(self._settablename) - self._db.close() - os.remove(self._resfilename) - os.remove(self._setfilename) - os.remove(self._chunkmapfilename) - - def test_convert(self): - conv = ConvSetChr2Chunk(self._db,self._settablename, self._chunkmaptable, self._settablename+"_onchk") - conv.convert() - obsFileName = "dummy_set.onchk" - self._db.exportDataToFile("dummy_set_onchk", obsFileName) - self._db.dropTable("dummy_set_onchk") - self.assertTrue(FileUtils.are2FilesIdentical(self._resfilename, obsFileName)) - os.remove(obsFileName) - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_ConvSetChr2Chunk ) ) -if __name__ == '__main__': - unittest.TextTestRunner(verbosity=2).run( test_suite ) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/Test_PathChunkConnector.py --- a/commons/pyRepetUnit/convCoord/test/Test_PathChunkConnector.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -import unittest -import time -import os -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.pyRepetUnit.convCoord.PathChunkConnector import PathChunkConnector -from commons.core.sql.DbMySql import DbMySql - - -class Test_PathChunkConnector( unittest.TestCase ): - - def setUp(self): - self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) - self._configFileName = "dummyConfigFile_%s" % ( self._uniqId ) - configF = open(self._configFileName, "w" ) - configF.write( "[repet_env]\n" ) - configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) - configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) - configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) - configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) - configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) - configF.close() - self._db = DbMySql( cfgFileName=self._configFileName ) - self._table = "dummyPathTable_%s" % ( self._uniqId ) - self._tpA = TablePathAdaptator( self._db, self._table ) - self._mapDict = {'chunk1': ('dmel_chr4', 1, 100000),'chunk2': ('dmel_chr4', 90001, 190000),'chunk3': ('dmel_chr4', 180001, 280000), } - self._mapFileName = "map_file.map" - - def tearDown(self): - self._db.close() - - def testTwoQueryOverlapsOnPlusStrand (self): - lines = [ - "1\tdmel_chr4\t95535\t95570\tsbj2\t125423\t125467\t7e-15\t82\t97.78\n", - "2\tdmel_chr4\t95545\t95576\tsbj2\t125457\t133465\t2e-38\t83\t65\n" - ] - - expectedList =[("dmel_chr4", 95535, 95576, "sbj2", 125423, 133465, 2e-38, 83,97.78)] - self._templateTest(lines, expectedList) - - def testTwoQueryOverlapsOnReverseStrand (self): - lines = [ - "1\tdmel_chr4\t95535\t95570\tsbj2\t125467\t125423\t7e-15\t82\t97.78\n", - "2\tdmel_chr4\t95545\t95576\tsbj2\t133465\t125457\t2e-38\t83\t65\n" - ] - - expectedList =[("dmel_chr4", 95535, 95576, "sbj2", 133465, 125423, 2e-38, 83,97.78)] - self._templateTest(lines, expectedList) - - def testTwoQueryOverlapsOnDifferentStrands (self): - lines = [ - "1\tdmel_chr4\t95535\t95570\tsbj2\t125423\t125467\t7e-15\t82\t97.78\n", - "2\tdmel_chr4\t95545\t95576\tsbj2\t133465\t125457\t2e-38\t83\t65\n" - ] - expectedList =[ - ("dmel_chr4", 95535, 95570, "sbj2", 125423, 125467, 7e-15, 82,97.78), - ("dmel_chr4", 95545, 95576, "sbj2", 133465, 125457, 2e-38, 83,65) - ] - self._templateTest(lines, expectedList) - - def _templateTest(self, datas2TestList, expectedList ): - pathFileName = "dummyPathFile_%s" % ( self._uniqId ) - _MockPathFile(pathFileName, datas2TestList) - - - self._db.createTable( self._table, "path", pathFileName ) - - _MockMapFile(self._mapFileName) - chunkConnector = PathChunkConnector(self._mapFileName, self._db, self._table, 0) - chunkConnector.run() - - sql_cmd = 'select * from %s' % (self._table) - self._db.execute(sql_cmd) - res = self._db.fetchall() - - for i in xrange(len(expectedList)): - resultTuple = res[i] - expectedTuple = expectedList[i] - self._assertExpectedTupleEqualsObsTuple(expectedTuple, resultTuple) - - self._db.dropTable( self._table ) - os.remove(pathFileName) - os.remove(self._mapFileName) - - def _assertExpectedTupleEqualsObsTuple(self, expectedTuple, resultTuple): - self.assertEquals(expectedTuple[0], resultTuple[1]) - self.assertEquals(expectedTuple[1], resultTuple[2]) - self.assertEquals(expectedTuple[2], resultTuple[3]) - self.assertEquals(expectedTuple[3], resultTuple[4]) - self.assertEquals(expectedTuple[4], resultTuple[5]) - self.assertEquals(expectedTuple[5], resultTuple[6]) - self.assertEquals(expectedTuple[6], resultTuple[7]) - self.assertEquals(expectedTuple[7], resultTuple[8]) - self.assertEquals(expectedTuple[8], resultTuple[9]) - - -class _MockPathFile: - - def __init__(self, fileName, lines): - path = open(fileName, "w"); - for line in lines: - path.write(line) - path.close - - -class _MockMapFile: - - def __init__ (self, fileName): - map = open(fileName, "w") - line1 = "chunk1" + '\t' + "dmel_chr4" + '\t' + "1" + '\t'+ "100000" + "\n" - line2 = "chunk2" + '\t' + "dmel_chr4" + '\t' + "90001" + '\t'+ "190000" + "\n" - line3 = "chunk3" + '\t' + "dmel_chr4" + '\t' + "180001" + '\t' + "280000" + "\n" - map.write(line1) - map.write(line2) - map.write(line3) - map.close - - -test_suite = unittest.TestSuite() -test_suite.addTest( unittest.makeSuite( Test_PathChunkConnector ) ) -if __name__ == "__main__": - unittest.TextTestRunner(verbosity=2).run( test_suite ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/convCoord/test/convCoordTestSuite.py --- a/commons/pyRepetUnit/convCoord/test/convCoordTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -import unittest -import sys -import TestConvCoordWithOverlapps -import TestConvMapChr2Chunk -import TestConvSetChr2Chunk -import TestConvPathChr2Chunk - -def main(): - commonsTestSuite = unittest.TestSuite() - commonsTestSuite.addTest(unittest.makeSuite(TestConvCoordWithOverlapps.Test_ConvCoordWithOverlaps,'test')) - commonsTestSuite.addTest(unittest.makeSuite(TestConvMapChr2Chunk.Test_ConvMapChr2Chunk,'test')) - commonsTestSuite.addTest(unittest.makeSuite(TestConvSetChr2Chunk.Test_ConvSetChr2Chunk,'test')) - commonsTestSuite.addTest(unittest.makeSuite(TestConvPathChr2Chunk.Test_ConvPathChr2Chunk,'test')) - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(commonsTestSuite) - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/doc/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/doc/api-objects.txt --- a/commons/pyRepetUnit/doc/api-objects.txt Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -commons.Checker commons.Checker-module.html -commons.Checker.DEFAULT_LOGGER_NAME commons.Checker-module.html#DEFAULT_LOGGER_NAME -commons.Checker.LOG_FILE commons.Checker-module.html#LOG_FILE -commons.IComponentWrapper commons.IComponentWrapper-module.html -commons.IDataProcessor commons.IDataProcessor-module.html -commons.Checker.Checker commons.Checker.Checker-class.html -commons.Checker.Checker.getLogger commons.Checker.Checker-class.html#getLogger -commons.Checker.Checker.__init__ commons.Checker.Checker-class.html#__init__ -commons.Checker.Checker.setLogger commons.Checker.Checker-class.html#setLogger -commons.Checker.Checker._handle commons.Checker.Checker-class.html#_handle -commons.Checker.IChecker.check commons.Checker.IChecker-class.html#check -commons.Checker.CheckerException commons.Checker.CheckerException-class.html -commons.Checker.CheckerException.msg commons.Checker.CheckerException-class.html#msg -commons.Checker.CheckerException.__init__ commons.Checker.CheckerException-class.html#__init__ -commons.Checker.ConfigChecker commons.Checker.ConfigChecker-class.html -commons.Checker.ConfigChecker.optionsDict commons.Checker.ConfigChecker-class.html#optionsDict -commons.Checker.ConfigChecker.check commons.Checker.ConfigChecker-class.html#check -commons.Checker.ConfigChecker.__init__ commons.Checker.ConfigChecker-class.html#__init__ -commons.Checker.ConfigChecker.sectionName commons.Checker.ConfigChecker-class.html#sectionName -commons.Checker.ConfigException commons.Checker.ConfigException-class.html -commons.Checker.ConfigException.messages commons.Checker.ConfigException-class.html#messages -commons.Checker.ConfigException.msg commons.Checker.ConfigException-class.html#msg -commons.Checker.ConfigException.__init__ commons.Checker.ConfigException-class.html#__init__ -commons.Checker.IChecker commons.Checker.IChecker-class.html -commons.Checker.IChecker.check commons.Checker.IChecker-class.html#check -commons.Checker._Logger commons.Checker._Logger-class.html -commons.Checker._Logger.getLogger commons.Checker._Logger-class.html#getLogger -commons.Checker._Logger._Logger__single commons.Checker._Logger-class.html#_Logger__single -commons.Checker._Logger.__init__ commons.Checker._Logger-class.html#__init__ -commons.IComponentWrapper.IComponentWrapper commons.IComponentWrapper.IComponentWrapper-class.html -commons.IComponentWrapper.IComponentWrapper.loadConfig commons.IComponentWrapper.IComponentWrapper-class.html#loadConfig -commons.IComponentWrapper.IComponentWrapper.run commons.IComponentWrapper.IComponentWrapper-class.html#run -commons.IComponentWrapper.IComponentWrapper.getComponent commons.IComponentWrapper.IComponentWrapper-class.html#getComponent -commons.IComponentWrapper.IComponentWrapper.clean commons.IComponentWrapper.IComponentWrapper-class.html#clean -commons.IDataProcessor.IDataProcessor commons.IDataProcessor.IDataProcessor-class.html -commons.IDataProcessor.IDataProcessor.run commons.IDataProcessor.IDataProcessor-class.html#run diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/doc/class-tree.html --- a/commons/pyRepetUnit/doc/class-tree.html Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ - - - - - Class Hierarchy - - - - - - - - - - - - - - - - - - - - -
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- Generated by Epydoc 3.0.1 on Fri Apr 10 16:39:01 2009 - - http://epydoc.sourceforge.net -
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Module Checker

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-

Created on 9 avr. 2009

- -
-

Author: - oinizan -

-
- - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - Checker
- A concrete checker implementation with a logging. -
-   - - CheckerException
- Exception raised during check. -
-   - - ConfigChecker
- A checker for config file. -
-   - - ConfigException
- A exception raised by check method class ConfigChecker -
-   - - IChecker
- Interface emulation for a checker -
-   - - _Logger -
- - - - - - - - - - - - -
- - - - - -
Variables[hide private]
-
-   - - DEFAULT_LOGGER_NAME = 'log02' -
-   - - LOG_FILE = '/home/oinizan/workspace/repet_pipe/pyRepetUnit/bla... -
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Variables Details[hide private]
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LOG_FILE

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Value:
- 
-'/home/oinizan/workspace/repet_pipe/pyRepetUnit/blaster/check/longconf\
-.ini'
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- - - - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/doc/commons.Checker-pysrc.html --- a/commons/pyRepetUnit/doc/commons.Checker-pysrc.html Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,259 +0,0 @@ - - - - - commons.Checker - - - - - - - - - - - - - - - - - - - - -
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Source Code for Module commons.Checker

-
-  1  ''' 
-  2  Created on 9 avr. 2009 
-  3   
-  4  @author: oinizan 
-  5  ''' 
-  6  import logging.config 
-  7  import ConfigParser 
-  8  from ConfigParser import NoSectionError 
-  9  from ConfigParser import NoOptionError 
- 10   
- 11  LOG_FILE = "/home/oinizan/workspace/repet_pipe/pyRepetUnit/blaster/check/longconf.ini" 
- 12  DEFAULT_LOGGER_NAME = "log02" 
- 13   
-
 14 -class IChecker(): 
-
 15      """ 
- 16      Interface emulation for a checker  
- 17      """ 
-
 18 -    def check(self, arg=""): 
-
 19          """ 
- 20          perform check, raise a CheckerException if error occured 
- 21           
- 22          @param arg:  a collecting parameter: put here all you need to perform check   
- 23          @type arg: choose the appropriate type 
- 24          """ 
- 25          pass 
-
 26   
-
 27 -class Checker (IChecker): 
-
 28      """ 
- 29      A concrete checker implementation with a logging. 
- 30      Logger instance is a singleton of logging module  
- 31      """ 
-
 32 -    def _handle (self): 
-
 33          try: 
- 34              single = _Logger() 
- 35          except _Logger, l: 
- 36              single = l 
- 37          return single     
-
 38       
-
 39 -    def __init__(self): 
-
 40          logger = self._handle() 
- 41          self._log = logger.getLogger() 
-
 42      
-
 43 -    def setLogger(self, logger): 
-
 44          """ 
- 45          set (change) default logger 
- 46           
- 47          @param logger: a new logger 
- 48          @type logger: class Logger  
- 49          """ 
- 50          self._log = logger 
-
 51   
-
 52 -    def getLogger(self): 
-
 53          """ 
- 54          returns the logger instance 
- 55          """ 
- 56          return self._log 
-
 57   
-
 58 -class CheckerException(Exception): 
-
 59      """ 
- 60      Exception raised during check.  
- 61       
- 62      @ivar msg : message embeded in Execption class    
- 63      @type msg: str 
- 64       
- 65      """ 
-
 66 -    def __init__(self,msg=""): 
-
 67          self.msg = msg 
- 68          Exception.__init__(self, msg) 
-
 69   
-
 70 -class ConfigChecker (IChecker): 
-
 71      """ 
- 72      A checker for config file.  
- 73      @ivar sectionName: section to check in config file 
- 74      @type sectionName: str 
- 75       
- 76      @ivar optionsDict: dict with option to check as keys and empty strings "" as values 
- 77      @type optionsDict: class Dict 
- 78      """ 
- 79   
-
 80 -    def __init__ (self, sectionName, optionsDict): 
-
 81          self._sectionName = sectionName 
- 82          self._optionsDict = optionsDict 
-
 83      """ 
- 84      Check options stored in optionsDict. 3 checks are performed: 
- 85      (i) config file existence, (ii) section existence, (iii) options existences 
- 86      If a check fail, raise a ConfigException with a list of messages 
- 87      """ 
-
 88 -    def check (self, configFile): 
-
 89          config = ConfigParser.ConfigParser() 
- 90          msg = [] 
- 91          try: 
- 92              config.readfp( open(configFile) ) 
- 93          except IOError, e: 
- 94              msg.append("CONFIG FILE not found - " + e.message) 
- 95              raise ConfigException("", msg)  
- 96   
- 97          if not (config.has_section(self._sectionName)): 
- 98              msg.append("[" + self._sectionName + "]" + " section not found - ") 
- 99              raise ConfigException("", msg) 
-100            
-101          isExceptionOccured = False         
-102          for key in self._optionsDict.keys(): 
-103              try: 
-104                  self._optionsDict[key] = config.get(self._sectionName, key)  
-105              except NoOptionError, e: 
-106                  msg.append("[" + self._sectionName + "]" + " - " + e.message) 
-107                  isExceptionOccured = True 
-108           
-109          if (isExceptionOccured): 
-110              raise ConfigException("", msg)  
-
111   
-
112 -class ConfigException(Exception): 
-
113       
-114      """ 
-115      A exception raised by check method class ConfigChecker 
-116       
-117      @ivar msg : message embeded in Execption class    
-118      @type msg: str 
-119       
-120      @ivar messages: list of messages 
-121      @type messages: Class list 
-122        
-123      """ 
-
124 -    def __init__(self,msg, messages=[]): 
-
125          self.messages = messages 
-126          Exception.__init__(self, msg) 
-
127   
-
128 -class _Logger: 
-
129       
-130      __single = None 
-131       
-
132 -    def __init__( self, loggerName ="" ): 
-
133          if _Logger.__single: 
-134              raise _Logger.__single 
-135          logging.config.fileConfig(LOG_FILE) 
-136          if (loggerName != ""): 
-137              self.__log = logging.getLogger(loggerName) 
-138          else: 
-139              self.__log = logging.getLogger(DEFAULT_LOGGER_NAME) 
-140          _Logger.__single = self 
-
141   
-
142 -    def getLogger(self): 
-
143          return self.__log 
-
144   
-
-
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Class Checker

source code

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-IChecker --+
-           |
-          Checker
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-

A concrete checker implementation with a logging. Logger instance is a - singleton of logging module

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_handle(self) - source code - -
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getLogger(self)
- returns the logger instance		 - source code - -
- -
-   - - - - - - -
setLogger(self, - logger)
- set (change) default logger		 - source code - -
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-

Inherited from IChecker: - check -

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Method Details[hide private]
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-

setLogger(self, - logger) -

- 		source code  -
- -

set (change) default logger

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  • logger (class Logger) - a new logger
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Class CheckerException

source code

-
-              object --+        
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-                              CheckerException
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-

Exception raised during check.

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__init__(self, - msg='')
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
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Inherited from exceptions.Exception: - __new__ -

-

Inherited from exceptions.BaseException: - __delattr__, - __getattribute__, - __getitem__, - __getslice__, - __reduce__, - __repr__, - __setattr__, - __setstate__, - __str__ -

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Inherited from object: - __hash__, - __reduce_ex__ -

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Inherited from exceptions.BaseException: - args, - message -

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__init__(self, - msg='') -
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x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

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Class ConfigChecker

source code

-
-IChecker --+
-           |
-          ConfigChecker
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-

A checker for config file.

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Instance Methods[hide private]
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-   - - - - - - -
__init__(self, - sectionName, - optionsDict) - source code - -
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check(self, - configFile)
- perform check, raise a CheckerException if error occured		 - source code - -
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Instance Variables[hide private]
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- class Dict - - optionsDict
- dict with option to check as keys and empty strings "" as - values -
- str - - sectionName
- section to check in config file -
- - - - - - -
- - - - - -
Method Details[hide private]
-
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check(self, - configFile) -

- 		source code  -
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perform check, raise a CheckerException if error occured

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-
    -
  • arg - a collecting parameter: put here all you need to perform check
    • -
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Class ConfigException

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A exception raised by check method class ConfigChecker

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__init__(self, - msg, - messages=[])
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Inherited from exceptions.Exception: - __new__ -

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Inherited from exceptions.BaseException: - __delattr__, - __getattribute__, - __getitem__, - __getslice__, - __reduce__, - __repr__, - __setattr__, - __setstate__, - __str__ -

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Inherited from exceptions.BaseException: - args, - message -

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__init__(self, - msg, - messages=[]) -
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x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

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Class IChecker

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Known Subclasses:
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Interface emulation for a checker

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check(self, - arg='')
- perform check, raise a CheckerException if error occured		 - source code - -
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check(self, - arg='') -

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perform check, raise a CheckerException if error occured

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  • arg (choose the appropriate type) - a collecting parameter: put here all you need to perform check
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Class _Logger

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Module IComponentWrapper

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Classes[hide private]
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- A interface wrapper for all pipelines component -
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Source Code for Module commons.IComponentWrapper

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- 1   
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 2 -class IComponentWrapper: 
-
 3      """ 
- 4       A interface wrapper for all pipelines component 
- 5      """ 
- 6       
-
 7 -    def run(self): 
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 8          """ 
- 9          run the component 
-10          """ 
-11          pass 
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12       
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13 -    def loadConfig(self, configParserInstance): 
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14          """ 
-15          load component config 
-16           
-17          @param configParserInstance: config parser where config file is loaded 
-18          @type  configParserInstance: class ConfigParser 
-19          """ 
-20          pass 
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21   
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22 -    def clean(self): 
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23          """ 
-24          clean files generated by run method 
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27       
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28 -    def getComponent (self): 
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29          """ 
-30          return component wrapped 
-31          """ 
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32   
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Class IComponentWrapper

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A interface wrapper for all pipelines component

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Instance Methods[hide private]
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clean(self)
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getComponent(self)
- return component wrapped		 - source code - -
- -
-   - - - - - - -
loadConfig(self, - configParserInstance)
- load component config		 - source code - -
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run(self)
- run the component		 - source code - -
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Method Details[hide private]
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loadConfig(self, - configParserInstance) -

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load component config

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  • configParserInstance (class ConfigParser) - config parser where config file is loaded
    • -
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Module IDataProcessor

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- A interface for all pipelines data processor -
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Source Code for Module commons.IDataProcessor

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 1 -class IDataProcessor: 
-
 2      """ 
- 3      A interface for all pipelines data processor 
- 4      """     
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 5 -    def run(self): 
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 6          """ 
- 7          run: process the data 
- 8          """ 
- 9          pass 
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Class IDataProcessor

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A interface for all pipelines data processor

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Instance Methods[hide private]
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run(self)
- run: process the data		 - source code - -
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   Trees      Indices      Help   
- - - - - -
  - - - - -
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-
- -

API Documentation

- -

This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python -objects defined by the project is divided into separate pages for each -package, module, and class. The API documentation also includes two -pages containing information about the project as a whole: a trees -page, and an index page.

- -

Object Documentation

- -

Each Package Documentation page contains:

-
    -
  • A description of the package.
    • -
  • A list of the modules and sub-packages contained by the - package.
    • -
  • A summary of the classes defined by the package.
    • -
  • A summary of the functions defined by the package.
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  • A detailed description of each function defined by the - package.
    • -
  • A detailed description of each variable defined by the - package.
    • -
- -

Each Module Documentation page contains:

-
    -
  • A description of the module.
    • -
  • A summary of the classes defined by the module.
    • -
  • A summary of the functions defined by the module.
    • -
  • A summary of the variables defined by the module.
    • -
  • A detailed description of each function defined by the - module.
    • -
  • A detailed description of each variable defined by the - module.
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- -

Each Class Documentation page contains:

-
    -
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    • -
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    • -
  • A description of the class.
    • -
  • A summary of the methods defined by the class.
    • -
  • A summary of the instance variables defined by the class.
    • -
  • A summary of the class (static) variables defined by the - class.
    • -
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    • -
  • A detailed description of each instance variable defined by the - class.
    • -
  • A detailed description of each class (static) variable defined - by the class.
    • -
- -

Project Documentation

- -

The Trees page contains the module and class hierarchies:

-
    -
  • The module hierarchy lists every package and module, with - modules grouped into packages. At the top level, and within each - package, modules and sub-packages are listed alphabetically.
    • -
  • The class hierarchy lists every class, grouped by base - class. If a class has more than one base class, then it will be - listed under each base class. At the top level, and under each base - class, classes are listed alphabetically.
    • -
- -

The Index page contains indices of terms and - identifiers:

-
    -
  • The term index lists every term indexed by any object's - documentation. For each term, the index provides links to each - place where the term is indexed.
    • -
  • The identifier index lists the (short) name of every package, - module, class, method, function, variable, and parameter. For each - identifier, the index provides a short description, and a link to - its documentation.
    • -
- -

The Table of Contents

- -

The table of contents occupies the two frames on the left side of -the window. The upper-left frame displays the project -contents, and the lower-left frame displays the module -contents:

- - - - - - - - - -
- Project
Contents
...		 - API
Documentation
Frame


-
- Module
Contents
 
...
  -

- -

The project contents frame contains a list of all packages -and modules that are defined by the project. Clicking on an entry -will display its contents in the module contents frame. Clicking on a -special entry, labeled "Everything," will display the contents of -the entire project.

- -

The module contents frame contains a list of every -submodule, class, type, exception, function, and variable defined by a -module or package. Clicking on an entry will display its -documentation in the API documentation frame. Clicking on the name of -the module, at the top of the frame, will display the documentation -for the module itself.

- -

The "frames" and "no frames" buttons below the top -navigation bar can be used to control whether the table of contents is -displayed or not.

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The Navigation Bar

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A navigation bar is located at the top and bottom of every page. -It indicates what type of page you are currently viewing, and allows -you to go to related pages. The following table describes the labels -on the navigation bar. Note that not some labels (such as -[Parent]) are not displayed on all pages.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
LabelHighlighted when...Links to...
[Parent](never highlighted) the parent of the current package
[Package]viewing a packagethe package containing the current object -
[Module]viewing a modulethe module containing the current object -
[Class]viewing a class the class containing the current object
[Trees]viewing the trees page the trees page
[Index]viewing the index page the index page
[Help]viewing the help page the help page
- -

The "show private" and "hide private" buttons below -the top navigation bar can be used to control whether documentation -for private objects is displayed. Private objects are usually defined -as objects whose (short) names begin with a single underscore, but do -not end with an underscore. For example, "_x", -"__pprint", and "epydoc.epytext._tokenize" -are private objects; but "re.sub", -"__init__", and "type_" are not. However, -if a module defines the "__all__" variable, then its -contents are used to decide which objects are private.

- -

A timestamp below the bottom navigation bar indicates when each -page was last updated.

- - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Fri Apr 10 16:39:01 2009 - - http://epydoc.sourceforge.net -
- - - - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/doc/identifier-index.html --- a/commons/pyRepetUnit/doc/identifier-index.html Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,267 +0,0 @@ - - - - - Identifier Index - - - - - - - - - - - - - - - - - - - - -
   Trees      Indices      Help   
- - - - - -
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-
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Identifier Index

-		 -[ - A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z - _ -] -
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- [hide private] - - - - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/TranslateInAllFramesAndReplaceStopByX.py --- a/commons/pyRepetUnit/fastaTranslation/allFrames/TranslateInAllFramesAndReplaceStopByX.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -from commons.core.seq.BioseqUtils import BioseqUtils - -class TranslateInAllFramesAndReplaceStopByX(object): - - def __init__(self): - self._inputFile = "" - self._outputFile = "" - - def setInputFile(self, input): - self._inputFile = input - - def setOutputFile(self, output): - self._outputFile = output - - def run(self): - """ - read a fasta file with nucleotide sequences and translate all sequences in all frames, write the result in a file - """ - if not FileUtils.isRessourceExists(self._inputFile): - raise Exception("Warning your input file %s does not exist!\n" % self._inputFile) - bioseqList = BioseqUtils.extractBioseqListFromFastaFile(self._inputFile) - bioseqListInAllFrames = BioseqUtils.translateBioseqListInAllFrames(bioseqList) - bioseqListTranslatedAndStopsReplace = BioseqUtils.replaceStopCodonsByXInBioseqList(bioseqListInAllFrames) - BioseqUtils.writeBioseqListIntoFastaFile(bioseqListTranslatedAndStopsReplace, self._outputFile) - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_F_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_F_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils - -class Test_F_TranslateAfastaFileInAllFrameAndReplaceStopsByX(unittest.TestCase): - - def setUp(self): - self._inputFile = "./datas/ConsensusTestFile_nt.fsa" - self._outputFile = "./datas/PreprocessOuputFile" - self._prg = "translateAfastaFileInAllFrameAndReplaceStopsByX_script.py" - - - def testAcceptanceTranslateAfastaFileInAllFrameAndReplaceStopsByX_script(self): - cmd = self._prg - cmd += " -i %s" % ( self._inputFile ) - cmd += " -o %s" % ( self._outputFile ) - os.system( cmd ) - self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "./datas/ConsensusTestFile_aaWithoutStop.fsa")) - os.system( "rm " + self._outputFile ) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_F_TranslateInAllFramesAndReplaceStopByX.py --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_F_TranslateInAllFramesAndReplaceStopByX.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX -from commons.core.seq.Bioseq import Bioseq -from commons.core.utils.FileUtils import FileUtils - -class Test_F_TranslateInAllFramesAndReplaceStopByX(unittest.TestCase): - - def setUp(self): - self.bioseq = Bioseq() - self.preProcess = TranslateInAllFramesAndReplaceStopByX() - self._inputFile = "./datas/test_input_nt.fa" - self._outputFile = "./datas/PreProcessResult.fa" - - - def testAcceptanceTranslateAfastaFileInAllFrame(self): - self.preProcess.setInputFile(self._inputFile) - self.preProcess.setOutputFile(self._outputFile) - self.preProcess.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._outputFile, "./datas/test_input_aa.fa")) - os.system("rm " + self._outputFile) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -import os -import unittest -from commons.core.utils.FileUtils import FileUtils - -class Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX(unittest.TestCase): - - def setUp(self): - self._inputFile = "dummyInputFile" - self._outputFile = "dummyOuputFile" - self._prg = "translateAfastaFileInAllFrameAndReplaceStopsByX_script.py" - - - def testTranslateAfastaFileInAllFrameAndReplaceStopsByX_script(self): - f = open(self._inputFile, "w") - f.write(">header1 description\n") - f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n") - f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n") - f.write(">header2\n") - f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n") - f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA") - f.close() - # expected fasta translated file - f = open("expectedTranslated.fa", "w") - f.write(">header1_1 description\n") - f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n") - f.write(">header1_2 description\n") - f.write("VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL\n") - f.write(">header1_3 description\n") - f.write("WLLVDQFMITMISRRCLVAPTNQQYNASRAX\n") - f.write(">header1_4 description\n") - f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n") - f.write(">header1_5 description\n") - f.write("QALLALYCXLVGATRHLREIIVIINXSTRSH\n") - f.write(">header1_6 description\n") - f.write("KLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT\n") - f.write(">header2_1\n") - f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n") - f.write(">header2_2\n") - f.write("VASSXSVYDHNDFTXVSRGYDXSTIXCEXSL\n") - f.write(">header2_3\n") - f.write("WLLVDQFMITMISRRCLVATTNQQYNASRAX\n") - f.write(">header2_4\n") - f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n") - f.write(">header2_5\n") - f.write("QALLALYCXLVVATRHLREIIVIINXSTRSH\n") - f.write(">header2_6\n") - f.write("KLYSHYIVDXSXPRDTYVKSLXSXTDQLEAT\n") - f.close() - - #normal launch - cmd = self._prg - cmd += " -i %s" % ( self._inputFile ) - cmd += " -o %s" % ( self._outputFile ) - os.system( cmd ) - self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa")) - os.system( "rm " + self._outputFile ) - - #verbose option - cmd = self._prg - cmd += " -i %s" % ( self._inputFile ) - cmd += " -o %s" % ( self._outputFile ) - cmd += " -v 1" - os.system( cmd ) - self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa")) - os.system( "rm " + self._outputFile ) - - #clean option - cmd = self._prg - cmd += " -i %s" % ( self._inputFile ) - cmd += " -o %s" % ( self._outputFile ) - cmd += " -c" - os.system( cmd ) - self.assertTrue( FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa" ) ) - self.assertFalse( FileUtils.isRessourceExists( self._inputFile ) ) - os.system( "rm " + self._outputFile) - os.system("rm expectedTranslated.fa") - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateInAllFramesAndReplaceStopByX.py --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateInAllFramesAndReplaceStopByX.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX -from commons.core.seq.Bioseq import Bioseq -from commons.core.utils.FileUtils import FileUtils - -class Test_TranslateInAllFramesAndReplaceStopByX(unittest.TestCase): - - def setUp(self): - self.bioseq = Bioseq() - self.preProcess = TranslateInAllFramesAndReplaceStopByX() - self._inputFile = "./datas/dummy.fa" - self._outputFile = "./datas/dummyoutput.fa" - - - def testRun(self): - self.preProcess.setInputFile(self._inputFile) - self.preProcess.setOutputFile(self._outputFile) - # real fasta file - f = open(self._inputFile, "w") - f.write(">header1 description\n") - f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n") - f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n") - f.write(">header2\n") - f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n") - f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA") - f.close() - # expected fasta translated file - f = open("./datas/expectedTranslated.fa", "w") - f.write(">header1_1 description\n") - f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n") - f.write(">header1_2 description\n") - f.write("VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL\n") - f.write(">header1_3 description\n") - f.write("WLLVDQFMITMISRRCLVAPTNQQYNASRAX\n") - f.write(">header1_4 description\n") - f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n") - f.write(">header1_5 description\n") - f.write("QALLALYCXLVGATRHLREIIVIINXSTRSH\n") - f.write(">header1_6 description\n") - f.write("KLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT\n") - f.write(">header2_1\n") - f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n") - f.write(">header2_2\n") - f.write("VASSXSVYDHNDFTXVSRGYDXSTIXCEXSL\n") - f.write(">header2_3\n") - f.write("WLLVDQFMITMISRRCLVATTNQQYNASRAX\n") - f.write(">header2_4\n") - f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n") - f.write(">header2_5\n") - f.write("QALLALYCXLVVATRHLREIIVIINXSTRSH\n") - f.write(">header2_6\n") - f.write("KLYSHYIVDXSXPRDTYVKSLXSXTDQLEAT\n") - f.close() - self.preProcess.run() - self.assertTrue(FileUtils.are2FilesIdentical("./datas/expectedTranslated.fa", self._outputFile)) - os.system("rm " + self._inputFile) - os.system("rm " + self._outputFile) - os.system("rm ./datas/expectedTranslated.fa") - # empty fasta file - #self.preProcess.translateAfastaFileInAllFrame() - #self.assertFalse(FileUtils.isRessourceExists(self._outputFile)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/ConsensusTestFile_aaWithoutStop.fsa --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/ConsensusTestFile_aaWithoutStop.fsa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ ->blumeria_Grouper_590_20:NoCat_1 -FRSYXNVXPTTXFVDLLVEGSLCNNEGXKDVNSTTLLNTDTRLLLIPIDSPCGISYXQQX -TTLTQGIRNLRSPNTSLSGLLIIEPSRIDNVYPNIEIIESSTPKPLINNCHXSSPDLSLY -SIISTLKNIC ->blumeria_Grouper_590_20:NoCat_2 -FDXIEMYNPLLSSWTCWXREAYAIMKDKRMSIRLLFXTQIPDSFXSQXIARAGSPINSSK -QRXHRVYAISVRQTPVCRDYXLSSLVGSTMCIPTXKXXKAQHPNPSSITAINHHLTYLCT -PXFQHXRIFV ->blumeria_Grouper_590_20:NoCat_3 -SIXLKCITHYLVRGLVGRGKLMQXXRIKGCQFDYSSKHRYQTPFNPNRXPVRDLLLTAVN -NANTGYTQSPFAKHQSVGTTNYRAXXDRQCVSQHRNNRKLNTQTPHQXLPLIITXLISVL -HNFNTXEYL ->blumeria_Grouper_590_20:NoCat_4 -YKYSXVLKLWSTEISQVMINGSYXXGVWVLSFLLFLCWDTHCRSYXARXLVVPTDWCLAN -GDCVYPVLALFTAVNRRSRTGYLLGLKGVWYLCLEEXSNXHPFILHYCISFPLPTSPRTK -XWVIHFNXIE ->blumeria_Grouper_590_20:NoCat_5 -TNILXCXNYGVQRXVRXXLMAVIDEGFGCXAFYYFYVGIHIVDPTRLDNXXSRQTGVWRT -EIAYTLCXRCLLLLIGDPARAIYWDXKESGICVXKSSRIDILLSFIIAXASLYQQVHELS -SGLYISIXSK ->blumeria_Grouper_590_20:NoCat_6 -QIFXSVEIMEYRDKSGDDXWQLLMRGLGVELSIISMLGYTLSILLGSIISSPDRLVFGER -RLRIPCVSVVYCCXXEIPHGLSIGIKRSLVSVFRRVVELTSFYPSLLHKLPSTNKSTNXV -VGYTFQXDR ->blumeria_Grouper_4152_12:NoCat_1 -GPAATNCAIAARKXTLMESTKFLSSPVESGXRAASTLLIAVEHIVNCAAFCLALRSSASI -AASNSGGCVFFLPAASSAGGCGASGGFSAPAALVDGVSALFAGLTSAGRGSAGTVMRFSG -ATTVFLGDPVGSKTCSASSGLEDAQTESARVFSFSTSASTISTSGTL ->blumeria_Grouper_4152_12:NoCat_2 -DRPPRIARLLLASRLXWSLQNFCLHRWRAVEELPRHCXXPSSILXIARLFVLPCAPPLRS -LQAILEGVYFFCLLLLVLEAAGPVEGFRLLLPXWMVFQPFSRASLLQVAVVLEPXCASRV -RRRFFWGIRWDPRLALRLLGWRMPKLNRRGFLASRLLRPPYLPRGH ->blumeria_Grouper_4152_12:NoCat_3 -TGRHELRDCCSQVDFDGVYKIFVFTGGERLKSCLDTANSRRAYCELRGFLSCPALLRFDR -CKQFWRVCIFSACCFXCWRLRGQWRVFGSCCLSGWCFSPFRGPHFCRSRXCWNRDALLGC -DDGFSGGSGGIQDLLCVFWAGGCPNXIGEGFXLLDFCVHHIYLGDI ->blumeria_Grouper_4152_12:NoCat_4 -QCPRGRYGGRRSREAKNPRRFSLGILQPRRRRASLGSHRIPQKNRRRTREAHHGSSTTAT -CRSEAREKGXNTIHXGSRSRKPSTGPAASSTRSSRQKKYTPSRIACSDRSGGAQGKTKSR -AIHNMLDGYXQCRGSSSTALHRXRQKFCRLHQSLLASSNRAIRGGRS ->blumeria_Grouper_4152_12:NoCat_5 -NVPEVDMVDAEVEKLKTLADSVWASSSPEDAEQVLDPTGSPRKTVVAPEKRITVPALPRP -AEVRPAKRAETPSTKAAGAENPPLAPQPPALEAAGRKNTHPPELLAAIEAEERRARQKAA -QFTICSTAISSVEAALQPLSTGEDKNFVDSIKVYLRAAIAQFVAAG ->blumeria_Grouper_4152_12:NoCat_6 -MSPRXIWWTQKSRSXKPSPIQFGHPPAQKTQSKSWIPPDPPEKPSSHPRSASRFQHYRDL -QKXGPRKGLKHHPLRQQEPKTLHWPRSLQHXKQQAEKIHTLQNCLQRSKRRSAGQDKKPR -NSQYARRLLAVSRQLFNRSPPVKTKILXTPSKSTCEQQSRNSWRPV diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/ConsensusTestFile_nt.fsa --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/ConsensusTestFile_nt.fsa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ ->blumeria_Grouper_590_20:NoCat -TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA -AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT -ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA -ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA -CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC -TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC -TCCATAATTTCAACACTNAAGAATATTTGTA ->blumeria_Grouper_4152_12:NoCat -GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA -AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC -GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC -GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC -TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT -TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT -GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG -CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC -ATATCTACCTCGGGGACATTG diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/test_input_aa.fa --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/test_input_aa.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,258 +0,0 @@ ->blumeria_Grouper_28830_3_1 -CGFXLISLXSQXFHVGVSWLRLINNIMRVELETNKTXIXFYNTGSPTYLNIPPHHVSQST -AHNLHGRVSINWDPQTIPLLKTSCPQLIXITSXLEILLWYHSNXILAEFLSVFLSCSSIR -RLPYHRLRTGCPSRTYAGNRFVPLYLLPNLYPPGDIKEXVLLLXQAATAHGPSXXGSILC -LRWRTRSTQSPGAXVRISAFSSWRXARILSLVAFILLTXERAIGAGCFLPSSSAQRRSSD -SVASRVYTGXEFSSSGGXVPKSKKXGLYPLGETLRLKFITASERAPASVILGESRRTLTS -MAFRTPFACSTLPFPLGLAGVVWTTCSCWLAXNRCASMPPKQPALSLIICFGFPKFWIIY -VSRGTVLAKSALGTKRDSSQPVAYSIALSKTWGPTXVXSIPHRVRGGAGTIGVKLPSNGS -GGFMSXQDLHFRTASXAARISSGCQNLRPNSRIVLPIDAWPWPSXTFTAVDTRSSYSKIS -SRVAAPDGPGASPTCCDGFFLMRCNLELYIAKLSRTQVAAIFRGSASPKVRNSVMHCRSM -RLSSCGCFISSISSSLSAPLWILEFSLSSVATFPSPSSLERNRTSQGRERKSARTFAFPR -RXIILILKCSIASKKRTILTGCSALVXIVRRDSWSVITVTSPPSTQXRQCCSDSKIPSNS -LSCAEXRCWVSFSFLEKXAMGCSTERSELLEHRMYGWSMTAPTNFWEASVSNMTGSLQSN -FFTTGDVVSASLILFHDXIDWSVRMTGQFLGPEDWSVSGPASWEKFLMRQRRXPAAFTNP -LISEVVVGIGLSLIAETFSGSAAMPCLEIWKPRKIPSETNSLHFEALRRRPXEANLEKIS -INRECNSAIESAQTATSSRSPATNGRNGSRTSSIKHWKVAGALHRPKGITSHSXTPKGVT -NAVFSEESLCIRICQNPFSRSRNAXKLCPAARXISSXAFGRGWACFFVILLSSLXSTQIR -QTVWLVWVSVFFWCXXQRCSPWSLTFAYELSRSCVAQESPRMACCCAGAISPRRGVLNWV -DNYPVSMRVFLSWESFIPFGGRDLSKSXRGIXLXYCREKLXCGMKGGLGAIXPLEYLKXX -RLFGLGEYXLXDXELVGQLSXEVAVCHLINIVAPVHGIKFVQVSHLLGMCHLGQLLETLX -IPESRMIQGDSSKETVQLKLHPXKLLGQGHQCLTFXKXXMYYKKSNIXRKTVKHNMLKSR -SQKKLKIGHRENELFVQKTFCVACHILPVEVVLLGVAQICPFLRPQSRYSGCPIHKFLHF -AFDIEWLQFRHRAAHLLFGLQGLFALDPNLLAQQGKXKXQALMNDRVVLQVLHIFYFSLI -GKFSXIYRXNATRCIXRLVHIPFVLLIPPALFSSTGSLSPSGLSFRNXSIRNACRELGMI -YLFLQCLVTQRRLAHTTLDQLWMRQMLEAFRLLTLRSELVHWTRNVXIHHPQVSTLXYRV -XLEPLDPQAPRWXVWGDYWKXWSRYVEVRVEYAASVYLXSEALPXHPKVGXRKLSGVVAQ -IVIESRRFLQLFVQMLSKATRVHHCRTVFXGYSLQLLPNRGVDXXLFFAPRXNLHPFPLQ -FXXPKQNMEAYVESSMIACGIIYSLCSHQQSAISIVVGIPRVFFYLPLLKGRADFQLRNA -KRNLGSTALFFALVQXHSMVRXLTGGINXXSHLCFAHHCLGWALFHRIAPRXRVFSXAET -RLAWLRVARRCLLKSQIAPPGMVFYFQMALLPKVERGLNFSKKFLFPRLHFYLLVWKLSR -SLQTFVXLEEKFVIGSLQTFDRFSWRDLLSLPLQLHXLRKNFRWLWFARQCDPSSSFPTE -HYSGRPXXLNRWXNAXKIWRRLKLGXPRIVRFSQQKYIILWLLVDQFMITMISRRCLVAP -TNQQYNASRAXDXXNVNFILXYRTANLFKYSPAPREPINSTQFARSGFHQLGST ->blumeria_Grouper_28830_3_2 -VASSXSVYDHNDFTXVSRGSDXSTIXCEXSLRLIKREFXSIIQDRQLIXIFPRTTXANQQ -RTICTVGFPSIGIHKLSPFSKLAVHSLFKLQVNXKFYYGITQTKSLLNFXVSFYPAPAYG -GYHTIDYELGVLHVHMPGIGLCRCTCCLICIHPVILRSRYYYYDKLLRPMARHSRAPSCV -FAGVLAVPSLRGRKYVXVPFLPGGKPVFYPXLLSYYXRRSVLLVRGVSFRVLRPRGAPLI -LWLHGYILDKNFPPPGAECRRVRSKGYTRWVRLFDXNSLPRVRERQLVXFXENPGELXPV -WLSERHLPVRLCHFLLAXLVWYGQPAVVGXLEIVVLLCLRSSQHCHXXSALAFQSSGXYT -XAEAQCXRSLHWELSGIPASLLRTQLHXARLGVLLEYDLYPTVSEEVLVLXELSFPVTGL -EVSXADRTCIFGQLREPRGSVRGAKTYALIPAXYCRLTHGLGPHEHLRPSILDPHIPRFL -VGLRRQMDQVHRLLVATGSFXXDAIWNCTSQNYLGPKWQLYLGEVPLLRLEIRXCTAGRC -GXVRVGALFPPSQVLFLHHFGFXSFRCRQXLHSLPLLPXREIEHHRDGRENQREHLLFRD -GRXSXYXNALXHLKNGPFXRAARLWSEXFVEIHGQLSPLRRRLLPSDANVVVTVKSQVIP -SLVLNNAAGYRLVFLRSKLWDAALNDRNCWSIACTVGVXLHPRTFGKRQFPIXREVSNQI -FLQLVMLXALVXYFSMIESIGPSEXQGNFXVQRIGPXVALLVGRNFXXDNVGNQLHLQIL -LFPRXLLAXACLXSLKLFRGLLQCHVXKYGNQGRFPLKQIACTLKHXGGDHRKRIXKKXV -STVSAILPLSLPRQLHRPGALRQMDGMALELLPXNTGKXLVRCIGRKAXLAIHRHRKESQ -MLFSLKSLCAYVSAKIRFPGRGMHRSYVLLRAEFHLEHLVGDGRVSSXSCXALYSQHKYA -KRFGXSGLASFFGVNNRGAAHGPLHLRMNXAGHVLHKKVPGWLVVAPGLYRLGGEFXIGL -TITPFLCGCFCLGRVLSHLAGEIYRKVEGEFNFDIVGKNCNAEXRVGWVPFDHWNIXSSE -DFSVWESINYRIKNWLVNXVEKLQFAIXXTSXPQFMEXSLSKCHICWECAIWDNSXRHCE -FLSPEXFKVIRAKKLCSXNCILRNCWARATNAXHFRNNRCIIRSQIFRERLXNITCXRAV -VKKNXKLDIGKMSYSCKKHSVWLAISFPXRLSFWGWLKFALSYGHKVGIRAVLFINFFIS -HSIXNGFNFVIELLIFYLAFRAYLLLIQIFWLNKESRSDRLXXTIVWCYRFYIFFIFHXL -VSFPEFIAETRRGVFSVWCIFPLFFXFHRRCFHQPAVFRPVACLSAIEAFVTLVVNWVXF -ICFCNVLXRKDVLPIRPWISYGCVKCWKLFAFXRXDRNWCIGLGMFEYIILKCPPCNTAC -DLNHSIRKLRAGEFGEIIGNDGPGTWKXESNMLPQYISSLRPYHDIRRXAKESFPESSRK -LXLSLVVSCSYSCKCCQRRPEYIIVEQYFKDTVYSSCPIEVLTDDCSSRRDEIFIHFHCN -SDSPSRIWKHMLNHQXLHVVXYIHYVLISKVQFPLWWEYRACFSICLFXRAVRIFSFGTR -KEIWEVPLYFSLLFSNIQWFVNXLAVXINSPIFVLLIIAXVGRCFIELRRGKGSFLRLKH -DWPGCGSRGAACXKVKXLLPVWFFIFRWPCFRKLKGDXIFRRSFCFHVFISTYXFGNXVV -HCRHLFDXKRNLXLGLFKPLIDSLGEIFCHCLCSFISFGKIFVGFGLPGNVILHQAFQLS -IIQADHDDXIGGEMRKKFGDVLNWDDLELXGSLNKNIXFCGFXLISLXSQXFHVGVSWLR -QINNIMRVELETNKTXISFYNTGPPTYLNIPPHHVSQSTAHNLHGRVSINWDP ->blumeria_Grouper_28830_3_3 -WLLVDQFMITMISRRCLVAPTNQQYNASRAXDXXNVNXILXYRIANLFKYSPAPREPINS -AQFARSGFHQLGSTNYPPSQNXLSTAYLNYKLIRNFIMVSLKLNPCXIFECLSILLQHTA -ATIPXTTNWVSFTYICREXVCAVVLVAXFVSTRXYXGVGIIIMTSCYGPWPVIVGLHLVS -SLAYSQYPVSGGVSTYKCLFFLEVSPYFIPSCFHTTNVGACYWCGVFPSEFFGPEALLXF -CGFTGIYWIRIFLLRGLSAEEXEVRAIPAGXDSSIEIHYREXESASXCNFRRIQENSDQY -GFQNAICLFDFAISSWPSWCGMDNLQLLASLKSLCFYASEAASIVTDNLLWLSKVLDNIR -EQRHSVSEVCIGNXAGFQPACCVLNCIEQDLGSYLSMIYTPPCQRRCWYYRSXASQXRVW -RFHELTGLAFSDSFVSREDQFGVPKPTPXFPHSIADXRMALALMNIYGRRYXILIFQDFX -XGCGARWTRCIAYLLRRVLFDEMQFGIVHRKIISDPSGSYIXGKCLSXGXKFGDALQVDA -VEFVWVLYFLHLKFSFCTTLDSRVFVVVSSYIPFPFFPREKXNITGTGEKISENICFSAT -VDNPDIKMLYSIXKTDHSDGLLGFGLNSSXRFMVSYHRYVAAFYPVTPMLXXQXNPKXFP -LLCXITLLGIVXFSXEVSYGMQHXTIGIVGASHVRLEYDCTHELLGSVSFQYDGKSPIKF -FYNWXCCKRXFDTFPXLNRLVRQNDRAIFRSRGLVREWPCXLGEIFNETTXVTSCIYKSS -YFRGSCWHRPVSDRXNFFGVCCNAMFRNMETKEDSLXNKXPALXSIEEETIGSESRKNKY -QPXVQFCHXVCPDSYIVQEPCDKWTEWLXNFFHKTLESSWCVAXAERHNXPFIDTERSHK -CCFLXRVFVHTYLPKSVFQVEECIEVMSCCALNFILSIWXGMGVFLRNLVKLSIVNTNTP -NGLVSLGXRLFLVLITEVQPMVPYICVXIEPVMCCTRKSPDGLLLRRGYIASEGSFKLGX -QLPRFYAGVSVLGEFYPIWRERFIEKLKGNLTLILXGKTVMRNEGWAGCHLTIGIFEVVK -TFRFGRVLIIGLRIGWSIKLRSCSLPFDKHRSPSSWNKVCPSVTSAGNVPSGTTPRDTVN -SXVQNDSRXFEQRNCAVKIASLEIVGPGPPMPDILEIIDVLXEVKYLEKDCETXHAEEPX -SKKTENWTXGKXVIRAKNILCGLPYPSRRGCPFGGGSNLPFPTATKXVFGLSYSXISSFR -IRYRMASISSSSCSSSIWPSGLICSXSKSSGSTRKVEVTGFDERSCGVTGFTYFLFFIDW -XVFLNLSLKRDEVYLAFGAYSLCSFDSTGAVFINRQSFAQWPVFPQLKHSXRLSXIGYDL -SVSAMSCDAKTSCPYDLGSAMDASNAGSFSPFDAEIGIGALDSECLNTSSSSVHLVIPRV -TXTTRSASSALVSLGRLLEMMVQVRGSESRICCLSISLVXGPTMTSEGRLKKAFRSRRAN -CNXVSSFLAVIRANVVKGDPSTSLSNSILRIQSTAPAQSRCXLMIVLRAEMKSSSISIAI -LIAQAEYGSICXIINDCMWYNIFIMFSSAKCNFHCGGNTARVFLFASFKGPCGFSASERE -KKSGKYRFIFRSCSVTFNGSLTDWRYKLIVPSLFCSSLLRLGVVSXNCAEVKGLFLGXNT -IGLVAGREALPAEKSNSSSRYGFLFSDGPASESXKGTEFFEEVFVSTSSFLLTSLEIKSF -IADICLTRREICDWVSSNLXSILLERSFVTAFAASLASEKFSLALVCPAMXSFIKLSNXA -LFRPTMMIEXVVKCVKNLETSXIGMTXNCEVLSTKIYNFVASSXSVYDHNDFTXVSRGSD -KSTIXCEXSLRLIKREFHSIIQDRQLIXIFPRTTXANQQHTICTVGFPSIGIH ->blumeria_Grouper_28830_3_4 -CGSQLMETRPCKLCAVDWLTWCGGIFKXVGGPVLXNEIHVLLVSSSTRIILLICRSHETP -TXNHCDHKLINXKPQNYIFLLREPHNSRSSQFKTSPNFLRISPPIQSSWSAXIMLSWKAX -XRITLPGKPKPTKIFPKLMKLQRQXQKISPRESIKGLKRPNHKFLFXSNKCLQXTTXFPN -XXVEMKTWKQKLLRKIQSPFNFRKQGHLKIKNHTGRSYLTFQQAAPRDPQPGQSCFSLRK -DPLPRRNSMKQRPTXAMMSKTKMGLLIYTASQLTNHXMLLNKSEKXSGTSQISFRVPKLK -IRTALXKRQIEKHARYSHHNGNCTLLMRTXXIYYTTCNHXXFNICFHILLGLSELQWKWM -KISSRREEQSSVNTSIGQELXTVSLKYCSTMMYSGRLXQHLHEXLQETTRLNYNLRDDSG -KLSLAYLRMSWXGLRLEIYXGSIFDSHFHVPGPSFPIISPNSPARSLRIEWFKSHAVLQG -GHLRMMYSNIPSPMHQFRSQRQKAKSFQHLTHPXLIQGRMGKTSLRHKTLQKQINHTQFT -TSVTNASIAERQATGRKTAGXXKQRRWNQKNKGNMHQTLNTPRRVSAINSGKLTNQXKIK -NMXNLXHHTIVHQSLSLLLSLLSQKIWIKSKXALKAKXKMSSSMTKLKPFYIECEMKKFM -NRTARIPTLWPXERANLSHPQKDNLYGKDMASHTECFLHEXLIFPMSNFQFFLTTALQHV -MFHSLSLNIXLLIIHLLFLKCQALVALAQQFLRMQFXLHSFFARITLNHSGLRNSQCLXE -LSQMAHSQQMXHLDKLYSMNWGYDVYQMANCNFSTXLTNQFLILXLILSQTEKSSLLQIF -QWSNGTQPTLHSALQFFPTISKLNSPSTFRXISPAKWDKTLPRQKHPHRNGVIVNPIXNS -PPRRYSPGATTSHPGTFLCNTXPAQFIRKCKGPWAAPLLLTPKKDANPDXPNRLAYLCXL -XRAXQDYEETRPSPTKCSRXNSARSRTXLLCIPRPGKRILADTYAQRLFRENSICDSFRC -LXMASYAFRPMQRTSYFPVFYGRSSRAIPSICRRAPGRCSCLGRLNGRIALTVDTYFFXI -RFLWSPPQCFKVQAICFRGNLPWFPYFXTWHCSRPRKSFSDQRQAYANNYLGNKRICKCS -WLPTLSHXKFLPTSRATHGPILWTXKLPCHSDGPIDSIMEKYQTSAYNITSCKKIXLETS -RHIGNXRFPKVRGCSHTPTVHAMLQQFRSFSAASHSLLLKKTKRYPAALFSTREGITWDF -TVTTTLASLGRRRRRNGDNXPXISTNYSDQSRAARQNGPFFRCYRAFXYQDYLPSRKSKC -SRXFSLPSLXCSISLXGRRGRECSYXRQRKLXNPKWCRKRTXDGGNKAPTRTQPHRPAVH -HRISNLRRGTSPKYSCHLGPRXFCDVQFQIASHQKEPVATSRRCTWSIWRRNPTRNLGIX -GSSIDGRKCSXGPRPCVNRQYYAGIRAXVLAPRTDPRGSRSCPKMQVLSAHETSRPVTGK -LNSYSTSTSSDTVGYRSYSSRTPSLAQCNXVRNRLAGIPLSSQCRLRXHCASAHVYYPEL -WKAKADYQXQCWLLRRHRSTTISSXPTTAGCPYHTSXAKRKWQSRTGKWRSESHTGQSSP -GFSXNYTSWRSLTRGNEFQSKSLTQRVXPLLLTLRHSAPGGGKFLSSIYPXSHRIRGAPL -GRRTRKETPRTNSTLLRXXYESNXGXNTGLPPGRKGTYTYLRPRRLGTASTPAKTQDGAL -LXRAMGRSSLSXXXYLLLNITGWIQIRQQVQRHKPIPGICTXRTPSSXSMVWXPPYAGAG -XKDTQKFSKDLVXVIPXXNFXLTCNLNKLWTASFEKGDSLWIPIDGNPTVQIVRCXLAHV -VRGNIXISWRSCIIEXNSRFISLKLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT ->blumeria_Grouper_28830_3_5 -VDPNXWKPDRANCVLLIGSRGAGEYLNKLAVLYYRMKFTFYXSQALLALYCXFVGATRHL -REIIVIINXSTRSHKIIYFCXENLTILGHPNLRRLQIFYAFHHLFNHHGRPEXCSVGKLD -EGSHCRANQSQRKFFRSXXSCKGSDKRSLQENRSKVXRDPITNFSSSQTNVCNERLNFQT -SKXKXRRGNKNFFEKFSPLSTFGSRAIXKXKTIPGGAIXLFSRQRLATRNQANRVSAXEK -TLYLGAILXNNAQPKQXXAKQRWDYXFIPPVSXRTIECYXTRAKNKAVLPRFLFAFRSXK -SARPFKRGKXKNTRGIPTTMEIALCXXEHNEYIIPHAIIDDSTYASIFCLGYQNCNGNGX -RFHLGAKNNHQSTPRLGRSCRLYPXNTVRQXCTRVAFDNICTNNCKKRRDSITICATTPE -SFLXPTFGCHGRASDXRYTEAAYSTLTSTYLDHHFQXSPQTHQRGACGSSGSSHTRYYKV -DTXGXCIQTFRVQCTNSDLSVKRRKASSIXRIHSXSKVVWARRLCVTRHCRNRXIIPNSR -QALRMLQLRKDRPLGERLPVDENSAGGIKRTKGICTKRXIHLVAFQRXIQENLPINEKXK -ICKTCNTTRSFIKACHFYFPCXARRFGSRANKPXRPNRRXAARXRNXSHSISNAKXRNLX -IGQPEYLLCGRRKGQIXATPKRTTSTGRIWQATQNVFCTNNSFSLCPIFSFFXLRLFSML -CFTVFLXIFDFLXYIYYFXNVRHWWPWPNNFXGCNFNCTVSLLESPXIILDSGIHSVSRS -CPRWHIPSRCDTWTNFIPXTGATMFIKWQTATSQLNXPTNSXSYNXYSPKPKSLHYFKYS -NGQMAPSPPFIPHYSFSLQYQSXIPLQLFDKSLPPNGIKLSQDRNTRIETGXLSTQFKTP -LRGDIAPAQQQAIRGLSCATHDRLNSYANVRDHGLHLCYXHQKKTLTQTNQTVWRICVDY -RELNKITKKHAHPLPNAQDEIQRAAGHNFYAFLDLENGFWQIRMHKDSSEKTAFVTPFGV -YEWLVMPFGLCNAPATFQCFMEEVLEPFRPFVAGLLDDVAVWADSMAELHSRLILIFSRF -ASYGLLLNASKCRLFVSEGIFLGFHISKHGIAADPEKVSAIRDRPMPTTTSEIRGFVNAA -GYLRCLIKNFSQLAGPLTDQSSGPKNCPVILTDQSIQSWKSIKLALTTSPVVKKFDWRLP -VILETDASQKFVGAVILQPYMRCSNNSDRSVLHPIAYFSRKLNDTQQRYSAQERELLGIL -LSLQHWRHWVEGGDVTVITDHESLRTIQTKAEQPVRMVRFLDAIEHFNIRIIYRRGKANV -LADFLSRPCDVLFLSREEGEGNVATDDNENSRIQSGAERELEMEEIKHPHELNRIDLQCI -TEFLTLGEALPLNIAATWVRDNFAMYNSKLHLIKKNPSQQVGDAPGPSGAATLLEILEYE -DLVSTAVNVHEGQGHASIGNTMRELGRRFWHPELILAAHEAVRKCKSCQLMKPPDPLLGS -LTPIVPAPPLTRWGIDHTQVGPQVLLNAIEYATGWLESRLVPNADFANTVPLLTYIIQNF -GKPKQIISDNAGCFGGIEAQRFQASQQLQVVHTTPARPRGNGKVEQANGVLKAILVRVLL -DSPKITLAGALSLAVMNFNRRVSPSGYSPYFLLFGTQPPEEENSYPVYTREATESEERLW -AEELGRKHPAPIARSYVSSMKATRDKIRAYLQEEKALIRTYAPGDWVLRVRQRRHKMEPY -YDGPWAVAACHNNNTYSLISPGGYKLGNKYNGTNLFPAYVREGHPVRSLWYGSRRMLEQD -RKTLKNSARIXFEXYHNKISNXLVIXISCGQLVLRRGIVCGSQLMETRPCKLCAVDWLTW -CGGIFKXVGDPVLXNXIHVLLVSSSTRIILLISRSHETPTXNHCDHKLINXKP ->blumeria_Grouper_28830_3_6 -WIPIDGNPTVQIVCCXLAHVVRGNIXISWRSCIIEXNSRFISLKLYSHYIVDLSEPRDTY -VKSLXSXTDQLEATKLYIFVERTSQFXVIPIXDVSKFFTHFTTYSIIMVGLNNAQLESLM -KDHIAGQTKANENFSEANEAAKAVTKDLSKRIDQRFEETQSQISLLVKQMSAMNDLISKL -VSRNEDVETKTSSKNSVPFQLSEAGPSENKKPYREELFDFSAGSASRPATRPIVFQPKKR -PFTSAQFYETTPNLSNDEQNKDGTINLYRQSVNEPLNVTEQERKIKRYFPDFFSRSEAEN -PHGPLKEANRKTRAVFPPQWKLHFADENIMNILYHMQSLMIQHMLPYSAWAIRIAMEMDE -DFISARRTIISQHLDWAGAVDCILKILFDNDVLGSPLTTFARITARNDETQLQFARRLRK -AFFSLPSDVMVGPQTRDILRQHIRLSLPRTWTIISNNLPKLTSAELADRVVQVTRGITRW -TLEDDVFKHSESNAPIPISASKGEKLPAFDASIADPRSYGQDVFASQDIAETDKSYPIHD -KRYECFNCGKTGHWAKDCRLMKTAPVESKEQREYAPNAKYTSSRFSDKFRKTYQSMKNKK -YVKPVTPHDRSSKPVTSTFLVEPEDLDQEQISPEGQIEDEQLDDEIEAILYRMRNEEIYE -XDSPNTYFVAVGKGKFEPPPKGQPLREGYGKPHRMFFARITHFPYVQFSVFFDYGSSACY -VSQSFSKYLTSYNTSIISKMSGIGGPGPTISKDAILTAQFLCSNHLESFWTQEFTVSLGV -VPDGTFPADVTLGQTLFHELGLRCLSNGKLQLLNLIDQPILNPIINTLPNRKVFTTSNIP -MVKWHPAHPSFRITVFPYNIKVKFPFNFSINLSRQMGXNSPKTETPAXKRGNCQPNLKLP -SEAIXPRRNNKPSGDFLVQHMTGSIHTQMXGTMGCTSVINTKKRRXPRLTKPFGVFVLTI -ESLTRLRRNTPIPYQMLKMKFSAQQDITSMHSSTWKTDFGRYVCTKTLQRKQHLXLLSVS -MNGXLCLSAYATHQLLSSVLWKKFXSHSVHLSQGSWTMXLSGQTQWQNCTHGXYLFFLDS -LPMVSSSMLQSAGYLFQRESSLVSIFLNMALQQTPKKFQRSETGLCQQLPRKXEDLXMQL -VTYVVSLKISPNXQGHSRTNPLDLKIALSFXRTNRFNHGKVSNXRLQHHQLXKNLIGDFP -SYWKLTLPKSSWVQSYSNRTCDAPTIPIVQCCIPXLTSQENXTIPSSVIQHKRGNYLGFY -CHYNIGVTGXKAATXRXXLTMNLYELFRPKPSSPSEWSVFXMLXSILISGLSTVAEKQMF -SLIFSPVPVMFYFSLGKKGKGMXLLTTTKTLESKVVQKENLRWRKXSTHTNSTASTCSAS -PNFXPXERHFPXIXLPLGSEIILRCTIPNCISSKRTRRNKXAMHLVHLAPQPYXKSWNMR -IXYRRPXMFMRAKAMRQSAILCGNXGVGFGTPNXSSRLTKLSENASPVSSXNLQTRYWEA -XLLXYQHLLXHGGVXIILKXDPKSCSMQLSTQQAGWNPAXFPMQTSLTLCLCSRILSRTL -ESQSRLSVTMLAASEAXKHNDFKLANNCRLSIPHQLGQEEMAKSNRQMAFXKPYWSEFSW -ILLKLHXLALSHSRXXISIEESHPAGIALTSYSSALSPRRRKILIQYIPVKPQNQRSASG -PKNSEGNTPHQXHAPTLVVXKQLGIKYGLTSRKKRHLYVLTPPETGYCEYASEDTRWSPT -MTGHGPXQLVIIIIPTPXYHRVDTNXATSTTAQTYSRHMYVKDTQFVVYGMVAAVCWSRI -ERHSKIQQGFSLSDTIIKFLINLXFKXAVDSXFXEGGXFVDPNXWKPDRANCALLIGSRG -AGEYLNKLAILYYRXKFTFYXSQALLALYCXLVGATRHLREIIVIINXSTRSH ->blumeria_Grouper_14770_3_1 -GXTDTVSLVXSCGRKNXLETSVLRCMVLSKTELIRVRLRVRISYQLRFLTSIYQSPWIIS -YDPCRCKSIYVQIYEPEIXSXIHVCRXXIRETFNLHLIHNHLMECXCEINANVRXTFREE -CADDNDIGRXIXXPNXPDLQMSYPWHSRIYNISTPLLTLHRGXIHKXKTVSIFIVISHLM -LVWXTRQWLYXYQKLKCINRCALVSVSLLYIYLRDFXLKEHVIVXASRLQFFPLXNDKRC -RYVXKHHLVLDCEQVQWQPYCQSRLLLGCCLQGIGEVRAKSRYIVWMRALLPCTQLRRLN ->blumeria_Grouper_14770_3_2 -VRPIQXVSYEVVEGRIDWKQVYXDVWFXVKLSXXEXDCVCAYLINXGFXPVFINLHGSXV -MIPVDVNLYTYRYMSQKYKAKYMCVGNRSEKPLTCIXYIIIXWNASVKXMPMYVKLSVRN -VLMTMIXEGEFDNLISRTYKXVILGIPGYTIFQHPSSLCIEDRYISEKLLVYLLSFLIXC -WYGRHASGCTSTKNXSAXIGVPWSRXAFCTYICEIFSXRNMXXCKRAVFNSFPCKMISDV -DMFRSIIXFWIVSKFNGSRIVSRDCCWDAVSKESVKSAQNPDILFGCERYCHVLSFAGXM ->blumeria_Grouper_14770_3_3 -LDRYSKSRMKLWKEELTGNKCIEMYGSEXNXADKSEIACAHILSTEVFDQYLSISMDHKL -XSLXMXIYIRTDIXARNIKLNTCVSVIDPRNLXPAFDTXSSDGMLVXNKCQCTLNFPXGM -CXXQXYRKVNLITXLAGLTNELSLAFQDIQYFNTPPHFASRIDTXVKNCXYIYCHFSSNA -GMVDTPVVVLVPKTEVHKSVCLGLGKPFVHISARFLAEGTCNSVSEPSSILSLVKXXAMS -ICLEASFSFGLXASSMAAVLSVEIAAGMLSPRNRXSPRKIQIYCLDASAIAMYSASQVE ->blumeria_Grouper_14770_3_4 -HSTCEAEYMAIALASKQYIWILRGLHRFLGDSIPAAISTDNTAAIELAHNPKLNDASKHI -DIAYHFTRERIEDGSLTLLHVPSAKNLADICTKGLPRPRHTDLCTSVFGTSTTTGVSTIP -ALDEKXQXIYXQFFTYVSILDAKXGGVLKYCISWNAKDNSFVSPANXVIKFTFLYHCHQH -IPHGKFNVHWHLFHTSIPSDDYVSNAGXRFLGSITDTHVFSFIFLAHISVRIXIYIYRDH -NLXSMEIDKYWSKTSVDKICAHAISLLSAQFYSEPYISIHLFPVNSSFHNFIRDLLYRSN ->blumeria_Grouper_14770_3_5 -IQPAKLSTWQXRSHPNNISGFCADFTDSLETASQQQSRLTIRLPLNLLTIQNXMMLLNIS -TSLIILQGKELKTARLHYYMFLQLKISQIYVQKAYRDQGTPIYALQFLVLVQPLACLPYQ -HXMRNDNKYTNSFSLMYLSSMQSEEGCXNIVYPGMPRITHLXVRLIRLSNSPSYIIVIST -FLTESLTYIGIYFTLAFHQMIMYQMQVKGFSDLLPTHMYLALYFWLIYLYVYRFTSTGII -TYDPWRLINTGQKPQLIRYAHTQSHSYQLSFTQNHTSQYTCFQSILPSTTSYETYCIGLT ->blumeria_Grouper_14770_3_6 -FNLRSXVHGNSARIQTIYLDFARTSPIPWRQHPSSNLDXQYGCHXTCSQSKTKXCFXTYR -HRLSFYKGKNXRRLAYTITCSFSXKSRRYMYKRLTETKAHRFMHFSFWYXYNHWRVYHTS -IRXEMTINILTVFHLCIYPRCKVRRGVEILYILECQGXLICKSGXLGYQIHLPISLSSAH -SSRKVXRTLAFISHXHSIRXLCIKCRLKVSRIYYRHTCIXLYISGSYICTYIDLHLQGSX -LMIHGDXXILVKNLSXXDMRTRNLTLISSVLLRTIHLNTLVSSQFFLPQLHTRLTVSVX ->blumeria_Grouper_1717_12_1 -ISSILPXRASKSXSNSFRSLSSVTGSNSLQNPMMKRSACAERVWNILPCSARNLVATIXG -DGVCWCGELRXLASXIGSTNCCVGCCDGGCGPLRTISTSXRVEHXVGRGGQEPASAEDWG -GMSEXGLWQCEIVDGIRRAXR ->blumeria_Grouper_1717_12_2 -FPVSCPEGPVSPDRIVFEVSRQXLVPTACRTQXXSALLVRSASGISCPVRRGIWSRRFEA -TEFVGAVSFDDSPRRLALQIVVWVVVMAVVARXGPFRRLDASNIELGGGAKSQPLRRTGA -AXVSEVCGSVRSXMVYGALEG ->blumeria_Grouper_1717_12_3 -FQYLALKGQXVLIEXFSKSLVSDWFQQLAEPNDEALCLCGARLEYPALFGEEFGRDDLRR -RSLLVRXASMTRLVDWLYKLLCGLLXWRLWPVKDHFDVLTRRTLSWEGGPRASLCGGLGR -HEXVRFVAVXDRRWYTARLK ->blumeria_Grouper_1717_12_4 -PFKRAVYHLRSHTATNLTHSCRPSPPQRLALGPPSQLNVRRVKTSKWSLTGHNRHHNNPH -NNLXSQSTRRVIEAHRTNKLRRLKSSRPNSSPNRAGYSRRAPHKQSASSLGSASCWNQSL -TRDFENYSIRTYWPFRARYWK ->blumeria_Grouper_1717_12_5 -PSSAPYTIYDLTLPQTSLTHAAPVLRRGWLLAPPPNSMFDASRRRNGPXRATTAITTTHT -TICRANLRGESSKLTAPTNSVASNRRDQIPRRTGQDIPDALRTSRALHHWVLQAVGTSHX -RETSKTIRSGLTGPSGQDTGN ->blumeria_Grouper_1717_12_6 -LQARRIPSTISHCHKPHSLMPPQSSAEAGSWPPLPTQCSTRQDVEMVLNGPQPPSQQPTQ -QFVEPIYEASHRSSPHQQTPSPQIVATKFLAEQGRIFQTRSAQAERFIIGFCKLLEPVTD -ERLRKLFDQDLLALQGKILE diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/test_input_nt.fa --- a/commons/pyRepetUnit/fastaTranslation/allFrames/tests/datas/test_input_nt.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,124 +0,0 @@ ->blumeria_Grouper_28830_3 -TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC -CGACTAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTNATTC -TATAATACAGGATCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACA -GCGCACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACAAACTATCCCCCTTCTC -AAAACTAGCTGTCCACAGCTTATTTAAATTACAAGTTAATTAGAAATTTTATTATGGTAT -CACTCAAACTAAATCCTTGCTGAATTTTTGAGTGTCTTTCTATCCTGCTCCAGCATACGG -CGGCTACCATACCATAGACTACGAACTGGGTGTCCTTCACGTACATATGCCGGGAATAGG -TTTGTGCCGTTGTACTTGTTGCCTAATTTGTATCCACCCGGTGATATTAAGGAGTAGGTA -TTATTATTATGACAAGCTGCTACGGCCCATGGCCCGTCATAGTAGGGCTCCATCTTGTGT -CTTCGCTGGCGTACTCGCAGTACCCAGTCTCCGGGGGCGTAAGTACGTATAAGTGCCTTT -TCTTCCTGGAGGTAAGCCCGTATTTTATCCCTAGTTGCTTTCATACTACTAACGTAGGAG -CGTGCTATTGGTGCGGGGTGTTTCCTTCCGAGTTCTTCGGCCCAGAGGCGCTCCTCTGAT -TCTGTGGCTTCACGGGTATATACTGGATAAGAATTTTCCTCCTCCGGGGGCTGAGTGCCG -AAGAGTAAGAAGTAAGGGCTATACCCGCTGGGTGAGACTCTTCGATTGAAATTCATTACC -GCGAGTGAGAGAGCGCCAGCTAGTGTAATTTTAGGAGAATCCAGGAGAACTCTGACCAGT -ATGGCTTTCAGAACGCCATTTGCCTGTTCGACTTTGCCATTTCCTCTTGGCCTAGCTGGT -GTGGTATGGACAACCTGCAGTTGTTGGCTAGCTTGAAATCGTTGTGCTTCTATGCCTCCG -AAGCAGCCAGCATTGTCACTGATAATCTGCTTTGGCTTTCCAAAGTTCTGGATAATATAC -GTGAGCAGAGGCACAGTGTTAGCGAAGTCTGCATTGGGAACTAAGCGGGATTCCAGCCAG -CCTGTTGCGTACTCAATTGCATTGAGCAAGACTTGGGGTCCTACTTGAGTATGATCTATA -CCCCACCGTGTCAGAGGAGGTGCTGGTACTATAGGAGTTAAGCTTCCCAGTAACGGGTCT -GGAGGTTTCATGAGCTGACAGGACTTGCATTTTCGGACAGCTTCGTGAGCCGCGAGGATC -AGTTCGGGGTGCCAAAACCTACGCCCTAATTCCCGCATAGTATTGCCGATTGACGCATGG -CCTTGGCCCTCATGAACATTTACGGCCGTCGATACTAGATCCTCATATTCCAAGATTTCT -AGTAGGGTTGCGGCGCCAGATGGACCAGGTGCATCGCCTACTTGTTGCGACGGGTTCTTT -TTGATGAGATGCAATTTGGAATTGTACATCGCAAAATTATCTCGGACCCAAGTGGCAGCT -ATATTTAGGGGAAGTGCCTCTCCTAAGGTTAGAAATTCGGTGATGCACTGCAGGTCGATG -CGGTTGAGTTCGTGTGGGTGCTTTATTTCCTCCATCTCAAGTTCTCTTTCTGCACCACTT -TGGATTCTAGAGTTTTCGTTGTCGTCAGTAGCTACATTCCCTTCCCCTTCTTCCCTAGAG -AGAAATAGAACATCACAGGGACGGGAGAGAAAATCAGCGAGAACATTTGCTTTTCCGCGA -CGGTAGATAATCCTGATATTAAAATGCTCTATAGCATCTAAAAAACGGACCATTCTGACG -GGCTGCTCGGCTTTGGTCTGAATAGTTCGTAGAGATTCATGGTCAGTTATCACCGTTACG -TCGCCGCCTTCTACCCAGTGACGCCAATGTTGTAGTGACAGTAAAATCCCAAGTAATTCC -CTCTCTTGTGCTGAATAACGCTGCTGGGTATCGTTTAGTTTTCTTGAGAAGTAAGCTATG -GGATGCAGCACTGAACGATCGGAATTGTTGGAGCATCGCATGTACGGTTGGAGTATGACT -GCACCCACGAACTTTTGGGAAGCGTCAGTTTCCAATATGACGGGAAGTCTCCAATCAAAT -TTTTTTACAACTGGTGATGTTGTAAGCGCTAGTTTGATACTTTTCCATGATTGAATCGAT -TGGTCCGTCAGAATGACAGGGCAATTTTTAGGTCCAGAGGATTGGTCCGTGAGTGGCCCT -GCTAGTTGGGAGAAATTTTTAATGAGACAACGTAGGTAACCAGCTGCATTTACAAATCCT -CTTATTTCCGAGGTAGTTGTTGGCATAGGCCTGTCTCTGATCGCTGAAACTTTTTCGGGG -TCTGCTGCAATGCCATGTTTAGAAATATGGAAACCAAGGAAGATTCCCTCTGAAACAAAT -AGCCTGCACTTTGAAGCATTGAGGAGGAGACCATAGGAAGCGAATCTAGAAAAAATAAGT -ATCAACCGTGAGTGCAATTCTGCCATTGAGTCTGCCCAGACAGCTACATCGTCCAGGAGC -CCTGCGACAAATGGACGGAATGGCTCTAGAACTTCTTCCATAAAACACTGGAAAGTAGCT -GGTGCGTTGCATAGGCCGAAAGGCATAACTAGCCATTCATAGACACCGAAAGGAGTCACA -AATGCTGTTTTCTCTGAAGAGTCTTTGTGCATACGTATCTGCCAAAATCCGTTTTCCAGG -TCGAGGAATGCATAGAAGTTATGTCCTGCTGCGCGCTGAATTTCATCTTGAGCATTTGGT -AGGGGATGGGCGTGTTTCTTCGTAATCTTGTTAAGCTCTCTATAGTCAACACAAATACGC -CAAACGGTTTGGTTAGTCTGGGTTAGCGTCTTTTTTTGGTGTTAATAACAGAGGTGCAGC -CCATGGTCCCTTACATTTGCGTATGAATTGAGCCGGTCATGTGTTGCACAAGAAAGTCCC -CGGATGGCTTGTTGTTGCGCCGGGGCTATATCGCCTCGGAGGGGAGTTTTAAATTGGGTT -GACAATTACCCCGTTTCTATGCGGGTGTTTCTGTCTTGGGAGAGTTTTATCCCATTTGGC -GGGAGAGATTTATCGAAAAGTTGAAGGGGAATTTAACTTTGATATTGTAGGGAAAAACTG -TAATGCGGAATGAAGGGTGGGCTGGGTGCCATTTGACCATTGGAATATTTGAAGTAGTGA -AGACTTTTCGGTTTGGGAGAGTATTAATTATAGGATTAAGAATTGGTTGGTCAATTAAGT -TGAGAAGTTGCAGTTTGCCATTTGATAAACATCGTAGCCCCAGTTCATGGAATAAAGTTT -GTCCAAGTGTCACATCTGCTGGGAATGTGCCATCTGGGACAACTCCTAGAGACACTGTGA -ATTCCTGAGTCCAGAATGATTCAAGGTGATTCGAGCAAAGAAACTGTGCAGTTAAAATTG -CATCCTTAGAAATTGTTGGGCCAGGGCCACCAATGCCTGACATTTTAGAAATAATAGATG -TATTATAAGAAGTCAAATATTTAGAGAAAGACTGTGAAACATAACATGCTGAAGAGCCGT -AGTCAAAAAAAACTGAAAATTGGACATAGGGAAAATGAGTTATTCGTGCAAAAAACATTC -TGTGTGGCTTGCCATATCCTTCCCGTAGAGGTTGTCCTTTTGGGGGTGGCTCAAATTTGC -CCTTTCCTACGGCCACAAAGTAGGTATTCGGGCTGTCCTATTCATAAATTTCTTCATTTC -GCATTCGATATAGAATGGCTTCAATTTCGTCATCGAGCTGCTCATCTTCTATTTGGCCTT -CAGGGCTTATTTGCTCTTGATCCAAATCTTCTGGCTCAACAAGGAAAGTAGAAGTGACAG -GCTTTGATGAACGATCGTGTGGTGTTACAGGTTTTACATATTTTTTATTTTTCATTGATT -GGTAAGTTTTCCTGAATTTATCGCTGAAACGCGACGAGGTGTATTTAGCGTTTGGTGCAT -ATTCCCTTTGTTCTTTTGATTCCACCGGCGCTGTTTTCATCAACCGGCAGTCTTTCGCCC -AGTGGCCTGTCTTTCCGCAATTGAAGCATTCGTAACGCTTGTCGTGAATTGGGTATGATT -TATCTGTTTCTGCAATGTCTTGTGACGCAAAGACGTCTTGCCCATACGACCTTGGATCAG -CTATGGATGCGTCAAATGCTGGAAGCTTTTCGCCTTTTGACGCTGAGATCGGAATTGGTG -CATTGGACTCGGAATGTTTGAATACATCATCCTCAAGTGTCCACCTTGTAATACCGCGTG -TGACTTGAACCACTCGATCCGCAAGCTCCGCGCTGGTGAGTTTGGGGAGATTATTGGAAA -TGATGGTCCAGGTACGTGGAAGTGAGAGTCGAATATGCTGCCTCAGTATATCTCTAGTCT -GAGGCCCTACCATGACATCCGAAGGTAGGCTAAAGAAAGCTTTCCGGAGTCGTCGCGCAA -ATTGTAATTGAGTCTCGTCGTTTCTTGCAGTTATTCGTGCAAATGTTGTCAAAGGCGACC -CGAGTACATCATTGTCGAACAGTATTTTAAGGATACAGTCTACAGCTCCTGCCCAATCGA -GGTGTTGACTGATGATTGTTCTTCGCGCCGAGATGAAATCTTCATCCATTTCCATTGCAA -TTCTGATAGCCCAAGCAGAATATGGAAGCATATGTTGAATCATCAATGATTGCATGTGGT -ATAATATATTCATTATGTTCTCATCAGCAAAGTGCAATTTCCATTGTGGTGGGAATACCG -CGCGTGTTTTTCTATTTGCCTCTTTTAAAGGGCCGTGCGGATTTTCAGCTTCGGAACGCG -AAAAGAAATCTGGGAAGTACCGCTTTATTTTTCGCTCTTGTTCAGTAACATTCAATGGTT -CGTTAACTGACTGGCGGTATAAATTAATAGTCCCATCTTTGTTTTGCTCATCATTGCTTA -GGTTGGGCGTTGTTTCATAGAATTGCGCCGAGGTAAAGGGTCTTTTCTTAGGCTGAAACA -CGATTGGCCTGGTTGCGGGTCGCGAGGCGCTGCCTGCTGAAAAGTCAAATAGCTCCTCCC -GGTATGGTTTTTTATTTTCAGATGGCCCTGCTTCCGAAAGTTGAAAGGGGACTGAATTTT -TCGAAGAAGTTTTTGTTTCCACGTCTTCATTTCTACTTACTAGTTTGGAAATTAAGTCGT -TCATTGCAGACATTTGTTTGACTAGAAGAGAAATTTGTGATTGGGTCTCTTCAAACCTTT -GATCGATTCTCTTGGAGAGATCTTTTGTCACTGCCTTTGCAGCTTCATTAGCTTCGGAAA -AATTTTCGTTGGCTTTGGTTTGCCCGGCAATGTGATCCTTCATCAAGCTTTCCAACTGAG -CATTATTCAGGCCGACCATGATGATTGAATAGGTGGTGAAATGCGTAAAAAATTTGGAGA -CGTCTTAAATTGGGATGACCTAGAATTGTGAGGTTCTCTCAACAAAAATATATAATTTTG -TGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCG -ACAAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTCATTCTA -TAATACAGGACCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACAGC -ACACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACA ->blumeria_Grouper_14770_3 -GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA -AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG -CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT -TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC -TAAATACATGTGTGTCGGTAATAGATCCGAGAAACCTTTAACCTGCATTTGATACATAAT -CATCTGATGGAATGCTAGTGTGAAATAAATGCCAATGTACGTTAAACTTTCCGTGAGGAA -TGTGCTGATGACAATGATATAGGAAGGTGAATTTGATAACCTAATTAGCCGGACTTACAA -ATGAGTTATCCTTGGCATTCCAGGATATACAATATTTCAACACCCCTCCTCACTTTGCAT -CGAGGATAGATACATAAGTGAAAAACTGTTAGTATATTTATTGTCATTTCTCATCTAATG -CTGGTATGGTAGACACGCCAGTGGTTGTACTAGTACCAAAAACTGAAGTGCATAAATCGG -TGTGCCTTGGTCTCGGTAAGCCTTTTGTACATATATCTGCGAGATTTTTAGCTGAAGGAA -CATGTAATAGTGTAAGCGAGCCGTCTTCAATTCTTTCCCTTGTAAAATGATAAGCGATGT -CGATATGTTTAGAAGCATCATTTAGTTTTGGATTGTGAGCAAGTTCAATGGCAGCCGTAT -TGTCAGTCGAGATTGCTGCTGGGATGCTGTCTCCAAGGAATCGGTGAAGTCCGCGCAAAA -TCCAGATATATTGTTTGGATGCGAGCGCTATTGCCATGTACTCAGCTTCGCAGGTTGAAT -G ->blumeria_Grouper_1717_12 -ATTTCCAGTATCTTGCCCTGAAGGGCCAGTAAGTCCTGATCGAATAGTTTTCGAAGTCTC -TCGTCAGTGACTGGTTCCAACAGCTTGCAGAACCCAATGATGAAGCGCTCTGCTTGTGCG -GAGCGCGTCTGGAATATCCTGCCCTGTTCGGCGAGGAATTTGGTCGCGACGATTTGAGGC -GACGGAGTTTGTTGGTGCGGTGAGCTTCGATGACTCGCCTCGTAGATTGGCTCTACAAAT -TGTTGTGTGGGTTGTTGTGATGGCGGTTGTGGCCCGTTAAGGACCATTTCGACGTCTTGA -CGCGTCGAACATTGAGTTGGGAGGGGGGGCCAAGAGCCAGCCTCTGCGGAGGACTGGGGC -GGCATGAGTGAGTGAGGTTTGTGGCAGTGTGAGATCGTAGATGGTATACGGCGCGCTTGA -AGGG - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/fastaTranslation/allFrames/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py --- a/commons/pyRepetUnit/fastaTranslation/allFrames/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,88 +0,0 @@ -#!/usr/bin/env python - -from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX -from commons.core.utils.FileUtils import FileUtils -import os -import sys -import getopt - -#------------------------------------------------------------------------------ - -def help(): - - """ - Give the command-line parameters. - """ - - print "" - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the nucleotidic input file (format='fasta')" - print " -o: name of the output file (default=inFileName+'_aa')" - print " -v: verbose (default=0/1/2)" - print " -c: clean" - print "" - -#------------------------------------------------------------------------------ - -def main(): - - inFileName = "" - outFileName = "" - verbose = 0 - clean = False - - try: - opts = getopt.getopt(sys.argv[1:],"hi:o:v:c")[0] - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - elif o == "-c": - clean = True - - if inFileName == "": - print "*** Error: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "beginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s_aa" % ( inFileName ) - - iTIAFARSBX = TranslateInAllFramesAndReplaceStopByX() - iTIAFARSBX.setInputFile( inFileName ) - iTIAFARSBX.setOutputFile( outFileName ) - iTIAFARSBX.run( ) - - if clean == True: - os.remove( inFileName ) - - if verbose > 0: - if FileUtils.isRessourceExists( outFileName ) and not(FileUtils.isEmpty( outFileName )): - print "%s finished successfully" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - else: - print "warning %s execution failed" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#------------------------------------------------------------------------------ - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/HmmpfamClusterComponent.py --- a/commons/pyRepetUnit/hmmer/HmmpfamClusterComponent.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ -import os -from pyRepet.launcher.Launcher import HmmpfamLauncher - - -class HmmpfamClusterComponent( object ): - - def __init__(self): - self._component = None - self._profilDatabank = "" - self._resultDir = "" - self._queryDir = "" - self._tmpDir = "" - self._jobDb = None - self._SGEQueue = "" - self._SGEGroupId = "" - - def loadConfig( self, config ): - self._profilDatabank = config.get( "profil_search","ProfilDatabank" ) - self._queryDir = config.get( "hmmer_config","query_dir" ) - self._tmpDir = config.get( "hmmer_config", "tmp_dir" ) - self._resultDir = config.get( "hmmer_config", "result_dir" ) - self._SGEQueue = config.get( "sge_config", "queue" ) - self._SGEGroupId = config.get( "sge_config", "groupid" ) - - def run(self): - params = {"param":"--informat FASTA -E 10", - "profilDB": self._profilDatabank, - "outputDir": self._resultDir, - "query": self._queryDir, - "job_table":"jobs", - "queue" : self._SGEQueue, - "groupid" : self._SGEGroupId, - "tmpDir": self._tmpDir, - "cDir" : "."} - self._component = HmmpfamLauncher(self._jobDb, params) - self._component.run() - - def clean (self): - dirToClean = self._tmpDir - os.system("rm " + dirToClean + "/*") - dirToClean = self._resultDir - os.system("rm " + dirToClean + "/*") - - def setProfilDatabank (self, profilDatabank): - self._profilDatabank = profilDatabank - - def getProfilDatabank(self): - return self._profilDatabank - - def setQueryDir(self, input): - self._queryDir = input - - def getQueryDir( self ): - return self._queryDir - - def setSubjectDir(self, input): - self._subjectDir = input - - def getSubjectDir( self ): - return self._subjectDir - - def setSGEQueue(self, queue): - self._SGEQueue = queue - - def getSGEQueue( self ): - return self._SGEQueue - - def setSGEGrouId(self, id): - self._SGEGroupId = id - - def getSGEGroupId( self ): - return self._SGEGroupId; - - def setTmpDir(self, tmpDir): - self._tmpDir = tmpDir - - def getTmpDir( self ): - return self._tmpDir - - def setResultDir(self, wkDir): - self._resultDir = wkDir - - def getResultDir(self): - return self._resultDir - - def setJobDb (self, jobDb): - self._jobDb = jobDb - - def getJobDb (self): - return self._jobDb - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/LaunchPreProcessHmmpfamPostProcessNotInParallel.py --- a/commons/pyRepetUnit/hmmer/LaunchPreProcessHmmpfamPostProcessNotInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,122 +0,0 @@ -import os -import unittest -from pyRepet.launcher.programLauncher import * -from pyRepet.util.file.FileUtils import * -import commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX -import commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing -import ConfigParser - -class LaunchPreProcessHmmpfamPostProcessNotInParallel: - - def __init__( self ): - - #for global analysis - self._configFile = "" - self._inputFile = "" - self._outputFile = "" - self.fileUtils = FileUtils() - self._programLauncherInstance = programLauncher() - #specific to PreProcess - self.bioseq = Bioseq() - self.preProcess = commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX.TranslateInAllFramesAndReplaceStopByX() - self._outputFilePreprocess = "" - #specific to PostProcess - self.hmmpfamOutputProcess = commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing.HmmpfamOutputProcessing() - - def _cleanTemporaryFiles(self, outputFilePreProcess, outputFileHmmpfam): - os.remove( outputFilePreProcess ) - os.remove( outputFileHmmpfam ) - - def _launchPostProcess(self, outputFileHmmpfam): - return self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(outputFileHmmpfam, self._outputFile) - - - def _launchHmmpfam(self, outputFilePreprocess): - config = ConfigParser.ConfigParser() - config.readfp(open(self._configFile)) - self._programLauncherInstance.reset(outputFilePreprocess) - outputFileHmmpfam = outputFilePreprocess + ".hmmpfamOut" - self._programLauncherInstance.setOutputFileName(outputFileHmmpfam) - self._programLauncherInstance.launchHmmpfam(evalFilter=config.get("profil_search", "Evalue"), inputFormat=config.get("profil_search", "InputFormat"), profilDatabank=config.get("profil_search", "ProfilDatabank")) - return outputFileHmmpfam - - - def _launchHmmpfamPreProcess(self): - self.preProcess.setInputFile(self._inputFile) - outputFilePreprocess = self._inputFile + ".translated" - self.preProcess.setOutputFile(outputFilePreprocess) - self.preProcess.run() - return outputFilePreprocess - - def setInputFile( self, input ): - self._inputFile = input; - - def setOutputFile( self, output ): - self._outputFile = output; - - def setConfigFile ( self, configFile ): - self._configFile = configFile - - def checkInputFile(self): - return self._checkFileExitsAndNotEmpty( self._inputFile ) - - def checkConfigFile(self): - return self._checkFileExitsAndNotEmpty( self._configFile ) - - def _checkFileExitsAndNotEmpty(self, fileName): - fileUtils = FileUtils() - if fileUtils.isRessourceExists(fileName) and not fileUtils.isFileEmpty(fileName): - return 1 - return 0 - - def run(self): - - if not self.checkInputFile(): - print "Warning : there is no input file : " + self._inputFile + "\n" - return 0 - if not self.checkConfigFile(): - print "Warning : there is no config file : " + self._configFile + "\n" - return 0 - outputFilePreProcess = self._launchHmmpfamPreProcess() - outputFileHmmpfam = self._launchHmmpfam(outputFilePreProcess) - self._launchPostProcess(outputFileHmmpfam) - self._cleanTemporaryFiles(outputFilePreProcess, outputFileHmmpfam) - - -if __name__ == "__main__": - main() - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -if __name__ == "__main__": - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/check/OldDetectFeatureConfigChecker.py --- a/commons/pyRepetUnit/hmmer/check/OldDetectFeatureConfigChecker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -''' -Created on 14 avr. 2009 - -@author: oinizan -''' -import re -from commons.core.checker.IChecker import IChecker -from commons.core.checker.OldConfigChecker import ConfigChecker -from commons.core.checker.ConfigException import ConfigException -from commons.core.checker.CheckerException import CheckerException - -class DetectFeatureConfigChecker (IChecker): - ''' - classdocs - ''' - def __init__(self): - ''' - Constructor - ''' - self._dict = {"te_hmmer" : "", - "te_blrn" : "" - } - self._specifiqueDict = {"te_hmmer_evalue" : "", - "te_hmm_profiles" : "" - } - - def _appendMessageToConfigExceptionMessage(self, messages): - appendedMessages = [] - for msg in messages: - if (re.match("\[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features'", msg)): - appendedMessages.append(msg + " whereas te_hmmer is set") - - if (re.match("\[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features'", msg)): - appendedMessages.append(msg + " whereas te_hmmer is set - Default value will be set") - - return appendedMessages - - - def check(self, configFile): - chk = ConfigChecker("detect_features", self._dict) - try : - chk.check(configFile) - except ConfigException, e : - raise e - - if self._dict["te_hmmer"] == "yes": - isErrorOccured = False - try: - chk = ConfigChecker("detect_features", self._specifiqueDict) - chk.check(configFile) - except ConfigException, e: - appendedMessages = self._appendMessageToConfigExceptionMessage(e.messages) - raise ConfigException("", appendedMessages) - - -if __name__ == "__main__": - pass diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/check/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/check/test/Test_OldDetectFeaturesConfigChecker.py --- a/commons/pyRepetUnit/hmmer/check/test/Test_OldDetectFeaturesConfigChecker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -import unittest -import re -import os -from commons.pyRepetUnit.hmmer.check.OldDetectFeatureConfigChecker import DetectFeatureConfigChecker -from commons.core.checker.ConfigException import ConfigException - -class Test_DetectFeaturesConfigChecker(unittest.TestCase): - - def setUp(self): - self._detectFeatureConfigChecker = DetectFeatureConfigChecker() - - def testWithDefaultLogger (self): - lineFound = False - try: - self._detectFeatureConfigChecker.check("dummyConfig") - except ConfigException, e: - for msg in e.messages: - if (re.match("CONFIG FILE not found.*", msg)): - lineFound = True - self.assertTrue(lineFound) - - def testWithNoConfigFile(self): - lineFound = False - try: - self._detectFeatureConfigChecker.check("dummyConfig") - except ConfigException, e: - for msg in e.messages: - if (re.match("CONFIG FILE not found.*", msg)): - lineFound = True - self.assertTrue(lineFound) - - def testWithNoSectionInConfigFile(self): - config = open("config.cfg", "w"); - config.close() - lineFound = False - try: - self._detectFeatureConfigChecker.check("config.cfg") - except ConfigException, e: - for msg in e.messages: - if (re.match("\[detect_features\] section not found.*", msg)): - lineFound = True - self.assertTrue(lineFound) - os.remove("config.cfg") - - def testMissingOptionsInConfig (self): - dict = {} - MockConfigFile("config.cfg", dict) - hmmProfilsFound = False - TE_BLRnFound = False - try : - self._detectFeatureConfigChecker.check("config.cfg") - except ConfigException, e: - for msg in e.messages: - if (re.match("\[detect_features\] - No option 'te_hmmer' in section: 'detect_features'", msg)): - hmmProfilsFound = True - if (re.match("\[detect_features\] - No option 'te_blrn' in section: 'detect_features'", msg)): - TE_BLRnFound = True - self.assertTrue(hmmProfilsFound) - self.assertTrue(TE_BLRnFound) - os.remove("config.cfg") - - def testOptionsIfHmmProfilsSetAtYESInConfig (self): - - dict = { - "TE_HMMER" : "yes", - "TE_BLRn" : "no" - } - - profilDatabankFound = False - evalueFound = False - MockConfigFile("config.cfg", dict) - try : - self._detectFeatureConfigChecker.check("config.cfg") - except ConfigException, e: - for msg in e.messages: - print msg - if (re.match("\[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features' whereas te_hmmer is set", msg)): - profilDatabankFound = True - if (re.match("\[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features' whereas te_hmmer is set - Default value will be set", msg)): - evalueFound = True - self.assertTrue(profilDatabankFound) - self.assertTrue(evalueFound) - os.remove("config.cfg") - - - def testOptionsIfHmmProfilsSetAtNOInConfig (self): - profilDatabankFound = False - inputFormatFound = False - evalueFound = False - dict = { - "TE_HMMER" : "no" - } - MockConfigFile("config.cfg", dict) - try : - self._detectFeatureConfigChecker.check("config.cfg") - except ConfigException, e: - for msg in e.messages: - if (re.match(".+INFO \[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features' whereas te_hmmer is set", msg)): - profilDatabankFound = True - if (re.match(".+INFO \[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features' whereas te_hmmer is set - Default value will be set", msg)): - evalueFound = True - self.assertFalse(profilDatabankFound) - self.assertFalse(inputFormatFound) - self.assertFalse(evalueFound) - os.remove("config.cfg") - - def testTE_BLRnAndTE_hmmerAtNoInConfig (self): - - dict = { - "TE_HMMER" : "no", - "TE_BLRn" : "no" - } - - exceptionNotRaised = True - MockConfigFile("config.cfg", dict) - try : - self._detectFeatureConfigChecker.check("config.cfg") - except ConfigException: - exceptionNotRaised = False - - self.assertTrue(exceptionNotRaised) - - os.remove("config.cfg") - -class MockConfigFile: - - def __init__ (self, fileName, optionsDict): - - self._fileName = fileName - config = open(fileName, "w"); - config.write("[detect_features]\n") - for key in optionsDict.keys(): - config.write(key + ":" + optionsDict[key] + "\n") - config.close() - - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/check/test/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/check/test/detectFeatureConfigCheckerTestSuite.py --- a/commons/pyRepetUnit/hmmer/check/test/detectFeatureConfigCheckerTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -''' -Created on 29 mai 2009 - -@author: oinizan -''' -import unittest -import sys -import TestDetectFeaturesConfigChecker - - - - -def main(): - - commonsTestSuite = unittest.TestSuite() - commonsTestSuite.addTest(unittest.makeSuite(TestDetectFeaturesConfigChecker.TestDetectFeaturesConfigChecker,'test')) - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(commonsTestSuite) - - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/HmmOutput.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmOutput.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -## List of Hmmpfam or Hmmscan Output (that are too lists). -# -class HmmOutput( object ): - - list; - - def __init__( self ): - self._hmmpfamOutput = [] - - ## append an output in the list of output - # - # @param list name of the list - # - def append( self, list ): - self._hmmpfamOutput.append(list) - - ## return the length of the list of output - def len (self): - return len(self._hmmpfamOutput) - - ## return the output corresponding at the element number index in the list of output - # - # @param index number of index - # - def get(self, index): - return self._hmmpfamOutput[index] - - ## return the list of output - def getList(self): - return self._hmmpfamOutput diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/HmmOutputProcessing.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmOutputProcessing.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -import os -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput - -##Concrete implementation for hmmscan and hmmpfam output methods -# -class HmmOutputProcessing (object): - - ## write a align file from a HmmOutput object - # - # @param fout handle of align file - # @param HmmOutput HmmOutput object in fact a list of hmmOutput containing datas required - # - def writeHmmOutputToAlignFile( self, pfamOutput, fout ): - for item in pfamOutput.getList(): - for i in item: - fout.write(i + "\t") - fout.write("0\n") - - ## read an output file from hmm profiles search program and write the corresponding .align file - # - # @param inputFile file - # @param outputFile file - # - def readHmmOutputsAndWriteAlignFile( self, inputFile, outputFile ): - if not os.path.exists(inputFile): - print "Warning your input file " + inputFile + " does not exist!\n" - return - file2parse = open( inputFile ) - pfamOutput = HmmOutput() - if outputFile == "": - print "Warning have to specify an output name file!\n" - return - fout = open(outputFile, "w") - while pfamOutput != None: - pfamOutput = self.readHmmOutput(file2parse) - if pfamOutput != None: - self.writeHmmOutputToAlignFile(pfamOutput, fout) - fout.close() - file2parse.close() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/HmmpfamOutputProcessing.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmpfamOutputProcessing.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput -import re -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing - -##Concrete implementation for specific methods -# -class HmmpfamOutputProcessing (HmmOutputProcessing): - - ##read an output from hmmpfam and return a array with results useful to build a .align file - # - # @param file handle of file generated by software searching hmm profiles - # - def readHmmOutput( self, hmmerOutputFile ): - #Tested with HMMER 2.3.2 on Linux (Debian) and on Unix (Solaris) - line = hmmerOutputFile.readline() - tabResult = None - aRecup = 0 - if (line == ""): - tabResult = None - return tabResult - tabResult = HmmOutput() - while not re.match("Alignments of top-scoring domains:.*", line): - line = hmmerOutputFile.readline() - m = re.match("Query sequence:\s*(.*)", line) - if m: - seqName = m.group(1) - #warning : do no use a return character because they change between several OS - if re.match("--------\s+-------\s+-----\s+-----\s+-----\s+-----\s+-----\s+-------.*", line): - aRecup = 1 - m = re.match("(\S+)\s+\d+\/\d+\s+(\d+)\s+(\d+)\s+.+\s+(\d+)\s+(\d+)\s+.+\s+(.+\.\d)\s+(.+)", line) - if m and aRecup == 1: - tabResult.append([seqName, m.group(2), m.group(3), m.group(1), m.group(4), m.group(5), m.group(7), m.group(6)]) - if line == "": - tabResult = None - return tabResult - return tabResult diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/HmmscanOutputProcessing.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/HmmscanOutputProcessing.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -import re -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing - -##Concrete implementation for hmmscan output specific methods -# -class HmmscanOutputProcessing (HmmOutputProcessing): - - ## read an hmmscan output from a file, return a array with results useful to build a .align file - # - # @param file handle of file generated by software searching hmm profiles - # - def readHmmOutput( self, hmmerOutputFile ): - #Tested with HMMER 3 on Linux - line = hmmerOutputFile.readline() - tabResult = None - if (line == ""): - tabResult = None - return tabResult - tabResult = HmmOutput() - - while line != "": - line = hmmerOutputFile.readline() - if not(re.match("^#.*$", line)) and line != "": - lLines = re.split("\s+", line) - seqName = lLines[3] - profilName = lLines[0] - iValue = lLines[12] - score = lLines[13] - queryCoordStart =lLines[17] - queryCoordEnd = lLines[18] - subjectCoordStart = lLines[15] - subjectCoordEnd = lLines[16] - tabResult.append([seqName, queryCoordStart, queryCoordEnd, profilName, subjectCoordStart, subjectCoordEnd, iValue, score]) - return tabResult - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmOutputProcessing.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmOutputProcessing.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing -from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing -from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing -from commons.core.utils.FileUtils import FileUtils - -class TestHmmOutputProcessing(unittest.TestCase): - - def setUp(self): - self.hmmOutput = HmmOutputProcessing() - self._inputFile = "./datas/test_hmmpfam_output" - self._outputFile = "./datas/dummyoutput.align" - self._inputFileScan2 = "./datas/hmmscanOutput" - self._outputFileScan2 = "./datas/hmmscanOutput.align" - - def test_writeHmmOutputToAlignFile(self): - output = open("./datas/output.align", "w") - output.write("SAR:satellite:satellite_5\t3\t9\tDUF751\t5\t11\t5.4\t5.4\t0\n") - output.write("SAR:satellite:satellite_5\t17\t23\tDUF751\t5\t11\t5.1\t5.5\t0\n") - output.write("SAR:satellite:satellite_5\t3\t21\tClenterotox\t173\t191\t0.66\t7.4\t0\n") - output.close() - pfamOutput = HmmOutput() - pfamOutput.append(["SAR:satellite:satellite_5", "3", "9", "DUF751", "5", "11", "5.4", "5.4"]) - pfamOutput.append(["SAR:satellite:satellite_5", "17", "23", "DUF751", "5", "11", "5.1", "5.5"]) - pfamOutput.append(["SAR:satellite:satellite_5", "3", "21", "Clenterotox", "173", "191", "0.66", "7.4"]) - fout = open("./datas/outputGen.align", "w") - self.hmmOutput.writeHmmOutputToAlignFile(pfamOutput, fout) - fout.close() - self.assertTrue(FileUtils.are2FilesIdentical("./datas/output.align", "./datas/outputGen.align")) - os.remove("./datas/output.align") - os.remove("./datas/outputGen.align") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmpfamOutputProcessing.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmpfamOutputProcessing.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing -from commons.core.utils.FileUtils import FileUtils - -class TestHmmpfamOutputProcessing(unittest.TestCase): - - def setUp(self): - self.fileUtils = FileUtils() - self.hmmpfamOutputProcess = HmmpfamOutputProcessing() - self._inputFile = "./datas/Outputhmmpfam" - self._inputFile2 = "./datas/test_hmmpfam_output" - self._outputFile = "./datas/dummyAlignFile.align" - - def testReadHmmOutput(self): - file = open( self._inputFile ) - pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file) - self.assertEqual(["7LES_DROME", "437", "522", "fn3", "1", "84", "8.8e-15", "48.3"], pfamOutput.get(0)) - self.assertEqual(["7LES_DROME", "825", "914", "fn3", "1", "84", "2.2e-06", "13.4"], pfamOutput.get(1)) - self.assertEqual(["7LES_DROME", "1292", "1389", "fn3", "1", "84", "1.2e-06", "15.9"], pfamOutput.get(2)) - self.assertEqual(["7LES_DROME", "1799", "1891", "fn3", "1", "84", "2.3e-19", "63.5"], pfamOutput.get(3)) - self.assertEqual(["7LES_DROME", "1899", "1978", "fn3", "1", "84", "1.5e-06", "15.2"], pfamOutput.get(4)) - self.assertEqual(["7LES_DROME", "1993", "2107", "fn3", "1", "84", "4.3e-07", "20.3"], pfamOutput.get(5)) - self.assertEqual(["7LES_DROME", "2209", "2483", "pkinase", "1", "294", "6e-95", "314.6"], pfamOutput.get(6)) - self.assertEqual(["7LES_DROME", "2223", "2284", "rrm", "1", "77", "0.72", "-40.4"], pfamOutput.get(7)) - file.close() - - def test_readHmmOutput_empty_file(self): - file = open( "./datas/OutputhmmpfamEmpty", "w" ) - file.close() - file = open( "./datas/OutputhmmpfamEmpty") - pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file) - file.close() - self.assertEqual(None, pfamOutput) - os.system("rm ./datas/OutputhmmpfamEmpty") - - def testParseHmmpfamOutput2Align(self): - self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile2, self._outputFile) - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertEqual(18, FileUtils.getNbLinesInSingleFile(self._outputFile)) - os.system("rm " + self._outputFile) - - def test_parseHmmpfamOutput2Align_empty_file(self): - file = open("./datas/dummy_hmmpfam_output", "w") - file.close() - self._inputFile = "./datas/dummy_hmmpfam_output" - self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile ) - self.assertTrue(FileUtils.isEmpty(self._outputFile)) - os.system("rm " + self._inputFile) - os.system("rm " + self._outputFile) - - def test_parseHmmpfamOutput2Align_file_not_exists(self): - self._inputFile = "./datas/dummy_hmmpfam_output" - self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile ) - self.assertFalse(FileUtils.isRessourceExists(self._outputFile)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmscanOutputProcessing.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmscanOutputProcessing.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing -from commons.core.utils.FileUtils import FileUtils - -class TestHmmscanOutputProcessing(unittest.TestCase): - - def setUp(self): - self.hmmscanOutputProcess = HmmscanOutputProcessing() - self._inputFile = "./datas/hmmscanOutputTab.txt" - self._inputFileScan2 = "./datas/hmmscanOutput" - self._outputFileScan2 = "./datas/hmmscanOutput.align" - self._outputFile = "./datas/dummyFile.align" - - def tearDown(self): - if os.path.exists(self._outputFile): - os.remove(self._outputFile) - - def testReadHmmerscanOutput(self): - file = open( self._inputFile ) - pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file) - self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2742", "2766", "rve", "50", "78", "2.4e+03", "-3.3"], pfamOutput.get(0)) - self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2951", "3101", "rve", "4", "168", "6.7e-30", "103.4"], pfamOutput.get(1)) - self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "3198", "3228", "Chromo", "4", "51", "8.5e-06", "24.7"], pfamOutput.get(2)) - self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2117", "2125", "GARS_A", "196", "204", "11", "2.5"], pfamOutput.get(3)) - file.close() - - def test_readHmmerscanOutput_empty_file(self): - file = open( "./datas/OutputhmmscanEmpty", "w" ) - file.close() - file = open( "./datas/OutputhmmscanEmpty") - pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file) - file.close() - self.assertEqual(None, pfamOutput) - os.system("rm ./datas/OutputhmmscanEmpty") - - def testParseHmmscanOutput2Align(self): - self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFileScan2, self._outputFile) - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileScan2, self._outputFile)) - os.system("rm " + self._outputFile) - - def test_parseHmmscanOutput2Align_empty_file(self): - file = open("./datas/dummy_hmmpfam_output", "w") - file.close() - self._inputFile = "./datas/dummy_hmmpfam_output" - self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile ) - self.assertTrue(FileUtils.isEmpty(self._outputFile)) - os.system("rm " + self._inputFile) - os.system("rm " + self._outputFile) - - def test_parseHmmscanOutput2Align_file_not_exists(self): - self._inputFile = "./datas/dummy_hmmpfam_output" - self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile ) - self.assertFalse(FileUtils.isRessourceExists(self._outputFile)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/Test_HmmOutput.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/Test_HmmOutput.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput - -class Test_HmmOutput(unittest.TestCase): - - def testAppend(self): - hmmpfamOutput = HmmOutput() - self.assertEquals(0, hmmpfamOutput.len()) - list = ["a","b"] - hmmpfamOutput.append(list) - self.assertEquals(1, hmmpfamOutput.len()) - list2 = ["c","d"] - hmmpfamOutput.append(list2) - self.assertEquals(2, hmmpfamOutput.len()) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/Outputhmmpfam --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/Outputhmmpfam Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ -hmmpfam - search one or more sequences against HMM database -HMMER 2.3.2 (Oct 2003) -Copyright (C) 1992-2003 HHMI/Washington University School of Medicine -Freely distributed under the GNU General Public License (GPL) -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -HMM file: myhmms -Sequence file: 7LES_DROME -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query sequence: 7LES_DROME -Accession: P13368 -Description: SEVENLESS PROTEIN (EC 2.7.1.112). - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain 314.6 6e-95 1 -fn3 Fibronectin type III domain 176.6 2e-53 6 -rrm -40.4 0.72 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -fn3 1/6 437 522 .. 1 84 [] 48.3 8.8e-15 -fn3 2/6 825 914 .. 1 84 [] 13.4 2.2e-06 -fn3 3/6 1292 1389 .. 1 84 [] 15.9 1.2e-06 -fn3 4/6 1799 1891 .. 1 84 [] 63.5 2.3e-19 -fn3 5/6 1899 1978 .. 1 84 [] 15.2 1.5e-06 -fn3 6/6 1993 2107 .. 1 84 [] 20.3 4.3e-07 -pkinase 1/1 2209 2483 .. 1 294 [] 314.6 6e-95 -rrm 1/1 2223 2284 .. 1 77 [] -40.4 0.72 - -Alignments of top-scoring domains: -fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 8.8e-15 - CS C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC - *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge - P saP + +++ ++ l ++W p + ngpi+gY++++ +++ g+ - 7LES_DROME 437 PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482 - - CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - + e+ vp sy+++ L++gt+Y++ + +n +G+Gp - 7LES_DROME 483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA 522 - -fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 2.2e-06 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.EC - *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp - ++P l++ ++ + +sW+ p++++ ++ + + +Ye+++ + - 7LES_DROME 825 GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869 - - CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC CCCC - knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-* - + +++ ++++++ g+ + l+ L+P+ Y++rV+A+n +G++G+++ - 7LES_DROME 870 VASQSAFSIRnIRGPI--FGLQRLQPDNLYQLRVRAINVDGepGEWT 914 - -fn3: domain 3 of 6, from 1292 to 1389: score 15.9, E = 1.2e-06 - CS CCCCCEEEE EEC CTTCCEEEEECCC CCCCCCCEEE - *->PsaPtnltv......tdv..tstsltlsWsppt....gngpitgYev - Ps+P++l+v ++ t++++ s++l+W++p+++++ Y + - 7LES_DROME 1292 PSQPRRLRVfverlaTALqeANVSAVLRWDAPEqgqeAPMQALEYHI 1338 - - CS EE.ECCCCCCCCCCEEECCCC CECECCEEEEECCCCEEEEEECCC - tyRqpknggewneltvpgttt.sytltgLkPgteYevrVqAvnggG.... - ++ + g e +e +++ ++ ++ L+P+ +Y+++V A+ ++++ - 7LES_DROME 1339 SC-W--VGSELHEELRLNQSAlEARVEHLQPDQTYHFQVEARVAATgaaa 1385 - - CS CCCC - GpeS<-* - G++S - 7LES_DROME 1386 GAAS 1389 - -fn3: domain 4 of 6, from 1799 to 1891: score 63.5, E = 2.3e-19 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC - *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge. - Ps+P+n++v+ +++ +l +sW pp++ +++ +Y++++ q++ +ge+ - 7LES_DROME 1799 PSPPRNFSVRVLSPRELEVSWLPPEqLRSESVYYTLHW-QQELDGEn 1844 - - CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - .......wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - +++++ + + + t+ ++ ltg kPg+ Y+++VqA+ + +++ S - 7LES_DROME 1845 vqdrrewEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTkSNSS 1891 - -fn3: domain 5 of 6, from 1899 to 1978: score 15.2, E = 1.5e-06 - CS CCCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCCC - *->PsaPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggewn - + l+ +++++sl+l+W p+ + ++++R ++ e - 7LES_DROME 1899 FAELPELQLLELGPYSLSLTWAGT--PDPLGSLQLECR---SSAEQL 1940 - - CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - +++v g+ t ++++ L+P t+Y+ r+ ++++G++ - 7LES_DROME 1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL 1978 - -fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 4.3e-07 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC - *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge. - Ps+P+ ++ + + + ++++W++++++++pi Y+++ ++++ + - 7LES_DROME 1993 PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038 - - CS CCCCEEECCCC CECECCEEEEE - ...........................wneltvpgttt.sytltgLkPgt - +++++++++++++ ++ + +++ ++++l+ +tt s++++ L + - 7LES_DROME 2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088 - - CS CCCCEEEEEE CCC CCCC - eYevrVqAvn.ggG.GpeS<-* - +rV+A++ ++G Gp+S - 7LES_DROME 2089 LLLFRVRARSlEHGwGPYS 2107 - -pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 6e-95 - *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr - ++ll+ lG+G+fG+Vy++++k+++++ ++VA+K l+k+++++ e - 7LES_DROME 2209 LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253 - - flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng - +l E+q++ +++H+NIvrl g++ + +++ l+mE+me GdL++ylr+ + - 7LES_DROME 2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302 - - ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld - +++++++++ ls e++ ++ ++++G +YL+++++vHRDL+ +N+L++ - 7LES_DROME 2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352 - - en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg - e +++++++ tvKi+DFGLAr++++++++++ + + p+++m+PE l + - 7LES_DROME 2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401 - - rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl - +++++DvW++Gv+++E+lt g ++ - 7LES_DROME 2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426 - - PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP - P+ ++ +e+++++k+ g+rl +p+ c e l++Ll c++ DP - 7LES_DROME 2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468 - - skRpGsatakeilnhpwf<-* - ++Rp +++ + n + - 7LES_DROME 2469 WERP---SFRRCYNTLHA 2483 - -rrm: domain 1 of 1, from 2223 to 2284: score -40.4, E = 0.72 - *->lfVgNL.......ppdvteedLkdlFskfGpi.vsikivkDhkektk - ++ g L+++++++p+ v + L++ s+f + +++++ + - 7LES_DROME 2223 VYEGQLktedseePQRVAIKSLRKGASEFAELlQEAQLMSN------ 2263 - - etgkskGfaFVeFeseedAekAlealnGkelggrklrv<-* - F+ e+ ++ l G+ ++ + - 7LES_DROME 2264 ------------FKH----ENIVR-LVGICFDTESISL 2284 - -// diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord -# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target -#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- -DNA_pol_B_2 PF03175.5 531 Polinton-1_DY:classII:Polinton_1 - 4927 3.7e-06 24.2 16.0 1 3 1.4e-09 3.7e-06 24.2 11.1 13 252 992 1214 987 1218 0.76 DNA polymerase type B, organellar and viral -DNA_pol_B_2 PF03175.5 531 Polinton-1_DY:classII:Polinton_1 - 4927 3.7e-06 24.2 16.0 2 3 0.11 2.9e+02 -2.0 0.2 393 433 1367 1397 1364 1398 0.85 DNA polymerase type B, organellar and viral -DNA_pol_B_2 PF03175.5 531 Polinton-1_DY:classII:Polinton_1 - 4927 3.7e-06 24.2 16.0 3 3 0.33 8.5e+02 -3.5 0.2 175 193 2832 2850 2827 2852 0.85 DNA polymerase type B, organellar and viral -ASFV_p27 PF06556.3 131 Polinton-1_DY:classII:Polinton_1 - 4927 2.4 5.8 1.6 1 1 0.0023 6 4.5 1.1 59 74 2633 2648 2626 2652 0.90 IAP-like protein p27 C-terminus -Ribosomal_S4 PF00163.11 110 Polinton-1_DY:classII:Polinton_1 - 4927 5.5 5.7 1.1 1 1 0.0068 18 4.1 0.7 39 72 3008 3041 3002 3043 0.92 Ribosomal protein S4/S9 N-terminal domain -Homo_sperm_syn PF06408.3 487 Polinton-1_DY:classII:Polinton_1 - 4927 6.3 2.4 0.3 1 1 0.0034 8.8 2.0 0.2 49 68 3966 3985 3960 3987 0.88 Homospermidine synthase -rve PF00665.18 169 Polinton-1_DY:classII:Polinton_4 - 4927 5.4e-30 103.7 1.8 1 2 0.7 2.4e+03 -3.3 0.0 50 78 2742 2766 2739 2766 0.80 Integrase core domain -rve PF00665.18 169 Polinton-1_DY:classII:Polinton_4 - 4927 5.4e-30 103.7 1.8 2 2 1.9e-33 6.7e-30 103.4 0.7 4 168 2951 3101 2947 3102 0.92 Integrase core domain -Chromo PF00385.16 69 Polinton-1_DY:classII:Polinton_4 - 4927 3.3e-06 26.0 0.0 1 1 2.5e-09 8.5e-06 24.7 0.0 4 51 3198 3228 3195 3239 0.75 'chromo' (CHRromatin Organisation MOdifier) domain -GARS_A PF01071.11 208 Polinton-1_DY:classII:Polinton_4 - 4927 7.6 3.0 0.7 1 1 0.0031 11 2.5 0.5 196 204 2117 2125 2117 2125 0.95 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -Polinton-1_DY:classII:Polinton_1 992 1214 DNA_pol_B_2 13 252 3.7e-06 24.2 0 -Polinton-1_DY:classII:Polinton_1 1367 1397 DNA_pol_B_2 393 433 2.9e+02 -2.0 0 -Polinton-1_DY:classII:Polinton_1 2832 2850 DNA_pol_B_2 175 193 8.5e+02 -3.5 0 -Polinton-1_DY:classII:Polinton_1 2633 2648 ASFV_p27 59 74 6 4.5 0 -Polinton-1_DY:classII:Polinton_1 3008 3041 Ribosomal_S4 39 72 18 4.1 0 -Polinton-1_DY:classII:Polinton_1 3966 3985 Homo_sperm_syn 49 68 8.8 2.0 0 -Polinton-1_DY:classII:Polinton_4 2742 2766 rve 50 78 2.4e+03 -3.3 0 -Polinton-1_DY:classII:Polinton_4 2951 3101 rve 4 168 6.7e-30 103.4 0 -Polinton-1_DY:classII:Polinton_4 3198 3228 Chromo 4 51 8.5e-06 24.7 0 -Polinton-1_DY:classII:Polinton_4 2117 2125 GARS_A 196 204 11 2.5 0 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutputTab.txt --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutputTab.txt Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord -# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target -#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- -rve PF00665.18 169 Polinton-1_DY:classII:Polinton_4 - 4927 5.4e-30 103.7 1.8 1 2 0.7 2.4e+03 -3.3 0.0 50 78 2742 2766 2739 2766 0.80 Integrase core domain -rve PF00665.18 169 Polinton-1_DY:classII:Polinton_4 - 4927 5.4e-30 103.7 1.8 2 2 1.9e-33 6.7e-30 103.4 0.7 4 168 2951 3101 2947 3102 0.92 Integrase core domain -Chromo PF00385.16 69 Polinton-1_DY:classII:Polinton_4 - 4927 3.3e-06 26.0 0.0 1 1 2.5e-09 8.5e-06 24.7 0.0 4 51 3198 3228 3195 3239 0.75 'chromo' (CHRromatin Organisation MOdifier) domain -GARS_A PF01071.11 208 Polinton-1_DY:classII:Polinton_4 - 4927 7.6 3.0 0.7 1 1 0.0031 11 2.5 0.5 196 204 2117 2125 2117 2125 0.95 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,321 +0,0 @@ -hmmpfam - search one or more sequences against HMM database -HMMER 2.3.2 (Oct 2003) -Copyright (C) 1992-2003 HHMI/Washington University School of Medicine -Freely distributed under the GNU General Public License (GPL) -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -HMM file: myhmms -Sequence file: test.fa -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query sequence: pkinase_full -Accession: [none] -Description: Dario rerio - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain 266.6 3.3e-80 1 -pkinase Protein kinase domain 265.4 7.6e-80 1 -rrm -42.5 2.5 1 -rrm -8.7 3.7 1 -fn3 Fibronectin type III domain -45.8 3.7 1 -fn3 Fibronectin type III domain -9.0 3.8 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -rrm 1/1 169 180 .. 66 77 .] -8.7 3.7 -fn3 1/1 197 200 .. 81 84 .] -9.0 3.8 -rrm 1/1 256 319 .. 1 77 [] -42.5 2.5 -pkinase 1/1 258 540 .. 1 294 [] 266.6 3.3e-80 -pkinase 1/1 258 537 .. 1 289 [. 265.4 7.6e-80 -fn3 1/1 434 506 .. 1 84 [] -45.8 3.7 - -Alignments of top-scoring domains: -rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7 - *->nGkelggrklrv<-* - n++ ++l v - pkinase_fu 169 NKQDPHQHRLSV 180 - -fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8 - CS CCCC - *->GpeS<-* - G eS - pkinase_fu 197 GGES 200 - -rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5 - *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks - +N++ +d+ e + F+ + +++ + - pkinase_fu 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285 - - kGfaFVeFeseedAekAlealnG.kelggrklrv<-* - + V++ +ee+ ++ ++++ + l++ + - pkinase_fu 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319 - -pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - ng........................gplsekeakkialQilrGleYLHs - + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + - pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402 - - ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY - +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p + - pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451 - - mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev - +m+PE ++++ y+s++DvW++Gv+L+E++++g - pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483 - - dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd - ++P+++ + ee+ + +++ g l +p+nc+ el+ - pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517 - - LlkkcLnkDPskRpGsatakeilnhpwf<-* - L++ c+ P++Rp ++ i h + - pkinase_fu 518 LMRLCWSGHPTDRP---SFASI--HRIL 540 - -pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - ng........................gplsekeakkialQilrGleYLHs - + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + - pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402 - - ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY - +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p + - pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451 - - mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev - +m+PE ++++ y+s++DvW++Gv+L+E++++g - pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483 - - dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd - ++P+++ + ee+ + +++ g l +p+nc+ el+ - pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517 - - LlkkcLnkDPskRpGsatakeil<-* - L++ c+ P++Rp ++ i+ - pkinase_fu 518 LMRLCWSGHPTDRP---SFASIH 537 - -fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.E - *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq - a ++++ + + ++W pp++ ++ + +++ Y v + + - pkinase_fu 434 IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477 - - CS CCCCCC CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC - pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-* - + + + ++ + ++V+ +g+ S - pkinase_fu 478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS 506 - -// - -Query sequence: pkinase_part -Accession: [none] -Description: Dario rerio - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain 101.5 1.7e-30 1 -pkinase Protein kinase domain -94.7 1.5e-05 1 -rrm -42.5 2.5 1 -rrm -8.7 3.7 1 -fn3 Fibronectin type III domain -9.0 3.8 1 -fn3 Fibronectin type III domain -52.2 5.9 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -rrm 1/1 169 180 .. 66 77 .] -8.7 3.7 -fn3 1/1 197 200 .. 81 84 .] -9.0 3.8 -fn3 1/1 233 299 .. 1 84 [] -52.2 5.9 -rrm 1/1 256 319 .. 1 77 [] -42.5 2.5 -pkinase 1/1 258 400 .] 1 116 [. 101.5 1.7e-30 -pkinase 1/1 258 400 .] 1 294 [] -94.7 1.5e-05 - -Alignments of top-scoring domains: -rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7 - *->nGkelggrklrv<-* - n++ ++l v - pkinase_pa 169 NKQDPHQHRLSV 180 - -fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8 - CS CCCC - *->GpeS<-* - G eS - pkinase_pa 197 GGES 200 - -fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9 - CS CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC - *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew - P + ++l ++ +s ls + p + i++ +R + ++g - pkinase_pa 233 PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267 - - CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC - neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-* - g ++ gL P + ++ + + ++S - pkinase_pa 268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS 299 - -rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5 - *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks - +N++ +d+ e + F+ + +++ + - pkinase_pa 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285 - - kGfaFVeFeseedAekAlealnG.kelggrklrv<-* - + V++ +ee+ ++ ++++ + l++ + - pkinase_pa 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319 - -pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - ng........................gplsekeakkialQilrGleYL<- - + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL - pkinase_pa 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL 400 - - * - - pkinase_pa - - - -pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05 - *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek - +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ - pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 - - .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr - ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr - pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 - - nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi - + - pkinase_pa 353 RC------------------------------------------------ 354 - - aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL - A++ s + +t++ ++ PE - pkinase_pa 355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377 - - yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee - +P s - pkinase_pa 378 --------------------------------YPPLS------------- 382 - - lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp - + + ++S+ + + - pkinase_pa 383 -----CQ------EQLSISKQVAAGM-----------A------------ 398 - - wf<-* - ++ - pkinase_pa 399 YL 400 - -// - -Query sequence: S13421 -Accession: [none] -Description: S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum. - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain -171.6 0.19 1 -rrm -32.5 0.26 1 -rrm -6.1 0.92 1 -fn3 Fibronectin type III domain -39.7 1.2 1 -pkinase Protein kinase domain -9.2 1.8 1 -fn3 Fibronectin type III domain -7.5 1.9 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -fn3 1/1 143 224 .. 1 84 [] -39.7 1.2 -pkinase 1/1 233 241 .. 1 9 [. -9.2 1.8 -rrm 1/1 440 456 .. 1 17 [. -6.1 0.92 -rrm 1/1 669 731 .. 1 77 [] -32.5 0.26 -pkinase 1/1 906 1127 .. 1 294 [] -171.6 0.19 -fn3 1/1 923 934 .. 1 12 [. -7.5 1.9 - -Alignments of top-scoring domains: -fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2 - CS C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC - *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew - + ++t+l++ dv ++ sWs+ +g+ + tg v R + ng + - S13421 143 IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185 - - CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - +++ ++ + + l L + + V v ++ +G - S13421 186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH 224 - -pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8 - *->yelleklGe<-* - +l+klGe - S13421 233 VSTLKKLGE 241 - -rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92 - *->lfVgNLppdvteedLkd<-* - + ++ L++ + d+ d - S13421 440 VIISFLNEGLRQADIVD 456 - -rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26 - *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG - V L+++d+ + + f i k++ D + - S13421 669 --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699 - - faFVeFeseedAekAlealnGkelggr.klrv<-* - + FV ++ + e+ ++ l k+++ +l++ - S13421 700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI 731 - -pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19 - *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes - ++l G++ ++ + ++ ++ ++ + ++VAv + ++ - S13421 906 FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942 - - ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy - + + L+ ++ fe + + v++ +d - S13421 943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980 - - lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde - l + +++ +s ++ Q+ lde - S13421 981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007 - - ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l - + ++ + LAr+l +++ + + +++++f+ +++ ++++l - S13421 1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047 - - egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif - +r s ++ W++++ vi+ ++ g - S13421 1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073 - - vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL - l++ +++ dp + + k l + ++++ ++l+ L +k++ - S13421 1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113 - - nkDPskRpGsatakeilnhpwf<-* - +k +k p +i f - S13421 1114 TKVFTKHP----DYQI----LF 1127 - -fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9 - CS CCCCCEEEEEEC - *->PsaPtnltvtdv<-* - + t+l++++v - S13421 923 INPITGLSAREV 934 - -// - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/hmmOutput/tests/hmmOutputTestSuite.py --- a/commons/pyRepetUnit/hmmer/hmmOutput/tests/hmmOutputTestSuite.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -import unittest -import sys -import TestHmmOutputProcessing -import Test_HmmOutput -import TestHmmpfamOutputProcessing -import TestHmmscanOutputProcessing - - -def main(): - - hmmOutputTestSuite = unittest.TestSuite() - hmmOutputTestSuite.addTest(unittest.makeSuite(TestHmmOutputProcessing.TestHmmOutputProcessing,'test')) - hmmOutputTestSuite.addTest(unittest.makeSuite(Test_HmmOutput.Test_HmmOutput,'test')) - hmmOutputTestSuite.addTest(unittest.makeSuite(TestHmmpfamOutputProcessing.TestHmmpfamOutputProcessing,'test')) - hmmOutputTestSuite.addTest(unittest.makeSuite(TestHmmscanOutputProcessing.TestHmmscanOutputProcessing,'test')) - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(hmmOutputTestSuite) - - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/ProfilesSearch.py --- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/ProfilesSearch.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,103 +0,0 @@ -import subprocess -import os -import sys - -## Prepare profiles databank and create command to search profiles from a profiles databank in a nucleotides databank -# -class ProfilesSearch(object): - - ## launch command to prepare profiles bank - # - # @param launch_1 string corresponding to pre command - # @param launch_2 string corresponding to post command - # @param config configParser object instance - # @param cDir string current directory - # @param verbose int (default = 0) - # - def prepareProfilesBank(self, launch_1, launch_2, config, cDir, verbose = 0): - bank = self._getBankBaseName(config) - prg = "hmmpress" - if verbose > 0: - print "prepare bank '%s'..." % ( bank ); sys.stdout.flush() - cmd = "" - cmd += prg + " -f " - cmd += "%s/%s " % ( cDir, bank ) - process = subprocess.Popen(cmd, shell = True) - process.communicate() - if process.returncode != 0: - raise Exception("ERROR when launching '%s'" % cmd) - - ## create command to detect Hmm profiles in a nt sequence file - # - # @param inFileName string name of input file - # @param launch_1 string corresponding to pre command - # @param launch_2 string corresponding to post command - # @param cDir string current directory - # @param tmpDir string temporary directory - # @param config configParser object instance - # @return cmd string command to launch - # - def detectHmmProfiles(self, inFileName, launch_1, launch_2, cDir, tmpDir, config): - bank = self._getBankBaseName(config) - evalueMax = config.get("detect_features","TE_HMMER_evalue") - - cmd = "" - - cmd += launch_1 - cmd += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py" - cmd += " -i %s" % ( inFileName ) - cmd += " -o %s_translated" % ( inFileName ) - cmd += launch_2 - - cmd += launch_1 - cmd += "hmmscan " - cmd += " -o %s_tr.hmmScanOut" % ( inFileName ) - cmd += " --domtblout %s_tr.hmmScanOutTab" % ( inFileName ) - cmd += " --noali -E " + evalueMax - cmd += " --cpu 1 " - cmd += "%s/%s" % ( cDir, bank ) + " " + "%s_translated" % ( inFileName ) - cmd += launch_2 - - cmd += "if os.path.exists( \"%s_translated\" ):\n" % ( inFileName ) - cmd += "\tos.remove( \"%s_translated\" )\n" % ( inFileName ) - - cmd += launch_1 - cmd += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py" - cmd += " -i %s_tr.hmmScanOutTab" % ( inFileName ) - cmd += " -o %s_profiles_%s.align" % ( inFileName, bank ) - cmd += " -T %s" % ( inFileName ) - cmd += " -p hmmscan" - cmd += " -c" - cmd += launch_2 - - cmd += launch_1 - cmd += os.environ["REPET_PATH"] + "/bin/matcher" - cmd += " -m %s_profiles_%s.align" % ( inFileName, bank ) - cmd += " -j" - cmd += " -E 10" - cmd += " -L 0" - cmd += " -v 1" - cmd += launch_2 - - cmd += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( cDir, inFileName, bank ) - cmd += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inFileName, bank, cDir ) - cmd += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( cDir, inFileName, bank ) - cmd += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inFileName, bank, cDir ) - cmd += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inFileName, bank ) - cmd += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inFileName, bank ) - cmd += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inFileName, bank ) - cmd += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inFileName, bank ) - cmd += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inFileName ) - cmd += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inFileName ) - - if tmpDir != cDir: - cmd += "if os.path.exists( \"%s\" ):\n" % ( bank ) - cmd += "\tos.remove( \"%s\" )\n" % ( bank ) - - return cmd - - def _getBankBaseName(self, config): - profilsHmmBank = config.get("detect_features", "TE_HMM_profiles") - bank = os.path.basename(profilsHmmBank) - return bank - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/Test_ProfilesSearch.py --- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/Test_ProfilesSearch.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ -import unittest -import os -import ConfigParser -import shutil -from commons.pyRepetUnit.hmmer.profilsSearchInTEClassifier.ProfilesSearch import ProfilesSearch - -class Test_ProfilesSearch(unittest.TestCase): - - - def setUp(self): - self._section = 'detect_features' - self._option1 = 'TE_HMM_profiles' - self._option2 = 'TE_HMMER_evalue' - self._config = ConfigParser.ConfigParser() - self._config.add_section(self._section) - self._config.set(self._section, self._option1, './datas/hmmbank_test') - self._config.set(self._section, self._option2, '10') - self._iProfilesSearch = ProfilesSearch() - self._launch1 = 'First Command\n' - self._launch2 = '\nSecond Command\n' - self._cDir = '.' - self._profileBank = self._config.get(self._section, self._option1) - self._bank = os.path.basename(self._profileBank) - shutil.copy(self._profileBank, self._cDir + "/" + self._bank) - - def tearDown(self): - os.remove(self._cDir + "/" + self._bank) - - def test_prepareProfilesBank(self): - hmmpressLaunched = False - self._iProfilesSearch.prepareProfilesBank( self._launch1, self._launch2, self._config, self._cDir ) - if ( os.path.exists(self._cDir + "/" + self._bank + ".h3m") \ - and os.path.exists(self._cDir + "/" + self._bank + ".h3i") \ - and os.path.exists(self._cDir + "/" + self._bank + ".h3f") \ - and os.path.exists(self._cDir + "/" + self._bank + ".h3p")) : - hmmpressLaunched = True - os.remove(self._cDir + "/" + self._bank + ".h3m") - os.remove(self._cDir + "/" + self._bank + ".h3i") - os.remove(self._cDir + "/" + self._bank + ".h3f") - os.remove(self._cDir + "/" + self._bank + ".h3p") - self.assertTrue(hmmpressLaunched) - - def test_detectHmmProfiles(self): - inputFileName = ' FileName' - dirTemp = 'Tempory directory' - eValueMax = self._config.get(self._section, self._option2) - - expCommand = self._launch1 - expCommand += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py" - expCommand += " -i %s" % ( inputFileName ) + " -o %s_translated" % ( inputFileName ) - expCommand += self._launch2 - - expCommand += self._launch1 - expCommand += "hmmscan " - expCommand += " -o %s_tr.hmmScanOut" % ( inputFileName ) - expCommand += " --domtblout %s_tr.hmmScanOutTab" % ( inputFileName ) - expCommand += " --noali " - expCommand += "-E " + eValueMax - expCommand += " --cpu 1" - expCommand += " " + self._cDir + "/" + self._bank + " " + "%s_translated" % ( inputFileName ) - - expCommand += self._launch2 - - expCommand += "if os.path.exists( \"%s_translated\" ):\n" % ( inputFileName ) - expCommand += "\tos.remove( \"%s_translated\" )\n" % ( inputFileName ) - - expCommand += self._launch1 - expCommand += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py" - expCommand += " -i %s_tr.hmmScanOutTab" % ( inputFileName ) - expCommand += " -o %s_profiles_%s.align" % ( inputFileName, self._bank ) - expCommand += " -T %s" % ( inputFileName ) - expCommand += " -p hmmscan" - expCommand += " -c" - expCommand += self._launch2 - - expCommand += self._launch1 - expCommand += os.environ["REPET_PATH"] + "/bin/matcher" - expCommand += " -m %s_profiles_%s.align" % ( inputFileName, self._bank ) - expCommand += " -j" - expCommand += " -E 10" - expCommand += " -L 0" - expCommand += " -v 1" - expCommand += self._launch2 - - expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( self._cDir, inputFileName, self._bank ) - expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inputFileName, self._bank, self._cDir ) - expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( self._cDir, inputFileName, self._bank ) - expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inputFileName, self._bank, self._cDir ) - expCommand += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inputFileName, self._bank ) - expCommand += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inputFileName, self._bank ) - expCommand += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inputFileName, self._bank ) - expCommand += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inputFileName, self._bank ) - expCommand += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inputFileName ) - expCommand += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inputFileName ) - - if dirTemp != dir: - expCommand += "if os.path.exists( \"%s\" ):\n" % ( self._bank ) - expCommand += "\tos.remove( \"%s\" )\n" % ( self._bank ) - - obsCommand = self._iProfilesSearch.detectHmmProfiles( inputFileName, self._launch1, self._launch2, self._cDir, dirTemp, self._config ) - self.assertEquals(expCommand, obsCommand) - - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/ConsensusFile_test.fa --- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/ConsensusFile_test.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,141 +0,0 @@ ->blumeria_Grouper_590_20:NoCat -TTTCGATCNTATTGAAATGTATAACCCACTACTTAGTTCGTGGACTTGTTGGTAGAGGGA -AGCTTATGCAATAATGAAGGATAAAAGGATGTCAATTCGACTACTCTTCTAAACACAGAT -ACCAGACTCCTTTTAATCCCAATAGATAGCCCGTGCGGGATCTCCTATTAACAGCAGTAA -ACAACGCTAACACAGGGTATACGCAATCTCCGTTCGCCAAACACCAGTCTGTCGGGACTA -CTAATTATCGAGCCTAGTAGGATCGACAATGTGTATCCCAACATAGAAATAATAGAAAGC -TCAACACCCAAACCCCTCATCAATAACTGCCATTAATCATCACCTGACTTATCTCTGTAC -TCCATAATTTCAACACTNAAGAATATTTGTA ->blumeria_Grouper_4152_12:NoCat -GGACCGGCCGCCACGAATTGCGCGATTGCTGCTCGCAAGTAGACTTTGATGGAGTCTACA -AAATTTTTGTCTTCACCGGTGGAGAGCGGTTGAAGAGCTGCCTCGACACTGCTAATAGCC -GTCGAGCATATTGTGAATTGCGCGGCTTTTTGTCTTGCCCTGCGCTCCTCCGCTTCGATC -GCTGCAAGCAATTCTGGAGGGTGTGTATTTTTTCTGCCTGCTGCTTCTAGTGCTGGAGGC -TGCGGGGCCAGTGGAGGGTTTTCGGCTCCTGCTGCCTTAGTGGATGGTGTTTCAGCCCTT -TTCGCGGGCCTCACTTCTGCAGGTCGCGGTAGTGCTGGAACCGTGATGCGCTTCTCGGGT -GCGACGACGGTTTTTCTGGGGGATCCGGTGGGATCCAAGACTTGCTCTGCGTCTTCTGGG -CTGGAGGATGCCCAAACTGAATCGGCGAGGGTTTTTAGCTTCTCGACTTCTGCGTCCACC -ATATCTACCTCGGGGACATTG ->blumeria_Grouper_28830_3 -TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC -CGACTAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTNATTC -TATAATACAGGATCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACA -GCGCACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACAAACTATCCCCCTTCTC -AAAACTAGCTGTCCACAGCTTATTTAAATTACAAGTTAATTAGAAATTTTATTATGGTAT -CACTCAAACTAAATCCTTGCTGAATTTTTGAGTGTCTTTCTATCCTGCTCCAGCATACGG -CGGCTACCATACCATAGACTACGAACTGGGTGTCCTTCACGTACATATGCCGGGAATAGG -TTTGTGCCGTTGTACTTGTTGCCTAATTTGTATCCACCCGGTGATATTAAGGAGTAGGTA -TTATTATTATGACAAGCTGCTACGGCCCATGGCCCGTCATAGTAGGGCTCCATCTTGTGT -CTTCGCTGGCGTACTCGCAGTACCCAGTCTCCGGGGGCGTAAGTACGTATAAGTGCCTTT -TCTTCCTGGAGGTAAGCCCGTATTTTATCCCTAGTTGCTTTCATACTACTAACGTAGGAG -CGTGCTATTGGTGCGGGGTGTTTCCTTCCGAGTTCTTCGGCCCAGAGGCGCTCCTCTGAT -TCTGTGGCTTCACGGGTATATACTGGATAAGAATTTTCCTCCTCCGGGGGCTGAGTGCCG -AAGAGTAAGAAGTAAGGGCTATACCCGCTGGGTGAGACTCTTCGATTGAAATTCATTACC -GCGAGTGAGAGAGCGCCAGCTAGTGTAATTTTAGGAGAATCCAGGAGAACTCTGACCAGT -ATGGCTTTCAGAACGCCATTTGCCTGTTCGACTTTGCCATTTCCTCTTGGCCTAGCTGGT -GTGGTATGGACAACCTGCAGTTGTTGGCTAGCTTGAAATCGTTGTGCTTCTATGCCTCCG -AAGCAGCCAGCATTGTCACTGATAATCTGCTTTGGCTTTCCAAAGTTCTGGATAATATAC -GTGAGCAGAGGCACAGTGTTAGCGAAGTCTGCATTGGGAACTAAGCGGGATTCCAGCCAG -CCTGTTGCGTACTCAATTGCATTGAGCAAGACTTGGGGTCCTACTTGAGTATGATCTATA -CCCCACCGTGTCAGAGGAGGTGCTGGTACTATAGGAGTTAAGCTTCCCAGTAACGGGTCT -GGAGGTTTCATGAGCTGACAGGACTTGCATTTTCGGACAGCTTCGTGAGCCGCGAGGATC -AGTTCGGGGTGCCAAAACCTACGCCCTAATTCCCGCATAGTATTGCCGATTGACGCATGG -CCTTGGCCCTCATGAACATTTACGGCCGTCGATACTAGATCCTCATATTCCAAGATTTCT -AGTAGGGTTGCGGCGCCAGATGGACCAGGTGCATCGCCTACTTGTTGCGACGGGTTCTTT -TTGATGAGATGCAATTTGGAATTGTACATCGCAAAATTATCTCGGACCCAAGTGGCAGCT -ATATTTAGGGGAAGTGCCTCTCCTAAGGTTAGAAATTCGGTGATGCACTGCAGGTCGATG -CGGTTGAGTTCGTGTGGGTGCTTTATTTCCTCCATCTCAAGTTCTCTTTCTGCACCACTT -TGGATTCTAGAGTTTTCGTTGTCGTCAGTAGCTACATTCCCTTCCCCTTCTTCCCTAGAG -AGAAATAGAACATCACAGGGACGGGAGAGAAAATCAGCGAGAACATTTGCTTTTCCGCGA -CGGTAGATAATCCTGATATTAAAATGCTCTATAGCATCTAAAAAACGGACCATTCTGACG -GGCTGCTCGGCTTTGGTCTGAATAGTTCGTAGAGATTCATGGTCAGTTATCACCGTTACG -TCGCCGCCTTCTACCCAGTGACGCCAATGTTGTAGTGACAGTAAAATCCCAAGTAATTCC -CTCTCTTGTGCTGAATAACGCTGCTGGGTATCGTTTAGTTTTCTTGAGAAGTAAGCTATG -GGATGCAGCACTGAACGATCGGAATTGTTGGAGCATCGCATGTACGGTTGGAGTATGACT -GCACCCACGAACTTTTGGGAAGCGTCAGTTTCCAATATGACGGGAAGTCTCCAATCAAAT -TTTTTTACAACTGGTGATGTTGTAAGCGCTAGTTTGATACTTTTCCATGATTGAATCGAT -TGGTCCGTCAGAATGACAGGGCAATTTTTAGGTCCAGAGGATTGGTCCGTGAGTGGCCCT -GCTAGTTGGGAGAAATTTTTAATGAGACAACGTAGGTAACCAGCTGCATTTACAAATCCT -CTTATTTCCGAGGTAGTTGTTGGCATAGGCCTGTCTCTGATCGCTGAAACTTTTTCGGGG -TCTGCTGCAATGCCATGTTTAGAAATATGGAAACCAAGGAAGATTCCCTCTGAAACAAAT -AGCCTGCACTTTGAAGCATTGAGGAGGAGACCATAGGAAGCGAATCTAGAAAAAATAAGT -ATCAACCGTGAGTGCAATTCTGCCATTGAGTCTGCCCAGACAGCTACATCGTCCAGGAGC -CCTGCGACAAATGGACGGAATGGCTCTAGAACTTCTTCCATAAAACACTGGAAAGTAGCT -GGTGCGTTGCATAGGCCGAAAGGCATAACTAGCCATTCATAGACACCGAAAGGAGTCACA -AATGCTGTTTTCTCTGAAGAGTCTTTGTGCATACGTATCTGCCAAAATCCGTTTTCCAGG -TCGAGGAATGCATAGAAGTTATGTCCTGCTGCGCGCTGAATTTCATCTTGAGCATTTGGT -AGGGGATGGGCGTGTTTCTTCGTAATCTTGTTAAGCTCTCTATAGTCAACACAAATACGC -CAAACGGTTTGGTTAGTCTGGGTTAGCGTCTTTTTTTGGTGTTAATAACAGAGGTGCAGC -CCATGGTCCCTTACATTTGCGTATGAATTGAGCCGGTCATGTGTTGCACAAGAAAGTCCC -CGGATGGCTTGTTGTTGCGCCGGGGCTATATCGCCTCGGAGGGGAGTTTTAAATTGGGTT -GACAATTACCCCGTTTCTATGCGGGTGTTTCTGTCTTGGGAGAGTTTTATCCCATTTGGC -GGGAGAGATTTATCGAAAAGTTGAAGGGGAATTTAACTTTGATATTGTAGGGAAAAACTG -TAATGCGGAATGAAGGGTGGGCTGGGTGCCATTTGACCATTGGAATATTTGAAGTAGTGA -AGACTTTTCGGTTTGGGAGAGTATTAATTATAGGATTAAGAATTGGTTGGTCAATTAAGT -TGAGAAGTTGCAGTTTGCCATTTGATAAACATCGTAGCCCCAGTTCATGGAATAAAGTTT -GTCCAAGTGTCACATCTGCTGGGAATGTGCCATCTGGGACAACTCCTAGAGACACTGTGA -ATTCCTGAGTCCAGAATGATTCAAGGTGATTCGAGCAAAGAAACTGTGCAGTTAAAATTG -CATCCTTAGAAATTGTTGGGCCAGGGCCACCAATGCCTGACATTTTAGAAATAATAGATG -TATTATAAGAAGTCAAATATTTAGAGAAAGACTGTGAAACATAACATGCTGAAGAGCCGT -AGTCAAAAAAAACTGAAAATTGGACATAGGGAAAATGAGTTATTCGTGCAAAAAACATTC -TGTGTGGCTTGCCATATCCTTCCCGTAGAGGTTGTCCTTTTGGGGGTGGCTCAAATTTGC -CCTTTCCTACGGCCACAAAGTAGGTATTCGGGCTGTCCTATTCATAAATTTCTTCATTTC -GCATTCGATATAGAATGGCTTCAATTTCGTCATCGAGCTGCTCATCTTCTATTTGGCCTT -CAGGGCTTATTTGCTCTTGATCCAAATCTTCTGGCTCAACAAGGAAAGTAGAAGTGACAG -GCTTTGATGAACGATCGTGTGGTGTTACAGGTTTTACATATTTTTTATTTTTCATTGATT -GGTAAGTTTTCCTGAATTTATCGCTGAAACGCGACGAGGTGTATTTAGCGTTTGGTGCAT -ATTCCCTTTGTTCTTTTGATTCCACCGGCGCTGTTTTCATCAACCGGCAGTCTTTCGCCC -AGTGGCCTGTCTTTCCGCAATTGAAGCATTCGTAACGCTTGTCGTGAATTGGGTATGATT -TATCTGTTTCTGCAATGTCTTGTGACGCAAAGACGTCTTGCCCATACGACCTTGGATCAG -CTATGGATGCGTCAAATGCTGGAAGCTTTTCGCCTTTTGACGCTGAGATCGGAATTGGTG -CATTGGACTCGGAATGTTTGAATACATCATCCTCAAGTGTCCACCTTGTAATACCGCGTG -TGACTTGAACCACTCGATCCGCAAGCTCCGCGCTGGTGAGTTTGGGGAGATTATTGGAAA -TGATGGTCCAGGTACGTGGAAGTGAGAGTCGAATATGCTGCCTCAGTATATCTCTAGTCT -GAGGCCCTACCATGACATCCGAAGGTAGGCTAAAGAAAGCTTTCCGGAGTCGTCGCGCAA -ATTGTAATTGAGTCTCGTCGTTTCTTGCAGTTATTCGTGCAAATGTTGTCAAAGGCGACC -CGAGTACATCATTGTCGAACAGTATTTTAAGGATACAGTCTACAGCTCCTGCCCAATCGA -GGTGTTGACTGATGATTGTTCTTCGCGCCGAGATGAAATCTTCATCCATTTCCATTGCAA -TTCTGATAGCCCAAGCAGAATATGGAAGCATATGTTGAATCATCAATGATTGCATGTGGT -ATAATATATTCATTATGTTCTCATCAGCAAAGTGCAATTTCCATTGTGGTGGGAATACCG -CGCGTGTTTTTCTATTTGCCTCTTTTAAAGGGCCGTGCGGATTTTCAGCTTCGGAACGCG -AAAAGAAATCTGGGAAGTACCGCTTTATTTTTCGCTCTTGTTCAGTAACATTCAATGGTT -CGTTAACTGACTGGCGGTATAAATTAATAGTCCCATCTTTGTTTTGCTCATCATTGCTTA -GGTTGGGCGTTGTTTCATAGAATTGCGCCGAGGTAAAGGGTCTTTTCTTAGGCTGAAACA -CGATTGGCCTGGTTGCGGGTCGCGAGGCGCTGCCTGCTGAAAAGTCAAATAGCTCCTCCC -GGTATGGTTTTTTATTTTCAGATGGCCCTGCTTCCGAAAGTTGAAAGGGGACTGAATTTT -TCGAAGAAGTTTTTGTTTCCACGTCTTCATTTCTACTTACTAGTTTGGAAATTAAGTCGT -TCATTGCAGACATTTGTTTGACTAGAAGAGAAATTTGTGATTGGGTCTCTTCAAACCTTT -GATCGATTCTCTTGGAGAGATCTTTTGTCACTGCCTTTGCAGCTTCATTAGCTTCGGAAA -AATTTTCGTTGGCTTTGGTTTGCCCGGCAATGTGATCCTTCATCAAGCTTTCCAACTGAG -CATTATTCAGGCCGACCATGATGATTGAATAGGTGGTGAAATGCGTAAAAAATTTGGAGA -CGTCTTAAATTGGGATGACCTAGAATTGTGAGGTTCTCTCAACAAAAATATATAATTTTG -TGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCG -ACAAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTCATTCTA -TAATACAGGACCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACAGC -ACACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACA ->blumeria_Grouper_14770_3 -GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA -AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG -CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT -TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC -TAAATACATGTGTGTCGGTAATAGATCCGAGAAACCTTTAACCTGCATTTGATACATAAT -CATCTGATGGAATGCTAGTGTGAAATAAATGCCAATGTACGTTAAACTTTCCGTGAGGAA -TGTGCTGATGACAATGATATAGGAAGGTGAATTTGATAACCTAATTAGCCGGACTTACAA -ATGAGTTATCCTTGGCATTCCAGGATATACAATATTTCAACACCCCTCCTCACTTTGCAT -CGAGGATAGATACATAAGTGAAAAACTGTTAGTATATTTATTGTCATTTCTCATCTAATG -CTGGTATGGTAGACACGCCAGTGGTTGTACTAGTACCAAAAACTGAAGTGCATAAATCGG -TGTGCCTTGGTCTCGGTAAGCCTTTTGTACATATATCTGCGAGATTTTTAGCTGAAGGAA -CATGTAATAGTGTAAGCGAGCCGTCTTCAATTCTTTCCCTTGTAAAATGATAAGCGATGT -CGATATGTTTAGAAGCATCATTTAGTTTTGGATTGTGAGCAAGTTCAATGGCAGCCGTAT -TGTCAGTCGAGATTGCTGCTGGGATGCTGTCTCCAAGGAATCGGTGAAGTCCGCGCAAAA -TCCAGATATATTGTTTGGATGCGAGCGCTATTGCCATGTACTCAGCTTCGCAGGTTGAAT -G ->blumeria_Grouper_1717_12 -ATTTCCAGTATCTTGCCCTGAAGGGCCAGTAAGTCCTGATCGAATAGTTTTCGAAGTCTC -TCGTCAGTGACTGGTTCCAACAGCTTGCAGAACCCAATGATGAAGCGCTCTGCTTGTGCG -GAGCGCGTCTGGAATATCCTGCCCTGTTCGGCGAGGAATTTGGTCGCGACGATTTGAGGC -GACGGAGTTTGTTGGTGCGGTGAGCTTCGATGACTCGCCTCGTAGATTGGCTCTACAAAT -TGTTGTGTGGGTTGTTGTGATGGCGGTTGTGGCCCGTTAAGGACCATTTCGACGTCTTGA -CGCGTCGAACATTGAGTTGGGAGGGGGGGCCAAGAGCCAGCCTCTGCGGAGGACTGGGGC -GGCATGAGTGAGTGAGGTTTGTGGCAGTGTGAGATCGTAGATGGTATACGGCGCGCTTGA -AGGG diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/DummyRepbase_aa.fa --- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/DummyRepbase_aa.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ ->GYPSY11_AG1p:classI:LTR_retrotransposon -AATTTNVFKKVPYTCNFYGRSCINMQKLLEKIEILDRTYDQVRQLNKCYRLCALTTLRNN -TKELYDEIQELLRKHESSIKDEILTTLVKKSRHLYYEINKCIKIHFERHPDSLNTTLSEN -QFDITIETKSDKMADIIELIKITTSLISKYDGNEKDLKGVVSNLNVLKKIVKPENRETII -ELVLGRLTGKARIVVGEAPKSIEDIVNKLQDRCSIKVTPEIVVSKMDNTKQTGTIEDFGS -IIEKLTQQLEEAYIAEEITPEVARKKATKSGISALSYGLKDGETKIIMRSSKFETLHEAI -EQAVKLELEDRTKKGKNEQTKILYSNATRNNRGYGNNYQGRNNYNRFTNNNNNRYQTQNP -PRFPPARYGHNNNRNNNNYRNNNFNNTRNQHANRQNNSNRNQYVQSNQRNNSNLQNNRAP -IHNTVTAEEQNNFLGQPQASENTQY ->GYPSY10_AG2p:classI:LTR_retrotransposon -AIRQPKFFRATRATKSSALHSGGDPEPTGGPALHKPIRATYTINVQKSNFIKTRLGLADS -ICNLFVDSGSDISIIKGNKVRPTQTYKPKDIVDIISVGEGTITTHGSTITDVIVEGKKIQ -QLFHIVPDNFKIPADGILGRDFFMDHRCIINYDTWIFSVKHDGEFLETPIEDTINDKTLI -PPRCEVIRKLDKLKELDTDAVVCAEQLQEDVLVGNCIVNKNYPFIKIINTSNKAKLVNIS -HIKTIPLNEFEIVKTNNHKNENRLAIIKELIRKENISEDTDTSFEQLLLSYNDIFHLPND -HLTTNNFYKQDIKLEDKRPVYIPNYKQNHSQGPEIKKQIEKMLQDDVIEHSVSHYNSPIL -LVPKKSSDEKKWRLVVDFRQLNKKLLPDKFPLPRIDSILDQLGRAKFFSTLDLMSGFHQI -PLEESSKKYTAFSSTDGHYQFKRLPFGLNISPNSFQRMMTIAMTGLTPECAFVYVDDIVV -VGASENHHLKNLEKVFDRLRHYNLKLNPEKSCFFKKEVTYLGHKITDKGILPDDSKYDSI -KNYPIPQNADDVRRYVAFCNYYRKFIPNFALKAKPLNSLLKKNTKFEWTQECQEAFEYLK -NTLISPQVLQYPDFSKPFILTTDASTMACGAVLAQEHGGKDMPICFASRTFTKGEANKAI -IEKELAAIHWAIMHFKHYLYGKKFTVKTDHRPIVYLFGMKNPSSKLTRMRLDLEEFDFTV -EFVKGKQNVVADALSRIKITSDEIKSINVITKSMSKPVTSDNVLGNTSESDQLKMFHALA -YDEVKDLPKLESSVKKNEDTIELIGKILNKRKSKELLSVRDIHLKTDIGLQEPLLVKDFQ -RRKEKSAIVQFIKNIEKKLVMKSITQLAISETDEIFKEVHPNELKQIANNHLKNIQILIY -TKPQKITNEKTINDILDKVHNTPTGGHIGQYKMYKKIRREYSWNKMKKTIKEFLDKCLTC -KLNKHQTKTAEPFVKTDTPNTPFEAVSIDTVGPFQKTNNNNRYAVTIQCNLTKHVTVIAI -PNKEANTVARAVIEKIMLIYGTNIKKFRTDMGTEYKNEIFKNISEILKIEHKFSTPYHPQ -TIGALERNHRCLNEYLRIFTNEHKDDWDDWINYYSFAYNTTPNLDHGYTPFELVFGRNER -ITPNVKDTYSPLYNYDDYSKEFKYRLKIAHNRTRKHIEQVKFKLLKEQQNINQVNFEIGD -QIALTNENRTKLDPVYKGPYKVKEINGPNMIIENTEGVVQKIHKNRAIKL ->ORF1p_TCN4#2:classI:LTR_retrotransposon -ALLSHQKIFFDTITPIEDQSKPRLRQDTPFPEMTTPPTDKESLQRKIKQIEDERKREREE -HKREMAELQAQMRGLLKREAEKRDLPPHNPATSSLPAKSESPHPPIMYDSLPQPKYSFPV -LSEHADAAAIHQHISKLRSIFTLMAAGYRYEPTAFEARKLAHAAQSLTGIRHLQFLEGDG -LQCRTFDDWAKAFKSAMLPLGWVSETEKKIYSLQPQLLRLDKIPLAIMDFKQWFALLKDS -DSPMSEDVATHWLRNHMTPGLLAELERDFGGENQLRQASLAELLKHMEICATRLLRYQSA -FAPIAPTRTPIAAVSPEASSPIDIAQWLNPRLPLPKGGAGRRARAHLASEQRCFLCRQPG -HKSPDCPKRKEPTAIAAVSTFDHEEAEFEQEEGEMFAEVLATHLAPELSVPPILLECRIG -TNGSPFLALFDTGATVTLVDPSLITTHQLQTYPSEQRRVVSLAGGARGPALQRRVGVEVC -IQNQVFALHGYVMPLHARYKVILGLDFIRSHGLLSGASRLGNLAPDLLGPVVASVTTADG -YXDLRLAILHEYHDIFPDNIGEVANYPPICDANSKVRHHINLTPGAIPFKSASYRSPHMW -RQQLIEEIQKHREAGRLRPSSSPWAAPAFLVKKENGKFRFICDYRGLNKVTTPDSTPVPN -VDDILHRAACGKIFAKIDLSDAFFQTLMHEPDIEKTAITTELGLFEWVVMPQGACNSPAT -QQRRLNEALRGLLGDSCEAYVDDIIVWAADAEDLDKRLRAVLAALRKSGLVCSPTKSEFF -RHKVKFLGHVISANHIGPDPAKLRTIASWPLPQSVKELRSFLGLLQYLRKFIPSLATHTR -TLTALLPPTPAAEKAWEKQQRALRKGQSPKDVLSWVWAWSSEATAAFEILKAKVAEISGL -RPLDYAAALSGECPIYLFTDASNHGTGAWLGQGPDPDHAFPVAYDSRSLSAAERNYPTHE -KELLAIVRALKLWRPLLLDVPIQVQTDHFTLKWFLQQRDLSERQKRWLGXLSRFDLRIDH -ISGVNNFIADALSRLGGVDDEQDGMETAEVSVAVLGLLGQDTSTITKVAQGYAQDQVMGA -WLQEEDRAPGVTLENVENGQGRSTSGVAMGRQAMCARYQX ->Neptune2_Ap_1p:classI:LINE -ANTRPVVDSENIDKYRNTAKKIGKYRNTASKVDEIPKLQKRGIRRNLLKDFDLFARRMRL -KDIFSRERNKQHPFHVKSTWEPPVQQSVALETFLEEVEFELANSPSKRPKDNLSPGERRA -LHNLLGDKTIIVKKADKGTTTVIMSREQKIKEGQILLNDLDNYRPLEKQMADETVEKIKQ -LTTSMLTESHIDEMTVKWLSQTPNPPRIPEFYTLTKIHRPTLVGRPIISGCDGPTERISC -FVDRLIQPIAQQQESYLKDSKDFINFIENTKLPKNTILASKDVTSLYTNIPQEEGITTVC -KAYEDFYKNRLPIPTNFLRRMLCLILKENSFQFNKRHYLQTHGTAMGTKMAVAFANIFMA -KIEKGIISKSIIKPLVWKRYIDDVFCLWDTNEDNIKEFVTRANHYHDNIKFTAEISDSEI -AFLGHKSVQRREIQQRLPPSMCKRIINKQRPFNTRNFYSCHPPGVKKGFIKGEALHLLRT -NSSHSTFNKNMQSFKTRLKNRGYPNEFLEKKGPX ->ERV45_MD_I_2p:classI:LTR_retrotransposon -ASSKHATGKLQTGPGPGPSKQWGNNCGAQSEKPIPSPTIRSLHRATPGSAGLDLCAASGL -ILTPDSPPALIPTGVKGPLPEGTMGLIIGRSSVSLRGIVVTPGVIDSDFTGELQIIVQPP -XKTVTIMKGQRIAQLLILPYVQTXNPILKTSRGQGGFGSSNWAFWVQEIKNSRPMKILNI -SGKNIEGLLDTGADTSCIAGKHWPPTWPTKISPSNLIGIGKITNAAQSSQILTWSDGNLS -GQFCPHVVPSLPVTIWGRDILSQMKVSLVTPEEDAQTPPNDEPLDFPEGPSPR diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/DummyRepbase_nt.fa --- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/DummyRepbase_nt.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,501 +0,0 @@ ->Polinton-1_DY:classII:Polinton -aaaaaaaaaacaagttgggtgtcattggaaaggatttttcaagccctttccaatggtatg -cttttcacgattctgaaattaaaaatacgacttttcataaaaactctcaaaattacaatt -gcacttcttcgcgcacaagcaatcttggaagggggtgtacctgcgcgcacaagcagtcat -aaggatgatcgcaagggtgggggtgagatttctgttcaaggctatgcaccttactgtgtc -ctcaattttctgggaaggtaactggtggttggattattagttgagaaatatttagaaata -tcaaacaaactggttatagggtcgtgtatacgtatatataaaaaatcatataatcataaa -accgttaaaaaaccgtcgttcccgtatattccagctactttcagctaaaagctatggagc -cgttgagaagaaaatctaaacaatctgaagtcatagcgactttcagcttaaggctaccca -cgttttaaatgtatgccttgcaaaatgttacttataaagtaacaatgactagtagtcacc -aataatttcatgatccctgactgcggtcatccgaaataattccctacagagatatgtatt -tcagattatctgtgatctgtctccattttcattatgctaggagaccccataaaatcaaat -atttatgactctttgaacctattatcgagaaagtcaagcggctatttacctgcatccaaa -cccatagctcgccctccttttctgacttccccattgcagtctgtgcagtctgcagtctgt -gaaggctccttaaatcgagaaccaatcaggtggattctaagagtagacaccccctgtaga -tgtcaaactctctaatcctcgtgtataaaaatggatccccttaaattgctcaggatcagt -tcttataatacctcagcactgcattcttataatataatttcggtcgaacttgctcgggat -atcacgtctaaccgttttaattgtttgtgtggactcaaaccatttactgtgaaaaatttt -aaaaacgaattaaaatatataaataaaatatatttataaaaaattcaaaatggaatcatc -agtggcttgtgatttgtgcaaccaatgcatcgaaattagtgagtttgtctctcattacgc -gaagtgctcagaacccagtaaagcctgcgaggctttaatgttaaactctaacattagatg -tgacttatgctctaatctagtaaaaaattgtgaatttgatgatcactaccaacgctgtga -aggaccccgaaatgcatttagcattttaatgggtagaggaaaactggatgaagaagaccg -ccctatgacatcagctaagtctataaaacgattgaggatggaagaggataaggaaatatc -taaccccccaaaaagaaaacaaattgacttaagaagggaactcttatgtcctactcagag -aacgtcaacatattttgaccgatatacataaaaatgcgtcggccagagaagttaagaaca -atgcgaatatcatattgcttacatcagagacgacatttccagtaaaatcatatcgaattg -atagtccattatttaaaagagtatataagtgtatatggtacatatataaagcaaacagat -gaaggagttacagtggaaacaatgaagcactttaaaactgcctacaaatctgtatacata 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-ttttctcgaaaactcagattcaatttttactctcagaatgacaaagttgtattgtgagtt -gtgttcggaaacaaaatcgtttgcttcacgcagcggtttaaaaaaacataccttaaaagt -gcataacttcagctatcaaaaatcaaaatcttcttattattgttgctttttctgtcccaa -tgaacgaaaattctggttgcgatataattacaatgttcatctcttgctgatgcacgatgc -agaattaaagagtatgcgtaaatcaatggaaagttatcaaataaagataaaacaagtttg -agaatttaattttgtaaaatagttttatttaataaatttctgtataatatagacaaatta -aaaacctagatcaaataaaacgtctagtaatgaatggtcatcttcatccttcattattcg -taaataaatgttgggttgacttggctcgatgaactgatcaaaaatatgatcatcatcagg -aaactcatagattataggatctgtgtgcagtatatccatatcgaaatgctgtgcacattg -catttcttgatcgtctccattgcctcgtataagatcatttaaaacgtcctgcgttgccgc -tccaaaaggaaaatcgctccactcaagagacgcaaattcacttccaatttttgtagtggg -ggtagatgacatagaagggtcaaatactcctcttaagaagcgatctatcgaatcctctgt -gtcgatagcctccacataaccttccttcgagccttcaattatttcgacatcagagtcttg -agttaatggaacatttattccatttactgagtcaacaaactctacagtaagatccattgg -tatgcagtgctgaggtattataagaactgatcctgagcaatttaaggggatccattttta -tacacgaggattagagagtttgacatctacagggggtgtctactcttagaatccacctga -ttggttctcgatttaaggagccttcacagactgcagactgcacagactgcaatggggaag -tcagaaaaggagggcgagctatgggtttggatgcaggtaaatagccgcttgactttctcg -ataataggttcaaagagtcataaatatttgattttatggggtctcctagcataatgaaaa -tggagacagatcacagataatctgaaatacatatctctgtagggaattatttcggatgac -cgcagtcagggatcatgaaattattggtgactactagtcattgttactttataagtaaca -ttttgcaaggcatacatttaaaacgtgggtagccttaagctgaaagtcgctatgacttca -gattgtttagattttcttctcaacggctccatagcttttagctgaaagtagctggaatat -acgggaacgacggttttttaacggttttatgattatatgattttttatatatacgtatac -acgaccctataaccagtttgtttgatatttctaaatatttctcaactaataatccaacca -ccagttaccttcccagaaaattgaggacacagtaaggtgcatagccttgaacagaaatct -cacccccacccttgcgatcatc ->INV2j_DB:classII:TIR -aaaaaaaaatacctactaattgtagggccctcaaaatgattccaaacttcagtgattttt -aattaatgacattcgcggtaagaaaaaatggaaacgataacttttcgaacgcaaattgag -aagaacgcaaaatgagccatacgagcaagttagcaaaaatgatctagtcaacctaactga -gcaagtgagccaaaatgagcaagtgagccatatcactaaccatacaacacatagactgga -caactagaacaaacttttttcacgaagcagattatgatttcccgtcctagtcatcttcgt -atttgctcggctctttaatttactgttcgggcagcgactcgcggacaaatttcaattttt -gtgagctgctggcttgtgcctgtgtagacacacatacgtacatacatatatatatatgag -aggcatagagagagtgagtgagtaaagaaagaatagcacacagcggacttcatatgagaa -taaaatcatttcgttcgagcgctggcagcgaactgaatatcaactgctgtattttcgctg -tccgaacagtaaattaaagatccgagcaaatacgaagatgactaggacgagaaatcataa -tctgcttcgtgcaaaaagtttgttctagttgtccagtctatgtgttgtatggttagtgca -tatatacatatgtgtacgtctgtgatgtgataataattatcgtcgagtatcacttgtata -ggcgtttgaatgaatactctgccttgggcatttgcatatttcttgcatgggtctcaaata -ttgggcgtgttcatacctcaacttaagattttgggttcaaattgcaggagaggtcaataa -atttgtattacataatttgacactatggctaaaatgggacatgttattt ->TELSAT_PG:satellite:satellite -aaaaaacgttaaattcaaatgatttaagacgtttggctaagaaattagaataatattcac -gttagtttaataaaaacaaataaaaaacatcgactttcgcatgattttagcattatttta -gtcaatttatcactaaatcgctctaaaaacgttaaattagcatgatttaagacgtttggc -taagaaattagaataatactcgcgttaatttactaaaaaaagctaaataacgtcgaattt -tgcttgattttagcacaaatttagtcaatttaacgctaaattgctttaagaaaattaaat -ttgcttgttttaagacgtttggctaagaaattagaataatactggcgttagtttaataaa -agcagctaaaaaacattgactattgcttgattttagcattattttggtcaatttatcgat -aaatcgcttt ->Neptune2_Ap:classI:LINE -gcgaatactcgccctgtggtggattcagaaaatatcgacaaataccgtaataccgcaaaa -aaaatcggcaaatatcgaaataccgcatcgaaagtcgatgaaataccgaaattgcaaaaa -cgtggtataaggcgcaaccttttaaaagactttgacctttttgcaagacgaatgcgcctc -aaagacattttttcacgggaaagaaacaaacaacaccctttccacgttaaatcaacatgg -gaaccaccggttcaacagtcagtggccttggaaaccttcctagaggaggtggaatttgaa -ctggcgaacagccctagtaagaggccaaaagacaacctatcacccggtgaaaggcgtgca -ttacataacctattaggtgacaaaactatcattgtaaagaaagccgataaaggaaccact -accgtaataatgagcagagaacaaaaaattaaagagggtcaaattctgttgaacgatctg -gataactacaggcccttagaaaaacaaatggctgacgaaacagttgaaaaaataaaacaa -ctaacaacgtctatgctcacagaaagccacattgacgaaatgacagtaaaatggctctcc -caaacaccaaatccacctagaattccagaattctatacactaacaaagattcacagacct -actttagtaggcagacctataatctctgggtgtgacggccccacagagagaatttcatgc -tttgtcgaccgcctcatacagccgatagcacaacaacaagaatcttatctgaaagattca -aaagattttataaacttcattgaaaacacaaaactgccaaagaacactatccttgcctca -aaggacgttactagcttatacacaaacattcctcaagaagaagggattacaactgtatgc -aaagcatacgaagacttctataaaaaccgtttaccaatccctactaatttcttgaggcga -atgctctgcctaatacttaaagagaattcatttcaatttaataaacgacattatctacaa -acccacggaacggctatgggaaccaaaatggccgtggcctttgcaaatattttcatggca -aaaatagaaaaaggcattatcagcaagagcataattaaaccgctagtttggaagagatat -attgacgatgtcttctgtctgtgggacacaaacgaagacaatatcaaggaatttgttaca -agggcaaaccactaccacgataatataaaatttacggctgaaatatcagactcagaaatt -gcattcttgggacacaaaagtgtacaaaggcgagagattcaacagagactcccaccctcg -atgtgcaaacgcattataaacaaacagagacctttcaatacacgaaatttttattcgtgt -catccaccaggcgtaaagaaaggattcataaaaggagaggcgctgcacctgctaagaaca -aattcgtcacactcgacgtttaacaaaaacatgcagagtttcaaaacacgcctaaagaac -agaggatacccaaatgagtttttagagaaaaaaggcccttgaaacaaagacaaaagcaca -aaaaataaaatattgcctt ->REP2-2_TT:classI:LINE -aaaaaactttccaaaaactttaattaagattcgaaaaaaacgaagcttaaaagtaaaaca -gagaagtacaaattaattaaaaaatcagaggaaaaacaagaaaaagtcaaacaaactatt -aaaagatatctaaataacgagcaaaacctactgaaaatgtctcaaagaagataaagcaat -aagaagcaagagagcttagcaaacaagcaaaaacaggaccaaacaatcaccatatctcct -aggaatgcatcagcggacacttaaaacatagaactcaaccgaaacatcttagaaaaccac -acaaccaagcaccaatcaaaaacctaatccagaaatttctgaaaagaaggtagatggcag -gaagagaggtttcagatcggcctacaagaataaggtagaaaaacaatatgaagaacagca -accagtgtcaactccactcccatctgaagagaattgtttaaatctgctgtaggagcccca -aatggtcataaataagtagccaagacccgaagccaaggaggttccaatcagcagcaatac -atcaatctcgtaaagatcaaatagcaatgatagtagcagtctaaaacagaaccacaacca -ctagcatcgacactcaagcatctctagacaagaaagtaaaccagccttgcaagaaccgaa -accggaacttccaacctccatcgatatcggcaataaaatctggaaattgtgtagatttga -cgcaggcatgaatggatgcagaaacagttcctaggattgcaagtttatccatttggactt -gatagaacaggtagctctaagcgacaaaaagaagctagccaatgtagcaatctggaactg -ggactaagctaagctagacagcaagtatcaaccttctgacaaggaccttctcaactcctg -ggtaaactcaaattcaaacgagggaaatcccctcttcatcaaatacaaaacaatgattga -ggagaaggatcctgaattcgtctaactcactaaagatctcacagctgagtaaatggaact -tgaagaactctaaaacgcattccaagtcaagaagcagcgctacatgtcggagctttcttc -aagactaagacagaaaattctattcaaaagcaggcaaaaggcctttgataaattgctttc -agaatcagcccagaagagaacagcagcatctgaagcagcattatctcaagaaagtagcag -catagaatatctcccaccatcccagtagaagtactcaaatcgatatcagatgataccaca -tcacaaggaacaatatctaccctttgaaaattcacagtattcctcactccagtagtagcc -aaaatctccaatacgaacttctcagcagcaacattattactagcaaaacaatactcaaag -ctaccagccacagcactaagcccataactggaatccaacttattagcactagcaatctaa -caattagagatttgaacccagctacaagccgtcctactactgaagaaatacatatgaaaa -ctccttgaaatgaaatattaacatctcatgcatcaataaggaagtgttttacctctacta -gagatgagttttgagtaaactcttatttaaagaatttggaaagttttaaaaagaacgtat -caaacaaaaaccctgtgtcttcttcatatttacatattgtagtccctcaacacgcttaaa -tatagctcattctctatccccaataattagcaccagcaaattacaataggctttgctctt -attataataatatatcacagatataaaatttattattactattttttaggtatattctaa -aaggaattaagaaggccataaaataaagcaaacaactaaagaacatctatataatgatta -gaccaaatcctatttatagatcaagcaagaagtcacaaacacaaacctcacagacaataa -agctagatttaagactcatctagtaaattaactcacacctcaactaacatgattctaacc -taaaaagtagctcctgctcaaatcaatcaatgtcctccaaacgacgtattaacaaagact -cgatgaacaaagtaaatcaataccttggctctaacaaaacttctccccctcaatattcac -cacaacaacatttaaaaagcaaaattattggctcttagctcacaattacaggcttcaata -ctcaaggagtagcaaaagctaacaaaagaaataagcaatactctacgctttacctccaaa -agcttttcgctgaaagcgatgctaccatactcttggagacaaattgcaaagaaaatatga -gagtggatatccataatccggactatattcaaatgaacaatcactgcaaagtacgctaaa -tgggtgcaggaacagcctctatccaccacaaggaaatcaaacttgcaccatacgtcgcaa -gcctcaataatgaaaaagtccttgcccaagtattaattcttgagaatcaatagagagttc -taatcatgggactacatctccaactctaggccaaccctattgaagaataagctctactcg -aagaaatcatctcgtaagtgctgcaagacaacaggctcaaccatatacttatctacgggg -acttcaacctcgatatctcaacctccaactcctcacacgcagatgtaaggaaagccggac -aaatcagaaggctcaaggacttcttgaaatcaaagaacttatacatacacagcacaaata -ggcacactagagaagcattcaagcagaacaaaatcataaaaactcaagtggacttcttca -taagctcgtttgctcctaattgcattctcaagattgaaacaattacacaggacgaaagca -acagaggcagtgatcattatcccatccgaattcaaattgacttgcaagttgcaaaggcta -gagaaatcaaaaaagtcatcaacttaaagtagctagatctcctatcctagaagcttcaaa -aattcattcgcagcagtccatagaatgacacagaaatcagagataaaattaacagcatta -aaggcaaacttgatctcaaataacaaaactcttaacagctaaggcgaaacataaaccaaa -gaataaatgtagttatcagggcaatccacaaacatgaaaaggtgctaatgattgattaaa -actcagcaaaaactagagcagaacatatgaaaacgcgtagaaaaatcatacagagcaaag -acaccataatccagcataaggtcagtgaaatactcaaagaatactatgccgaatcaacga -aaaaagtccaatcactctttaaaacaaacattaagcgatattattagaacatcaagagag -tatgcagcttaggcaacaagtcaaatgttctaaacacctcaagcggaccagttgaaaact -cgaacaaagaactcttatttgatagtaaagatatctaaaacgaaataagcaaatacttca -aagaacactataaatgtgaaacacacgtcaattactatcacaccattgggcaacttagca -gcagcgaaatagacactctcattcagtcttcagaaactctctacagcagcaggaacaagg -ccttctccaacgattatatcaaagataagtgctttttcccaccaaattacagcgaaatct -ctaacgccatgcaaagcattccttgctccaaaactaccaagaagcaaatgatttctgaga -aaatgctctctcaatagtagcatagagacacaaacctcagaacactcctcaaagacatcc -tcactaacccagactccttcagacagaccttcaatgcgaggtaaatctacctcctaaaga -gcgaaagcagataaattatcaactgtagacccatcacgattcagtcctcagctattaaaa -tcctggaaaatgcaatgctccagcatgtccaaaagctcaaagatgaagggaaggttaaag -attttcacatcagccaatgtggcttccaaaagaatcgaagcacaatcatcaacatttgca -gaactattgctctcatccaaagtacagtagccaagaaagaaaacagagttgccatcttcg -tagatgtcaagagtgctttcgatagcgtcaaccacgaacagctgttctaagcactgcgaa -atcaaggctttgacgatattttcatcaaatctgtcgcctttctctactagcactgtcgca -tcaatgggtaccaaatcgggagaggagtcatccagggaggaaaattatcgcctatcctgt -tcaattacctctatgaagaagtcagagtgaaaatccttgaaatctggaagagtaagaagt -tggattgtcaagacctccactttgagctcttcgccgatgacatgctaatcattctcaaaa -agtacaagctcacagcaaccctccttgaagtcctcaagcaagcgtatagagacataaatc -tccaaatcaatgaatccaagacgaaaatcatgctaatcggcaagcaggaaacctacataa -aggactcactcaaactaaggcaagcgaagggcatagatcttgtcatggagttcaagtacc -ttggcttagtcatcaacaatgtgggcaaaatccacaaagatgtagctaagaaagtagaaa -aggcaaagaatctcacacaaatgctcaagaggtggcgctacaacaagctaggtgttatcc -cttgcctccttctctggtagctctttataaaatcgcagctataatacgcttcagcaatca -tgatcacatcagcctaaagcgaaaaatgcatgagaagtcttcgaaacatgtacaactctt -cccttagggacatacttggactcaacaggaacacttcaatctcaactatctgtgcagttc -ttggcatcgaaaacattgagtctatgattctcaactgctacaacaacctaatgagccaaa -ttaacgctgataaacgaatctaaatgtagttcaaagtcttcactaaaaacattaaattag -acatggctagcaggcatcaacagctgctacaagcagctactcataaggacagcagagtca -aacaaagattttggtggtagttcaacaacaagtacgatgatctcattaaactcaacatat -atctctagaaccctgctggacaattctgctggaaatgttaaaggttctacaagggcggca -gttggctctactgtcagcacaaaaaagaagcttggatggaactccaaaagatattaaata -ctacctccaaggcagaaatagtcagtgtgctcaatcttagaaacacggattggcaaaagt -tttctatagacataaaaaaaagtattcaagagtgggctagactcctggtctattaagaca -tttctaaggtcagatgaaagaaaaaatcagctcccaaaatttaaaattctcactcaaaaa -aaaaaaaaacttaaagaatcattcaagaatttgcaggcccttttcaatgtgagccaagta -ttgaacaaacgcccttcatgtttgttcaaatggaagaaatagtgaggagtttctttaata -accatgaagttactgtcttatacaatgtgagtcatgtatagtatatgtacatccataact -attaaaaaaaaactgaaagaatcacccatgaagtttaagccctatacaatgtgagtcatg -tatagaacaagcccttcatgtttgttcaaagtggaggcaatagtgaggagtttctttaat -aaccatgaagttactgtcctatacaatgtgagtcatgtatagtatatgtacatccatact -attaaataaatttaaagaatcacccatgaagtttaagccctatacaatgtgagtcatgta -tagaacaagcccttcatgtttgttcaaagtggaggcaatagtgaggagtttctttaataa -ccatgaagttactgtcctatacaatgtgagtcatgtatagtatatgtacatccataacta -ttaaaaaaaactgaaagaatcacccatgaagtttaagccctatacatgtatagaacaagc -ccttcatgtttgttcaaaagtaagaataaattatttttcatgttaagcgcaaataaataa -ttaaaaataataaacaataaattaaataaattaattgactcggaacaataaatagaaaaa -ggttattaaattaccaaattgttctggaattaatgagaaaaagaggaaactgggtgtata -ttaaatattcaaaaatcagatattgattgaattattaaaaattaataatttggaaaatac -ctaaaaataaataaaaattatctatataaatataataaaaataaattttaagatgtattc -tgagtgcatttatatgtgcgagtttttctattctattctatc ->GYPSY10_I:classI:LTR_retrotransposon -gacgcccaacgcgcttaagtgtcgtaataacgtaaactccgtaataaaaatatctaaaaa -tcaaggtctcgtaaccgggttttctttgaaaacgcttcggactcgcacgctgcacaacaa -cagtgaacatcaacacacaaacaaaaatatctaatgcaaaagtaaaacaacgccgcacaa -gcaacagtgaaaaccgctgcatatcaacagtaaacagctaaaacgacagccagaggataa -acggtcaaccagcaaccgtcttcgctgcattttaatataccaatataacatgtaagtgag -atctttattttcaatttacctcttttaacgtcaaccagatatgtgtgccatttttgaaaa -aaatacaaaactcataataaataacgaataaaacaaataaaaagagtgaatacaattaaa -actttaagtatagtgattttaatttacaaattgattagaaaaaaaaaaatgaagaatgaa -aatttaagtctttcctaagaagtaattctttctcatacaaagatatcattgtccgatgta -tagaaatagtatcgaaaacaacgacagtgacgaggacttaatacagagctataaagacat -aagaaacaataaccaacatgggggttacattgacggtactgagaccgacgaagatataga -attaaaaaacttaatagacggctttacagacagagtaaaaatggttaacgatcaagaatt -tcaaaatcaacctcaggaccttcaacaagaggcaacaccaacacaggaacaggcgaaaac -ctcaggtaccattagtaataaagatgtaattagactcatggaagcggccgtaaatggtgc -actagtgcaccagcatcaacaaaaaatattctcagacaagcttaaagaggttgaaaatag -gcagagaataaacgatggtggacccttagtggtatacgagcaaataccacataatgctgc -tattccttgtaatgaaccactagacttggtaaagtccatacccagttttgacggaaaaca -agatgaatatgtggtatgaagaaccgcagcagttaacgcctacgaaatctaccataataa -tataataatatataatagctagaatgggctgcgcatgtgcagaacaaactccaatcgagg -tgacgcagcagcaaatggttactatgcgtcagggagatcttcctctaatgacttttataa -tgagattgagagaaagctaactcttattattagtaggacttttttgtcttatgagacaaa -tactgccgctatcttaaaaaatagatcacggcaggacgctttgaacgcttttgtgaccgg -gctaaaaaaatcagtccgaaatgtagttctctcagctgcgcccaaagatttgccatcagc -attggccgtggctcaacggacagagtcctgcaatgaacgagcctggttcgttgcaagctt -taataaaaatgtagaagaaaaatcttacaattcagaaaaccgtcgccaaggtaaccgttt -tcataacaccccacaaagtaataaccacaacaactcccagggtgctttccagagaaacta -aaacaataatccaccgtgcactagtaatcaagctaatggctctcaattttctaaaaacca -aagataaaaaggccaagcgcatcagaacaatgaatcaaaaaatcttcgataaggttatac -gcaaaacctaggtcctgaacccatggacgtcgatcccacatcacgttctaaattcaggag -cgaacggagagctcgcagtagtcaacggttgaaccagaacaagagcagtcaaatgaccag -gagtatagggtaaagtcatcctacgaagcagcggaaatcgaggctgataacacgtccgat -tccgaatcatgtaattttttaggggacgtccctgctcccccaaataattcgttcgatagc -ggggcgagaaattaggttactgttggatacagaagcctccaaaaattacataaaacctct -aacagaattaaaacacttcaaaccggtggaaacaccatttgaagtcacatcaatccatgg -tcatacaaaaatagaacaaaagtgtctgatccatctattcaatgttaagtcatacttctt -cttgttaaacaacctgaacgaatatgaaggaattgttagactggatttgccaaaaaaggt -caatgcaaaaattgatctaacaaaaaacatcatcgagcatgatcatggtacggagcaaat -tttttactcaaaatgcaggaatggtaactttattaacatcgatgacgtggacgtgccgaa -agccataaacgaaaatttcaaaaagatgatcaaaaacagatcaaaagcctttgcggaccc -aaacgattccctccccttcaaaatgaatacggtcgccacgatccgcactgacggggaacc -cgtatattcaaaactttacccatatccgatgggtgtagccgatttcgtcaatacggaggt -taagcaacatctagcagacggaataataaggccatcccggtcgccttacaataacccaat -ttgggttgttgataagaagggttttggcggagaaggtcataggaagaaacgtctcgttat -taacttcaggaaactgaatcaaaaaacaattgatgacaagtatcctataccattcatatc -gaccatactgtcgaactttggaaaagctcagtacttcacgactcttgatctgaagtcggg -cttccatcaaattgagccctcggagcgctttcgagaaaagacagctttttagtagtatga -attctgcagacttccctttgctttaaaaaatgcgcctagtattttccaatagacgatgtt -ctgagagaacacatcggcaaaactcgctatgtctacgtcgatgacgtaatatttttctcc -caaacaatggagagtcatgccaacgatataaacacggttctgaaaactttgtgcgatgca -ggtatgagagtgtctgtagaaaaatctatgttctttaaagagaacgtagaatatttggga -ttcatagtgtcccgagggggaattaaaacttcacccgaaagggttaaggctataaaacaa -tttaaacctccatcgacattgttaagtctcaggtcatttctgggattggccagttattat -ataatagatgtttcataaaggggctttttagcatcgcaagacctctgacgaatattctaa -aaggtgacaacggaaaaattggtgctaccactcaaagaaagtcaaactggaacgagcagc -gaaaatcattcgaaaaactaagaaacaccctggagtctgaggatgtcattttggcatacc -cagattccactcagccatttgacttgaaaactgacgcctctggaagcggcctaggggctg -ttcttttacagatttaatcggcagcggcagaaatcaccgcaaattgcagaacgtgttccg -aagcaaaacaccaatcgtcacccagtgcaacaaaccatagcggaaacatcaattcctggt -tacactggggaaagtatccacatagatatattttggactgatcaaaagcattttctaacc -tgtatcgacaagttttcaaaatccgctatagtccaaccaatcgattcaagagcaatcgta -gatatcaaaactccgatactacaactaataaatctgttcaccaaaataaaaacagtttac -tgcgacaatgaaagatctatcaattcacaaaccatacgaaccatcctagaaaataggtat -ggtatacgggtctcaaatgcgcacccgttgcacagcacatctaatggccaagttgagaga -tttcatagcaccctaggggaaatcgcacggtgcatcaagatagatcaaaacataaccgag -acgagcgaccttattctattcggaacaatagaataggacagaactgtccactcggttaca -attaaaaagggtcatgaaatagttcacgctattccaccagattttacgagcaccataaga -gacaaaatcaaagaggcccaagagaaaacacttaggtactcaaatgcacacaaatgcaat -aaacagtaccaaataggcgaaaaaatctggttaaaaaaccaacagacgcctgggtaccaa -attaacgccactctgctcagaagaggtcatcgaggctgatctcggcacgacagtgcttat -tatggagcaacgaacattacatcgtacgagacttacgcggacgagacgaaacacgcgatg -gatttcttcgagaaggagcacatgagacgggtacttgaaacggactaggaacgaatagag -actcttctggacacactaaaggtacgtcacagacatgcccgtagtcttaatttctcttaa 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->blumeria_Grouper_14770_3 -GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA -AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG -CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT -TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/hmmbank_test --- a/commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/datas/hmmbank_test Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19248 +0,0 @@ -HMMER2.0 [2.3.2] -NAME DUF234 -ACC PF03008.6 -DESC Archaea bacterial proteins of unknown function -LENG 100 -ALPH Amino -RF no -CS no -MAP yes -COM hmmbuild -f -F HMM_fs.ann SEED.ann -COM hmmcalibrate --seed 0 HMM_fs.ann -NSEQ 19 -DATE Tue Apr 22 17:16:17 2008 -CKSUM 5535 -GA 15.0000 15.0000; -TC 15.4000 15.4000; -NC 14.9000 14.9000; -XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 -NULT -4 -8455 -NULE 595 -1558 85 338 -294 453 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-11 blumeria_Grouper_4152_12:NoCat 382 407 V-ATPase_G 2 10 0.017 2 0 -12 blumeria_Grouper_4152_12:NoCat 136 228 XhoI 202 172 4.3e-05 9 0 -13 blumeria_Grouper_4152_12:NoCat 479 497 DUF1798 40 35 0.011 1 0 -14 blumeria_Grouper_4152_12:NoCat 294 365 DUF881 237 214 0.0052 4 0 -15 blumeria_Grouper_4152_12:NoCat 84 131 LBP_BPI_CETP 209 191 0.012 1 0 -16 blumeria_Grouper_4152_12:NoCat 230 247 SOCS_box 6 1 0.031 2 0 -2 blumeria_Grouper_28830_3 786 1229 rve 169 1 1.4e-23 77 0 -3 blumeria_Grouper_28830_3 4061 4108 zf-CCHC 18 3 1.7e-09 29 0 -4 blumeria_Grouper_590_20:NoCat 271 324 DUF234 5 22 0.0047 3 0 -5 blumeria_Grouper_590_20:NoCat 331 357 DUF1414 1 9 0.02 2 0 -6 blumeria_Grouper_590_20:NoCat 90 113 CPW_WPC 1 9 0.024 1 0 -7 blumeria_Grouper_590_20:NoCat 119 148 DUF46 182 173 0.00034 6 0 -8 blumeria_Grouper_4152_12:NoCat 337 381 Peptidase_S29 1 15 0.0034 4 0 -9 blumeria_Grouper_4152_12:NoCat 62 79 Toxin_18 50 55 0.014 4 0 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestAcceptanceHmmpfamAndParse2alignInparallel.py --- a/commons/pyRepetUnit/hmmer/tests/TestAcceptanceHmmpfamAndParse2alignInparallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -import os -import sys -import unittest -import pyRepet.seq.fastaDB -from sets import Set -import ConfigParser -from pyRepet.launcher.programLauncher import * -from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher -from pyRepet.sql.RepetJobMySQL import * -from pyRepet.util.file.FileUtils import * -import commons.pyRepetUnit.dbSplit.LauncherDbSplit -import commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align - -CONFIG_FILE = "datas/configTestAcceptanceHmmpfamAndParse2alignLauncherInparallel.cfg" -CURRENT_DIR = os.getcwd() - -class TestAcceptanceHmmpfamLauncherAndParse2alignInparallel(unittest.TestCase): - - def setUp(self): - self._config = ConfigParser.ConfigParser() - self._config.readfp( open(CONFIG_FILE) ) - self._batchFilesList = [] - self._batchFilesBatchesList = [] - self._inputFile = self._config.get("dbSplit_config", "input_file") - self._programLauncherInstance = programLauncher() - self._outputFileNotInparallel = self._config.get("hmmer_config", "output_file") - self._hmmpfamOutput2align = commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align.HmmpfamOutput2align() - os.chdir(CURRENT_DIR) - - def _launchHmmpfamAndParseNotInParallel(self): - self._programLauncherInstance.reset(self._inputFile) - self._programLauncherInstance.setOutputFileName(self._outputFileNotInparallel) - self._programLauncherInstance.launchHmmpfam(evalFilter=self._config.get("profil_search", "Evalue"), inputFormat=self._config.get("profil_search", "InputFormat"), profilDatabank=self._config.get("profil_search", "ProfilDatabank")) - self._hmmpfamOutput2align.setInputFile(self._outputFileNotInparallel) - self._outputFileParsingNotInparallel = self._config.get("hmmpfam2align_config", "output_file") - self._hmmpfamOutput2align.setOutputFile(self._outputFileParsingNotInparallel) - self._hmmpfamOutput2align.run() - - - def _countNblinesInAllResultsFilesInParallel(self, fileUtils): - result_dir = self._config.get("hmmer_config", "result_dir") - dirFiles = fileUtils.listFilesInDir(result_dir) - listPath = [] - for file in dirFiles: - listPath.append(file) - - nbLinesInAlignFilesInparallel = fileUtils.countLinesInFiles(listPath) - return nbLinesInAlignFilesInparallel - - - def _launchHmmpfamAndParseInParallel(self): - user = self._config.get("db_config", "user") - host = self._config.get("db_config", "host") - passwd = self._config.get("db_config", "passwd") - dbName = self._config.get("db_config", "dbname") - jobDb = RepetJob(user, host, passwd, dbName) - params = {"param": "--informat " + self._config.get("profil_search", "InputFormat") + " -E " + self._config.get("profil_search", "Evalue"), "profilDB": self._config.get("profil_search", "ProfilDatabank"), "outputDir": self._config.get("hmmer_config", "result_dir"), "query": self._config.get("hmmer_config", "query_dir"), "job_table": "jobs", "queue": self._config.get("sge_config", "queue"), "groupid": self._config.get("sge_config", "groupid"), "tmpDir": self._config.get("hmmer_config", "tmp_dir"), "scriptToLaunch": self._config.get("parse_config", "scriptToLaunch"), "cDir" : "."} - self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params) - self.hmmpfamAndParse2align.run() - - - def _splitInputFile(self, dbSplit): - dbSplit.setInFileName(self._inputFile) - dbSplit.setIsNewDir(True) - dbSplit.setNbSequences(3) - dbSplit.run() - - def testAcceptanceHmmpfamAndParse2alignHasRunInparallel (self): - - dbSplit = commons.pyRepetUnit.dbSplit.LauncherDbSplit.LauncherDbSplit() - self._splitInputFile(dbSplit) - self._launchHmmpfamAndParseInParallel() - fileUtils = FileUtils() - nbLinesInAlignFilesInparallel = self._countNblinesInAllResultsFilesInParallel(fileUtils) - dbSplit.clean() - self._launchHmmpfamAndParseNotInParallel() - nbLinesInAlignFileNotInparallel = fileUtils.countLinesInAFile(self._outputFileParsingNotInparallel) - self.assertEqual(nbLinesInAlignFilesInparallel,nbLinesInAlignFileNotInparallel) - self._clean() - - def _clean(self): - - dirToClean = self._config.get( "hmmer_config", "tmp_dir" ) - os.system("rm " + dirToClean + "/*") - dirToClean = self._config.get( "hmmer_config", "result_dir" ) - os.system("rm " + dirToClean + "/*") - os.system("rm HmmpfamJob*.e*") - os.system("rm HmmpfamJob*.o*") - os.remove(self._outputFileNotInparallel) - os.remove(self._outputFileParsingNotInparallel) - - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamAndParse2alignLauncherInParallel.py --- a/commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamAndParse2alignLauncherInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -import os -import sys -import unittest -from sets import Set -import ConfigParser -from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher -from pyRepet.sql.RepetJobMySQL import * -from pyRepet.util.file.FileUtils import * - -CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg" -CURRENT_DIR = os.getcwd() - -class TestFunctionalHmmpfamLauncherAndParse2alignInparallel(unittest.TestCase): - - def setUp(self): - self._config = ConfigParser.ConfigParser() - self._config.readfp( open(CONFIG_FILE) ) - os.chdir(CURRENT_DIR) - - def testHmmpfamAndParse2alignHasRunInparallel (self): - user = self._config.get( "db_config","user" ) - host = self._config.get( "db_config","host" ) - passwd = self._config.get( "db_config","passwd" ) - dbName = self._config.get( "db_config","dbname" ) - jobDb = RepetJob(user , host , passwd , dbName) - params = {"param":"--informat FASTA -E 10", - "profilDB": self._config.get("profil_search", "ProfilDatabank"), - "outputDir": self._config.get("hmmer_config", "result_dir"), - "query": self._config.get("hmmer_config", "query_dir"), - "job_table":"jobs", - "queue" : self._config.get("sge_config", "queue"), - "groupid" : self._config.get("sge_config", "groupid"), - "tmpDir": self._config.get("hmmer_config", "tmp_dir"), - "scriptToLaunch": self._config.get("parse_config", "scriptToLaunch"), - "cDir" : "."} - self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params) - self.hmmpfamAndParse2align.run() - fileUtils = FileUtils() - dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir")) - dirSet = Set(dirFiles) - alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut.align", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut.align"]) - self.assertTrue( alignFileSet.issubset(dirSet)) - self._clean() - - def _clean(self): - - dirToClean = self._config.get( "hmmer_config", "tmp_dir" ) - os.system("rm " + dirToClean + "/*") - dirToClean = self._config.get( "hmmer_config", "result_dir" ) - os.system("rm " + dirToClean + "/*") - os.system("rm HmmpfamJob*.e*") - os.system("rm HmmpfamJob*.o*") - - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py --- a/commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -import os -import sys -import unittest -from sets import Set -import ConfigParser -from pyRepet.sql.RepetJobMySQL import * -from pyRepet.util.file.FileUtils import * -import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent - -CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg" -CURRENT_DIR = os.getcwd() - -class TestFunctionalHmmpfamClusterComponent(unittest.TestCase): - - def setUp(self): - os.chdir(CURRENT_DIR) - self._config = ConfigParser.ConfigParser() - self._config.readfp( open(CONFIG_FILE) ) - self._hmmer = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent() - - def testHmmpfamHasRunInparallel (self): - user = self._config.get( "db_config","user" ) - host = self._config.get( "db_config","host" ) - passwd = self._config.get( "db_config","passwd" ) - dbName = self._config.get( "db_config","dbname" ) - jobDb = RepetJob(user , host , passwd , dbName) - self._hmmer.setJobDb(jobDb) - self._hmmer.loadConfig(self._config) - self._hmmer.run() - fileUtils = FileUtils() - dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir")) - dirSet = Set(dirFiles) - alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut"]) - self.assertTrue(alignFileSet.issubset(dirSet)) - self._hmmer.clean() - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestHmmpfamAndParse2alignLauncher.py --- a/commons/pyRepetUnit/hmmer/tests/TestHmmpfamAndParse2alignLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -import unittest -import os -import sys - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher -from pyRepet.sql.RepetJobMySQL import * - -class TestHmmpfamAndParse2alignLauncher(unittest.TestCase): - - def testConstructor(self): - - params = { - "query" : "toto", - "job_table":"fakeTable", - "queue" : "fakeQueue", - "groupid" : "fakeId", - "tmpDir" : "fakeDir", - "cDir" : "." - } - - hmmpfam = HmmpfamAndParse2alignLauncher("toto", params) - - self.assertEquals("toto", hmmpfam.query) - self.assertEquals("fakeTable", hmmpfam.job_table) - self.assertEquals("fakeQueue", hmmpfam.queue) - self.assertEquals("fakeId", hmmpfam.groupid) - self.assertEquals("fakeDir", hmmpfam.tmpdir) - - - def testCmd_start(self): - - fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa" - expectedCmdStart = "hmmpfam --informat FASTA -E 10 /workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms test_input_aa.fa > /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut" - - user = "oinizan" - host = "pisano" - passwd = "oinizan" - dbName = "repet_oinizan" - jobDb = RepetJob(user , host , passwd , dbName) - params = {"param":"--informat FASTA -E 10", - "query" : "toto", - "job_table":"fake", - "queue" : "fake", - "groupid" : "fake", - "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms", - "tmpDir" : "fakeDir", - "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas", - "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py", - "cDir" : "." - } - self.hmmpfam = HmmpfamAndParse2alignLauncher(jobDb, params) - self.assertEquals(expectedCmdStart, self.hmmpfam.cmd_start ( fullInFileName )) - - - def testCmd_finish(self): - - fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa" - user = "oinizan" - host = "pisano" - passwd = "oinizan" - dbName = "repet_oinizan" - jobDb = RepetJob(user , host , passwd , dbName) - params = {"param":"--informat FASTA -E 10", - "query" : "toto", - "job_table":"fake", - "queue" : "fake", - "groupid" : "fake", - "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms", - "tmpDir" : "fakeDir", - "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas", - "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py", - "cDir" : "." - } - self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params) - expectedCmdFinish = "os.system( \"/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py -i /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut -o /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut.align -c\" )\n" - self.assertEquals(expectedCmdFinish, self.hmmpfamAndParse2align.cmd_finish ( fullInFileName )) - - - -if __name__ == "__main__": - unittest.main() - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py --- a/commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -import os -import unittest -import ConfigParser -import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent -from pyRepet.sql.RepetJobMySQL import * -from pyRepet.util.file.FileUtils import * - -class TestHmmpfamClusterComponent(unittest.TestCase): - - def setUp(self): - - self.component = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent() - - def testLoadConfig(self): - config = open("tmpConfig.cfg", "w") - config.write("[profil_search]\n") - config.write("ProfilDatabank: /repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms\n") - config.write("[hmmer_config]\n") - config.write("result_dir: /repet_results\n") - config.write("query_dir: /repet_datas/hmmer_in_parallel\n") - config.write("tmp_dir: /repet_tmp\n") - config.write("[sge_config]\n") - config.write("queue: main.q\n") - config.write("groupid: fake\n") - config.close() - config = ConfigParser.ConfigParser() - config.readfp( open("tmpConfig.cfg") ) - self.component.loadConfig(config) - self.assertEquals( "/repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms", self.component.getProfilDatabank() ) - self.assertEquals( "/repet_results", self.component.getResultDir() ) - self.assertEquals( "/repet_datas/hmmer_in_parallel", self.component.getQueryDir() ) - self.assertEquals( "/repet_tmp", self.component.getTmpDir() ) - self.assertEquals( "main.q", self.component.getSGEQueue() ) - self.assertEquals( "fake", self.component.getSGEGroupId() ) - os.system("rm tmpConfig.cfg") - - def testClean (self): - fileUtils = FileUtils() - if (fileUtils.isRessourceExists("dummyTmpDir")): - os.system("rm -r dummyTmpDir") - - if (fileUtils.isRessourceExists("dummyResultDir")): - os.system("rm -r dummyResultDir") - - os.mkdir("dummyTmpDir") - os.system("touch dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py") - os.system("touch dummyTmpDir/srptJob2_fake_HmmpfamJob1_2009-3-11_12394.py") - os.system("touch dummyTmpDir/srptJob3_fake_HmmpfamJob1_2009-3-11_12394.py") - os.system("touch dummyTmpDir/srptJob4_fake_HmmpfamJob1_2009-3-11_12394.py") - - os.mkdir("dummyResultDir") - os.system("touch dummyResultDir/batch_1.fa.hmmpfamOut") - os.system("touch dummyResultDir/batch_2.fa.hmmpfamOut") - os.system("touch dummyResultDir/batch_3.fa.hmmpfamOut") - os.system("touch dummyResultDir/batch_4.fa.hmmpfamOut") - - self.component.setTmpDir("dummyTmpDir") - self.component.setResultDir("dummyResultDir") - - self.component.clean() - - self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py")) - self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob2_2009-3-11_12394.py")) - self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob3_2009-3-11_12394.py")) - self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob4_2009-3-11_12394.py")) - self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_1.fa.hmmpfamOut")) - self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_2.fa.hmmpfamOut")) - self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_3.fa.hmmpfamOut")) - self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_4.fa.hmmpfamOut")) - - os.system("rm -r dummyTmpDir") - os.system("rm -r dummyResultDir") - - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestHmmpfamLauncher.py --- a/commons/pyRepetUnit/hmmer/tests/TestHmmpfamLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -import unittest -import os -import sys - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -from pyRepet.launcher.Launcher import HmmpfamLauncher -from pyRepet.sql.RepetJobMySQL import * - -class TestHmmpfamLauncher(unittest.TestCase): - - def testConstructor(self): - - params = { - "query" : "toto", - "job_table":"fakeTable", - "queue" : "fakeQueue", - "groupid" : "fakeId", - "tmpDir" : "fakeDir", - "cDir" : "." - } - - hmmpfam = HmmpfamLauncher("toto", params) - - self.assertEquals("toto", hmmpfam.query) - self.assertEquals("fakeTable", hmmpfam.job_table) - self.assertEquals("fakeQueue", hmmpfam.queue) - self.assertEquals("fakeId", hmmpfam.groupid) - self.assertEquals("fakeDir", hmmpfam.tmpdir) - - - def testCmd_start(self): - - fullInFileName = "/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa" - expectedCmdStart = "hmmpfam --informat FASTA -E 10 /workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms test_input_aa.fa > /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut" - user = "oinizan" - host = "pisano" - passwd = "oinizan" - dbName = "repet_oinizan" - jobDb = RepetJob(user , host , passwd , dbName) - params = {"param":"--informat FASTA -E 10", - "query" : "toto", - "job_table":"fake", - "queue" : "fake", - "groupid" : "fake", - "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms", - "tmpDir" : "fakeDir", - "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas", - "cDir" : "."} - self.hmmpfam = HmmpfamLauncher(jobDb, params) - self.assertEquals(expectedCmdStart, self.hmmpfam.cmd_start ( fullInFileName )) - - def testCmd_finish(self): - - fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa" - expectedCmdFinish = "" - - user = "oinizan" - host = "pisano" - passwd = "oinizan" - dbName = "repet_oinizan" - jobDb = RepetJob(user , host , passwd , dbName) - params = {"param":"--informat FASTA -E 10", - "query" : "toto", - "job_table":"fake", - "queue" : "fake", - "groupid" : "fake", - "tmpDir" : "fakeDir", - "cDir" : "." - } - self.hmmpfam = HmmpfamLauncher(jobDb, params) - self.assertEquals(expectedCmdFinish, self.hmmpfam.cmd_finish ( fullInFileName )) - - -if __name__ == "__main__": - unittest.main() - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.py --- a/commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.hmmer.LaunchPreProcessHmmpfamPostProcessNotInParallel import * -from pyRepet.util.file.FileUtils import * -import ConfigParser - -if (not os.environ.has_key("REPET_PATH")): - print "*** Error: no environment variable REPET_PATH" - exit =1 - -if (not os.environ.has_key("PYTHONPATH")): - print "*** Error: no environment variable PYTHONPATH" - exit =1 - -if (exit == 1): - sys.exit(1) - -CONFIG_FILE = "datas/configTestLaunchPreProcessHmmpfamPostProcessNotInParallel.cfg" -CURRENT_DIR = os.getcwd() - -class TestLaunchPreProcessHmmpfamPostProcessNotInParallel(unittest.TestCase): - - def setUp( self ): - os.chdir(CURRENT_DIR) - self._LaunchPreProcessHmmpfamPostProcess = LaunchPreProcessHmmpfamPostProcessNotInParallel() - self._configFile = CONFIG_FILE - config = ConfigParser.ConfigParser() - config.readfp(open(self._configFile)) - self._InputFile = config.get("hmmer_config", "input_file") - self._OutputFile = config.get("hmmer_config", "output_file") - self.fileUtils = FileUtils() - - def testRun(self): - #Normal launch - self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile ) - self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( self._OutputFile ) - self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile ) - self._LaunchPreProcessHmmpfamPostProcess.run() - self.assertTrue(self.fileUtils.isRessourceExists(self._OutputFile)) - self.assertFalse(self.fileUtils.isFileEmpty(self._OutputFile)) - os.system("rm " + self._OutputFile) - #without config file - configFile = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/configdummy.cfg" - self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( configFile ) - self._LaunchPreProcessHmmpfamPostProcess.run() - self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) - #without input file - InputFile = "" - self._LaunchPreProcessHmmpfamPostProcess.setInputFile( InputFile ) - self._LaunchPreProcessHmmpfamPostProcess.run() - self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) - #without output file - self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile ) - self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile ) - OutputFile = "" - self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( OutputFile ) - self._LaunchPreProcessHmmpfamPostProcess.run() - self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) - - - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/TestProgramLauncher.py --- a/commons/pyRepetUnit/hmmer/tests/TestProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -import os -import unittest -from pyRepet.launcher.programLauncher import * -from pyRepet.util.file.FileUtils import * -import ConfigParser - -if (not os.environ.has_key("REPET_PATH")): - print "*** Error: no environment variable REPET_PATH" - exit =1 - -if (not os.environ.has_key("PYTHONPATH")): - print "*** Error: no environment variable PYTHONPATH" - exit =1 - -if (exit == 1): - sys.exit(1) - -CONFIG_FILE = "datas/config.cfg" -CURRENT_DIR = os.getcwd() - -class TestProgramLauncher(unittest.TestCase): - - def setUp(self): - os.chdir(CURRENT_DIR) - self._programLauncherInstance = programLauncher() - self._configFile = CONFIG_FILE - config = ConfigParser.ConfigParser() - config.readfp( open(self._configFile) ) - self._configFile = CONFIG_FILE - config = ConfigParser.ConfigParser() - config.readfp(open(self._configFile)) - self._inputFile = config.get("hmmer_config", "input_file") - self._outputFile = config.get("hmmer_config", "output_file") - self.fileUtils = FileUtils() - - def testLaunchHmmpfam(self): - config = ConfigParser.ConfigParser() - config.readfp( open(self._configFile) ) - self._programLauncherInstance.reset( self._inputFile ) - self._programLauncherInstance.setOutputFileName( self._outputFile ) - self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"), - inputFormat=config.get("profil_search","InputFormat"), - profilDatabank=config.get("profil_search","ProfilDatabank")) - self.assertTrue(self.fileUtils.isRessourceExists(self._outputFile)) - self.assertFalse(self.fileUtils.isFileEmpty(self._outputFile)) - os.system( "rm " + self._outputFile) - self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa2.fa" - self._programLauncherInstance.reset( self._inputFile ) - self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"), - inputFormat=config.get("profil_search","InputFormat"), - profilDatabank=config.get("profil_search","ProfilDatabank")) - self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile)) - #No output file - self._outputFile = "" - self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa.fa" - self._programLauncherInstance.reset( self._inputFile ) - self._programLauncherInstance.setOutputFileName( self._outputFile ) - self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"), - inputFormat=config.get("profil_search","InputFormat"), - profilDatabank=config.get("profil_search","ProfilDatabank")) - self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile)) - os.chdir(CURRENT_DIR) - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/datas/Outputhmmpfam --- a/commons/pyRepetUnit/hmmer/tests/datas/Outputhmmpfam Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ -hmmpfam - search one or more sequences against HMM database -HMMER 2.3.2 (Oct 2003) -Copyright (C) 1992-2003 HHMI/Washington University School of Medicine -Freely distributed under the GNU General Public License (GPL) -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -HMM file: myhmms -Sequence file: 7LES_DROME -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query sequence: 7LES_DROME -Accession: P13368 -Description: SEVENLESS PROTEIN (EC 2.7.1.112). - -Scores for sequence family classification (score includes all domains): -Model Description Score E-value N --------- ----------- ----- ------- --- -pkinase Protein kinase domain 314.6 6e-95 1 -fn3 Fibronectin type III domain 176.6 2e-53 6 -rrm -40.4 0.72 1 - -Parsed for domains: -Model Domain seq-f seq-t hmm-f hmm-t score E-value --------- ------- ----- ----- ----- ----- ----- ------- -fn3 1/6 437 522 .. 1 84 [] 48.3 8.8e-15 -fn3 2/6 825 914 .. 1 84 [] 13.4 2.2e-06 -fn3 3/6 1292 1389 .. 1 84 [] 15.9 1.2e-06 -fn3 4/6 1799 1891 .. 1 84 [] 63.5 2.3e-19 -fn3 5/6 1899 1978 .. 1 84 [] 15.2 1.5e-06 -fn3 6/6 1993 2107 .. 1 84 [] 20.3 4.3e-07 -pkinase 1/1 2209 2483 .. 1 294 [] 314.6 6e-95 -rrm 1/1 2223 2284 .. 1 77 [] -40.4 0.72 - -Alignments of top-scoring domains: -fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 8.8e-15 - CS C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC - *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge - P saP + +++ ++ l ++W p + ngpi+gY++++ +++ g+ - 7LES_DROME 437 PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482 - - CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - + e+ vp sy+++ L++gt+Y++ + +n +G+Gp - 7LES_DROME 483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA 522 - -fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 2.2e-06 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.EC - *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp - ++P l++ ++ + +sW+ p++++ ++ + + +Ye+++ + - 7LES_DROME 825 GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869 - - CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC CCCC - knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-* - + +++ ++++++ g+ + l+ L+P+ Y++rV+A+n +G++G+++ - 7LES_DROME 870 VASQSAFSIRnIRGPI--FGLQRLQPDNLYQLRVRAINVDGepGEWT 914 - -fn3: domain 3 of 6, from 1292 to 1389: score 15.9, E = 1.2e-06 - CS CCCCCEEEE EEC CTTCCEEEEECCC CCCCCCCEEE - *->PsaPtnltv......tdv..tstsltlsWsppt....gngpitgYev - Ps+P++l+v ++ t++++ s++l+W++p+++++ Y + - 7LES_DROME 1292 PSQPRRLRVfverlaTALqeANVSAVLRWDAPEqgqeAPMQALEYHI 1338 - - CS EE.ECCCCCCCCCCEEECCCC CECECCEEEEECCCCEEEEEECCC - tyRqpknggewneltvpgttt.sytltgLkPgteYevrVqAvnggG.... - ++ + g e +e +++ ++ ++ L+P+ +Y+++V A+ ++++ - 7LES_DROME 1339 SC-W--VGSELHEELRLNQSAlEARVEHLQPDQTYHFQVEARVAATgaaa 1385 - - CS CCCC - GpeS<-* - G++S - 7LES_DROME 1386 GAAS 1389 - -fn3: domain 4 of 6, from 1799 to 1891: score 63.5, E = 2.3e-19 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC - *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge. - Ps+P+n++v+ +++ +l +sW pp++ +++ +Y++++ q++ +ge+ - 7LES_DROME 1799 PSPPRNFSVRVLSPRELEVSWLPPEqLRSESVYYTLHW-QQELDGEn 1844 - - CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - .......wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - +++++ + + + t+ ++ ltg kPg+ Y+++VqA+ + +++ S - 7LES_DROME 1845 vqdrrewEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTkSNSS 1891 - -fn3: domain 5 of 6, from 1899 to 1978: score 15.2, E = 1.5e-06 - CS CCCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCCC - *->PsaPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggewn - + l+ +++++sl+l+W p+ + ++++R ++ e - 7LES_DROME 1899 FAELPELQLLELGPYSLSLTWAGT--PDPLGSLQLECR---SSAEQL 1940 - - CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC - eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* - +++v g+ t ++++ L+P t+Y+ r+ ++++G++ - 7LES_DROME 1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL 1978 - -fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 4.3e-07 - CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC - *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge. - Ps+P+ ++ + + + ++++W++++++++pi Y+++ ++++ + - 7LES_DROME 1993 PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038 - - CS CCCCEEECCCC CECECCEEEEE - ...........................wneltvpgttt.sytltgLkPgt - +++++++++++++ ++ + +++ ++++l+ +tt s++++ L + - 7LES_DROME 2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088 - - CS CCCCEEEEEE CCC CCCC - eYevrVqAvn.ggG.GpeS<-* - +rV+A++ ++G Gp+S - 7LES_DROME 2089 LLLFRVRARSlEHGwGPYS 2107 - -pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 6e-95 - *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr - ++ll+ lG+G+fG+Vy++++k+++++ ++VA+K l+k+++++ e - 7LES_DROME 2209 LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253 - - flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng - +l E+q++ +++H+NIvrl g++ + +++ l+mE+me GdL++ylr+ + - 7LES_DROME 2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302 - - ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld - +++++++++ ls e++ ++ ++++G +YL+++++vHRDL+ +N+L++ - 7LES_DROME 2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352 - - en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg - e +++++++ tvKi+DFGLAr++++++++++ + + p+++m+PE l + - 7LES_DROME 2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401 - - rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl - +++++DvW++Gv+++E+lt g ++ - 7LES_DROME 2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426 - - PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP - P+ ++ +e+++++k+ g+rl +p+ c e l++Ll c++ DP - 7LES_DROME 2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468 - - skRpGsatakeilnhpwf<-* - ++Rp +++ + n + - 7LES_DROME 2469 WERP---SFRRCYNTLHA 2483 - -rrm: domain 1 of 1, from 2223 to 2284: score -40.4, E = 0.72 - *->lfVgNL.......ppdvteedLkdlFskfGpi.vsikivkDhkektk - ++ g L+++++++p+ v + L++ s+f + +++++ + - 7LES_DROME 2223 VYEGQLktedseePQRVAIKSLRKGASEFAELlQEAQLMSN------ 2263 - - etgkskGfaFVeFeseedAekAlealnGkelggrklrv<-* - F+ e+ ++ l G+ ++ + - 7LES_DROME 2264 ------------FKH----ENIVR-LVGICFDTESISL 2284 - -// diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/datas/config.cfg --- a/commons/pyRepetUnit/hmmer/tests/datas/config.cfg Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -[profil_search] - -Evalue: 10 -InputFormat: FASTA -ProfilDatabank: ./datas/myhmms - -[hmmer_config] -input_file: ./datas/test_input_aa.fa -output_file: ./datas/hmmpfam_output - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/datas/configTestAcceptanceHmmpfamAndParse2alignLauncherInparallel.cfg --- a/commons/pyRepetUnit/hmmer/tests/datas/configTestAcceptanceHmmpfamAndParse2alignLauncherInparallel.cfg Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -[db_config] -user: oinizan -host: pisano -passwd: oinizan -dbname:repet_oinizan - -[profil_search] -Evalue: 10 -InputFormat: FASTA -ProfilDatabank: /home/oinizan/repet_integration/repet_pipe/pyRepetUnit/hmmer/tests/datas/myhmms - -[hmmer_config] -output_file: ./datas/hmmpfam_output -result_dir: /home/oinizan/repet_integration/repet_results -query_dir: /home/oinizan/repet_integration/repet_pipe/pyRepetUnit/hmmer/tests/batches -tmp_dir: 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-701 -1378 * * - 293 -6409 -5751 -7614 -7636 2593 -7311 -4003 -5084 -7219 -150 -151 -6210 -7172 -849 -6723 -6510 -6299 -1387 4881 2807 470 - - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - - -1 -10749 -11791 -894 -1115 -701 -1378 * * - 294 -4057 -3817 -6415 -5791 3203 -1638 -4541 1679 -5412 765 1434 -5333 -5617 -4930 -5182 -4791 -3987 1226 750 -3959 471 - - * * * * * * * * * * * * * * * * * * * * - - * * * * * * * * 0 -// diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/datas/test_input_aa.fa --- a/commons/pyRepetUnit/hmmer/tests/datas/test_input_aa.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,258 +0,0 @@ ->blumeria_Grouper_28830_3_1 -CGF*LISL*SQ*FHVGVSWLRLINNIMRVELETNKT*IXFYNTGSPTYLNIPPHHVSQST -AHNLHGRVSINWDPQTIPLLKTSCPQLI*ITS*LEILLWYHSN*ILAEFLSVFLSCSSIR -RLPYHRLRTGCPSRTYAGNRFVPLYLLPNLYPPGDIKE*VLLL*QAATAHGPS**GSILC -LRWRTRSTQSPGA*VRISAFSSWR*ARILSLVAFILLT*ERAIGAGCFLPSSSAQRRSSD -SVASRVYTG*EFSSSGG*VPKSKK*GLYPLGETLRLKFITASERAPASVILGESRRTLTS -MAFRTPFACSTLPFPLGLAGVVWTTCSCWLA*NRCASMPPKQPALSLIICFGFPKFWIIY -VSRGTVLAKSALGTKRDSSQPVAYSIALSKTWGPT*V*SIPHRVRGGAGTIGVKLPSNGS -GGFMS*QDLHFRTAS*AARISSGCQNLRPNSRIVLPIDAWPWPS*TFTAVDTRSSYSKIS -SRVAAPDGPGASPTCCDGFFLMRCNLELYIAKLSRTQVAAIFRGSASPKVRNSVMHCRSM -RLSSCGCFISSISSSLSAPLWILEFSLSSVATFPSPSSLERNRTSQGRERKSARTFAFPR -R*IILILKCSIASKKRTILTGCSALV*IVRRDSWSVITVTSPPSTQ*RQCCSDSKIPSNS -LSCAE*RCWVSFSFLEK*AMGCSTERSELLEHRMYGWSMTAPTNFWEASVSNMTGSLQSN -FFTTGDVVSASLILFHD*IDWSVRMTGQFLGPEDWSVSGPASWEKFLMRQRR*PAAFTNP -LISEVVVGIGLSLIAETFSGSAAMPCLEIWKPRKIPSETNSLHFEALRRRP*EANLEKIS -INRECNSAIESAQTATSSRSPATNGRNGSRTSSIKHWKVAGALHRPKGITSHS*TPKGVT -NAVFSEESLCIRICQNPFSRSRNA*KLCPAAR*ISS*AFGRGWACFFVILLSSL*STQIR -QTVWLVWVSVFFWC**QRCSPWSLTFAYELSRSCVAQESPRMACCCAGAISPRRGVLNWV -DNYPVSMRVFLSWESFIPFGGRDLSKS*RGI*L*YCREKL*CGMKGGLGAI*PLEYLK** -RLFGLGEY*L*D*ELVGQLS*EVAVCHLINIVAPVHGIKFVQVSHLLGMCHLGQLLETL* -IPESRMIQGDSSKETVQLKLHP*KLLGQGHQCLTF*K**MYYKKSNI*RKTVKHNMLKSR -SQKKLKIGHRENELFVQKTFCVACHILPVEVVLLGVAQICPFLRPQSRYSGCPIHKFLHF -AFDIEWLQFRHRAAHLLFGLQGLFALDPNLLAQQGK*K*QALMNDRVVLQVLHIFYFSLI -GKFS*IYR*NATRCI*RLVHIPFVLLIPPALFSSTGSLSPSGLSFRN*SIRNACRELGMI -YLFLQCLVTQRRLAHTTLDQLWMRQMLEAFRLLTLRSELVHWTRNV*IHHPQVSTL*YRV -*LEPLDPQAPRW*VWGDYWK*WSRYVEVRVEYAASVYL*SEALP*HPKVG*RKLSGVVAQ -IVIESRRFLQLFVQMLSKATRVHHCRTVF*GYSLQLLPNRGVD**LFFAPR*NLHPFPLQ -F**PKQNMEAYVESSMIACGIIYSLCSHQQSAISIVVGIPRVFFYLPLLKGRADFQLRNA -KRNLGSTALFFALVQ*HSMVR*LTGGIN**SHLCFAHHCLGWALFHRIAPR*RVFS*AET -RLAWLRVARRCLLKSQIAPPGMVFYFQMALLPKVERGLNFSKKFLFPRLHFYLLVWKLSR -SLQTFV*LEEKFVIGSLQTFDRFSWRDLLSLPLQLH*LRKNFRWLWFARQCDPSSSFPTE -HYSGRP**LNRW*NA*KIWRRLKLG*PRIVRFSQQKYIILWLLVDQFMITMISRRCLVAP -TNQQYNASRA*D**NVNFIL*YRTANLFKYSPAPREPINSTQFARSGFHQLGST ->blumeria_Grouper_28830_3_2 -VASS*SVYDHNDFT*VSRGSD*STI*CE*SLRLIKREFXSIIQDRQLI*IFPRTT*ANQQ -RTICTVGFPSIGIHKLSPFSKLAVHSLFKLQVN*KFYYGITQTKSLLNF*VSFYPAPAYG -GYHTIDYELGVLHVHMPGIGLCRCTCCLICIHPVILRSRYYYYDKLLRPMARHSRAPSCV -FAGVLAVPSLRGRKYV*VPFLPGGKPVFYP*LLSYY*RRSVLLVRGVSFRVLRPRGAPLI -LWLHGYILDKNFPPPGAECRRVRSKGYTRWVRLFD*NSLPRVRERQLV*F*ENPGEL*PV -WLSERHLPVRLCHFLLA*LVWYGQPAVVG*LEIVVLLCLRSSQHCH**SALAFQSSG*YT -*AEAQC*RSLHWELSGIPASLLRTQLH*ARLGVLLEYDLYPTVSEEVLVL*ELSFPVTGL -EVS*ADRTCIFGQLREPRGSVRGAKTYALIPA*YCRLTHGLGPHEHLRPSILDPHIPRFL -VGLRRQMDQVHRLLVATGSF**DAIWNCTSQNYLGPKWQLYLGEVPLLRLEIR*CTAGRC -G*VRVGALFPPSQVLFLHHFGF*SFRCRQ*LHSLPLLP*REIEHHRDGRENQREHLLFRD -GR*S*Y*NAL*HLKNGPF*RAARLWSE*FVEIHGQLSPLRRRLLPSDANVVVTVKSQVIP -SLVLNNAAGYRLVFLRSKLWDAALNDRNCWSIACTVGV*LHPRTFGKRQFPI*REVSNQI -FLQLVML*ALV*YFSMIESIGPSE*QGNF*VQRIGP*VALLVGRNF**DNVGNQLHLQIL -LFPR*LLA*ACL*SLKLFRGLLQCHV*KYGNQGRFPLKQIACTLKH*GGDHRKRI*KK*V -STVSAILPLSLPRQLHRPGALRQMDGMALELLP*NTGK*LVRCIGRKA*LAIHRHRKESQ -MLFSLKSLCAYVSAKIRFPGRGMHRSYVLLRAEFHLEHLVGDGRVSS*SC*ALYSQHKYA -KRFG*SGLASFFGVNNRGAAHGPLHLRMN*AGHVLHKKVPGWLVVAPGLYRLGGEF*IGL -TITPFLCGCFCLGRVLSHLAGEIYRKVEGEFNFDIVGKNCNAE*RVGWVPFDHWNI*SSE -DFSVWESINYRIKNWLVN*VEKLQFAI**TS*PQFME*SLSKCHICWECAIWDNS*RHCE -FLSPE*FKVIRAKKLCS*NCILRNCWARATNA*HFRNNRCIIRSQIFRERL*NITC*RAV -VKKN*KLDIGKMSYSCKKHSVWLAISFP*RLSFWGWLKFALSYGHKVGIRAVLFINFFIS -HSI*NGFNFVIELLIFYLAFRAYLLLIQIFWLNKESRSDRL**TIVWCYRFYIFFIFH*L -VSFPEFIAETRRGVFSVWCIFPLFF*FHRRCFHQPAVFRPVACLSAIEAFVTLVVNWV*F -ICFCNVL*RKDVLPIRPWISYGCVKCWKLFAF*R*DRNWCIGLGMFEYIILKCPPCNTAC -DLNHSIRKLRAGEFGEIIGNDGPGTWK*ESNMLPQYISSLRPYHDIRR*AKESFPESSRK -L*LSLVVSCSYSCKCCQRRPEYIIVEQYFKDTVYSSCPIEVLTDDCSSRRDEIFIHFHCN -SDSPSRIWKHMLNHQ*LHVV*YIHYVLISKVQFPLWWEYRACFSICLF*RAVRIFSFGTR -KEIWEVPLYFSLLFSNIQWFVN*LAV*INSPIFVLLIIA*VGRCFIELRRGKGSFLRLKH -DWPGCGSRGAAC*KVK*LLPVWFFIFRWPCFRKLKGD*IFRRSFCFHVFISTY*FGN*VV -HCRHLFD*KRNL*LGLFKPLIDSLGEIFCHCLCSFISFGKIFVGFGLPGNVILHQAFQLS -IIQADHDD*IGGEMRKKFGDVLNWDDLEL*GSLNKNI*FCGF*LISL*SQ*FHVGVSWLR -QINNIMRVELETNKT*ISFYNTGPPTYLNIPPHHVSQSTAHNLHGRVSINWDP ->blumeria_Grouper_28830_3_3 -WLLVDQFMITMISRRCLVAPTNQQYNASRA*D**NVNXIL*YRIANLFKYSPAPREPINS -AQFARSGFHQLGSTNYPPSQN*LSTAYLNYKLIRNFIMVSLKLNPC*IFECLSILLQHTA -ATIP*TTNWVSFTYICRE*VCAVVLVA*FVSTR*Y*GVGIIIMTSCYGPWPVIVGLHLVS -SLAYSQYPVSGGVSTYKCLFFLEVSPYFIPSCFHTTNVGACYWCGVFPSEFFGPEALL*F -CGFTGIYWIRIFLLRGLSAEE*EVRAIPAG*DSSIEIHYRE*ESAS*CNFRRIQENSDQY -GFQNAICLFDFAISSWPSWCGMDNLQLLASLKSLCFYASEAASIVTDNLLWLSKVLDNIR -EQRHSVSEVCIGN*AGFQPACCVLNCIEQDLGSYLSMIYTPPCQRRCWYYRS*ASQ*RVW -RFHELTGLAFSDSFVSREDQFGVPKPTP*FPHSIAD*RMALALMNIYGRRY*ILIFQDF* -*GCGARWTRCIAYLLRRVLFDEMQFGIVHRKIISDPSGSYI*GKCLS*G*KFGDALQVDA -VEFVWVLYFLHLKFSFCTTLDSRVFVVVSSYIPFPFFPREK*NITGTGEKISENICFSAT -VDNPDIKMLYSI*KTDHSDGLLGFGLNSS*RFMVSYHRYVAAFYPVTPML**Q*NPK*FP -LLC*ITLLGIV*FS*EVSYGMQH*TIGIVGASHVRLEYDCTHELLGSVSFQYDGKSPIKF -FYNW*CCKR*FDTFP*LNRLVRQNDRAIFRSRGLVREWPC*LGEIFNETT*VTSCIYKSS -YFRGSCWHRPVSDR*NFFGVCCNAMFRNMETKEDSL*NK*PAL*SIEEETIGSESRKNKY -QP*VQFCH*VCPDSYIVQEPCDKWTEWL*NFFHKTLESSWCVA*AERHN*PFIDTERSHK -CCFL*RVFVHTYLPKSVFQVEECIEVMSCCALNFILSIW*GMGVFLRNLVKLSIVNTNTP -NGLVSLG*RLFLVLITEVQPMVPYICV*IEPVMCCTRKSPDGLLLRRGYIASEGSFKLG* -QLPRFYAGVSVLGEFYPIWRERFIEKLKGNLTLIL*GKTVMRNEGWAGCHLTIGIFEVVK -TFRFGRVLIIGLRIGWSIKLRSCSLPFDKHRSPSSWNKVCPSVTSAGNVPSGTTPRDTVN -S*VQNDSR*FEQRNCAVKIASLEIVGPGPPMPDILEIIDVL*EVKYLEKDCET*HAEEP* -SKKTENWT*GK*VIRAKNILCGLPYPSRRGCPFGGGSNLPFPTATK*VFGLSYS*ISSFR -IRYRMASISSSSCSSSIWPSGLICS*SKSSGSTRKVEVTGFDERSCGVTGFTYFLFFIDW -*VFLNLSLKRDEVYLAFGAYSLCSFDSTGAVFINRQSFAQWPVFPQLKHS*RLS*IGYDL -SVSAMSCDAKTSCPYDLGSAMDASNAGSFSPFDAEIGIGALDSECLNTSSSSVHLVIPRV -T*TTRSASSALVSLGRLLEMMVQVRGSESRICCLSISLV*GPTMTSEGRLKKAFRSRRAN -CN*VSSFLAVIRANVVKGDPSTSLSNSILRIQSTAPAQSRC*LMIVLRAEMKSSSISIAI -LIAQAEYGSIC*IINDCMWYNIFIMFSSAKCNFHCGGNTARVFLFASFKGPCGFSASERE -KKSGKYRFIFRSCSVTFNGSLTDWRYKLIVPSLFCSSLLRLGVVS*NCAEVKGLFLG*NT -IGLVAGREALPAEKSNSSSRYGFLFSDGPASES*KGTEFFEEVFVSTSSFLLTSLEIKSF -IADICLTRREICDWVSSNL*SILLERSFVTAFAASLASEKFSLALVCPAM*SFIKLSN*A -LFRPTMMIE*VVKCVKNLETS*IGMT*NCEVLSTKIYNFVASS*SVYDHNDFT*VSRGSD -KSTI*CE*SLRLIKREFHSIIQDRQLI*IFPRTT*ANQQHTICTVGFPSIGIH ->blumeria_Grouper_28830_3_4 -CGSQLMETRPCKLCAVDWLTWCGGIFK*VGGPVL*NEIHVLLVSSSTRIILLICRSHETP -T*NHCDHKLIN*KPQNYIFLLREPHNSRSSQFKTSPNFLRISPPIQSSWSA*IMLSWKA* -*RITLPGKPKPTKIFPKLMKLQRQ*QKISPRESIKGLKRPNHKFLF*SNKCLQ*TT*FPN -**VEMKTWKQKLLRKIQSPFNFRKQGHLKIKNHTGRSYLTFQQAAPRDPQPGQSCFSLRK -DPLPRRNSMKQRPT*AMMSKTKMGLLIYTASQLTNH*MLLNKSEK*SGTSQISFRVPKLK -IRTAL*KRQIEKHARYSHHNGNCTLLMRT**IYYTTCNH**FNICFHILLGLSELQWKWM -KISSRREEQSSVNTSIGQEL*TVSLKYCSTMMYSGRL*QHLHE*LQETTRLNYNLRDDSG -KLSLAYLRMSW*GLRLEIY*GSIFDSHFHVPGPSFPIISPNSPARSLRIEWFKSHAVLQG -GHLRMMYSNIPSPMHQFRSQRQKAKSFQHLTHP*LIQGRMGKTSLRHKTLQKQINHTQFT -TSVTNASIAERQATGRKTAG**KQRRWNQKNKGNMHQTLNTPRRVSAINSGKLTNQ*KIK -NM*NL*HHTIVHQSLSLLLSLLSQKIWIKSK*ALKAK*KMSSSMTKLKPFYIECEMKKFM -NRTARIPTLWP*ERANLSHPQKDNLYGKDMASHTECFLHE*LIFPMSNFQFFLTTALQHV -MFHSLSLNI*LLIIHLLFLKCQALVALAQQFLRMQF*LHSFFARITLNHSGLRNSQCL*E -LSQMAHSQQM*HLDKLYSMNWGYDVYQMANCNFST*LTNQFLIL*LILSQTEKSSLLQIF -QWSNGTQPTLHSALQFFPTISKLNSPSTFR*ISPAKWDKTLPRQKHPHRNGVIVNPI*NS -PPRRYSPGATTSHPGTFLCNT*PAQFIRKCKGPWAAPLLLTPKKDANPD*PNRLAYLC*L -*RA*QDYEETRPSPTKCSR*NSARSRT*LLCIPRPGKRILADTYAQRLFRENSICDSFRC -L*MASYAFRPMQRTSYFPVFYGRSSRAIPSICRRAPGRCSCLGRLNGRIALTVDTYFF*I -RFLWSPPQCFKVQAICFRGNLPWFPYF*TWHCSRPRKSFSDQRQAYANNYLGNKRICKCS -WLPTLSH*KFLPTSRATHGPILWT*KLPCHSDGPIDSIMEKYQTSAYNITSCKKI*LETS -RHIGN*RFPKVRGCSHTPTVHAMLQQFRSFSAASHSLLLKKTKRYPAALFSTREGITWDF -TVTTTLASLGRRRRRNGDN*P*ISTNYSDQSRAARQNGPFFRCYRAF*YQDYLPSRKSKC -SR*FSLPSL*CSISL*GRRGRECSY*RQRKL*NPKWCRKRT*DGGNKAPTRTQPHRPAVH -HRISNLRRGTSPKYSCHLGPR*FCDVQFQIASHQKEPVATSRRCTWSIWRRNPTRNLGI* -GSSIDGRKCS*GPRPCVNRQYYAGIRA*VLAPRTDPRGSRSCPKMQVLSAHETSRPVTGK -LNSYSTSTSSDTVGYRSYSSRTPSLAQCN*VRNRLAGIPLSSQCRLR*HCASAHVYYPEL -WKAKADYQ*QCWLLRRHRSTTISS*PTTAGCPYHTS*AKRKWQSRTGKWRSESHTGQSSP -GFS*NYTSWRSLTRGNEFQSKSLTQRV*PLLLTLRHSAPGGGKFLSSIYP*SHRIRGAPL -GRRTRKETPRTNSTLLR**YESN*G*NTGLPPGRKGTYTYLRPRRLGTASTPAKTQDGAL -L*RAMGRSSLS***YLLLNITGWIQIRQQVQRHKPIPGICT*RTPSS*SMVW*PPYAGAG -*KDTQKFSKDLV*VIP**NF*LTCNLNKLWTASFEKGDSLWIPIDGNPTVQIVRC*LAHV -VRGNI*ISWRSCIIEXNSRFISLKLYSHYIVD*SEPRDTYVKSL*S*TDQLEAT ->blumeria_Grouper_28830_3_5 -VDPN*WKPDRANCVLLIGSRGAGEYLNKLAVLYYRMKFTFY*SQALLALYC*FVGATRHL -REIIVIIN*STRSHKIIYFC*ENLTILGHPNLRRLQIFYAFHHLFNHHGRPE*CSVGKLD -EGSHCRANQSQRKFFRS**SCKGSDKRSLQENRSKV*RDPITNFSSSQTNVCNERLNFQT -SK*K*RRGNKNFFEKFSPLSTFGSRAI*K*KTIPGGAI*LFSRQRLATRNQANRVSA*EK -TLYLGAIL*NNAQPKQ**AKQRWDY*FIPPVS*RTIECY*TRAKNKAVLPRFLFAFRS*K -SARPFKRGK*KNTRGIPTTMEIALC**EHNEYIIPHAIIDDSTYASIFCLGYQNCNGNG* -RFHLGAKNNHQSTPRLGRSCRLYP*NTVRQ*CTRVAFDNICTNNCKKRRDSITICATTPE -SFL*PTFGCHGRASD*RYTEAAYSTLTSTYLDHHFQ*SPQTHQRGACGSSGSSHTRYYKV -DT*G*CIQTFRVQCTNSDLSVKRRKASSI*RIHS*SKVVWARRLCVTRHCRNR*IIPNSR -QALRMLQLRKDRPLGERLPVDENSAGGIKRTKGICTKR*IHLVAFQR*IQENLPINEK*K -ICKTCNTTRSFIKACHFYFPC*ARRFGSRANKP*RPNRR*AAR*RN*SHSISNAK*RNL* -IGQPEYLLCGRRKGQI*ATPKRTTSTGRIWQATQNVFCTNNSFSLCPIFSFF*LRLFSML -CFTVFL*IFDFL*YIYYF*NVRHWWPWPNNF*GCNFNCTVSLLESP*IILDSGIHSVSRS -CPRWHIPSRCDTWTNFIP*TGATMFIKWQTATSQLN*PTNS*SYN*YSPKPKSLHYFKYS -NGQMAPSPPFIPHYSFSLQYQS*IPLQLFDKSLPPNGIKLSQDRNTRIETG*LSTQFKTP -LRGDIAPAQQQAIRGLSCATHDRLNSYANVRDHGLHLCY*HQKKTLTQTNQTVWRICVDY -RELNKITKKHAHPLPNAQDEIQRAAGHNFYAFLDLENGFWQIRMHKDSSEKTAFVTPFGV -YEWLVMPFGLCNAPATFQCFMEEVLEPFRPFVAGLLDDVAVWADSMAELHSRLILIFSRF -ASYGLLLNASKCRLFVSEGIFLGFHISKHGIAADPEKVSAIRDRPMPTTTSEIRGFVNAA -GYLRCLIKNFSQLAGPLTDQSSGPKNCPVILTDQSIQSWKSIKLALTTSPVVKKFDWRLP -VILETDASQKFVGAVILQPYMRCSNNSDRSVLHPIAYFSRKLNDTQQRYSAQERELLGIL -LSLQHWRHWVEGGDVTVITDHESLRTIQTKAEQPVRMVRFLDAIEHFNIRIIYRRGKANV -LADFLSRPCDVLFLSREEGEGNVATDDNENSRIQSGAERELEMEEIKHPHELNRIDLQCI -TEFLTLGEALPLNIAATWVRDNFAMYNSKLHLIKKNPSQQVGDAPGPSGAATLLEILEYE -DLVSTAVNVHEGQGHASIGNTMRELGRRFWHPELILAAHEAVRKCKSCQLMKPPDPLLGS -LTPIVPAPPLTRWGIDHTQVGPQVLLNAIEYATGWLESRLVPNADFANTVPLLTYIIQNF -GKPKQIISDNAGCFGGIEAQRFQASQQLQVVHTTPARPRGNGKVEQANGVLKAILVRVLL -DSPKITLAGALSLAVMNFNRRVSPSGYSPYFLLFGTQPPEEENSYPVYTREATESEERLW -AEELGRKHPAPIARSYVSSMKATRDKIRAYLQEEKALIRTYAPGDWVLRVRQRRHKMEPY -YDGPWAVAACHNNNTYSLISPGGYKLGNKYNGTNLFPAYVREGHPVRSLWYGSRRMLEQD -RKTLKNSARI*FE*YHNKISN*LVI*ISCGQLVLRRGIVCGSQLMETRPCKLCAVDWLTW -CGGIFK*VGDPVL*NXIHVLLVSSSTRIILLISRSHETPT*NHCDHKLIN*KP ->blumeria_Grouper_28830_3_6 -WIPIDGNPTVQIVCC*LAHVVRGNI*ISWRSCIIE*NSRFISLKLYSHYIVDLSEPRDTY -VKSL*S*TDQLEATKLYIFVERTSQF*VIPI*DVSKFFTHFTTYSIIMVGLNNAQLESLM -KDHIAGQTKANENFSEANEAAKAVTKDLSKRIDQRFEETQSQISLLVKQMSAMNDLISKL -VSRNEDVETKTSSKNSVPFQLSEAGPSENKKPYREELFDFSAGSASRPATRPIVFQPKKR -PFTSAQFYETTPNLSNDEQNKDGTINLYRQSVNEPLNVTEQERKIKRYFPDFFSRSEAEN -PHGPLKEANRKTRAVFPPQWKLHFADENIMNILYHMQSLMIQHMLPYSAWAIRIAMEMDE -DFISARRTIISQHLDWAGAVDCILKILFDNDVLGSPLTTFARITARNDETQLQFARRLRK -AFFSLPSDVMVGPQTRDILRQHIRLSLPRTWTIISNNLPKLTSAELADRVVQVTRGITRW -TLEDDVFKHSESNAPIPISASKGEKLPAFDASIADPRSYGQDVFASQDIAETDKSYPIHD -KRYECFNCGKTGHWAKDCRLMKTAPVESKEQREYAPNAKYTSSRFSDKFRKTYQSMKNKK -YVKPVTPHDRSSKPVTSTFLVEPEDLDQEQISPEGQIEDEQLDDEIEAILYRMRNEEIYE -*DSPNTYFVAVGKGKFEPPPKGQPLREGYGKPHRMFFARITHFPYVQFSVFFDYGSSACY -VSQSFSKYLTSYNTSIISKMSGIGGPGPTISKDAILTAQFLCSNHLESFWTQEFTVSLGV -VPDGTFPADVTLGQTLFHELGLRCLSNGKLQLLNLIDQPILNPIINTLPNRKVFTTSNIP -MVKWHPAHPSFRITVFPYNIKVKFPFNFSINLSRQMG*NSPKTETPA*KRGNCQPNLKLP -SEAI*PRRNNKPSGDFLVQHMTGSIHTQM*GTMGCTSVINTKKRR*PRLTKPFGVFVLTI -ESLTRLRRNTPIPYQMLKMKFSAQQDITSMHSSTWKTDFGRYVCTKTLQRKQHL*LLSVS -MNG*LCLSAYATHQLLSSVLWKKF*SHSVHLSQGSWTM*LSGQTQWQNCTHG*YLFFLDS -LPMVSSSMLQSAGYLFQRESSLVSIFLNMALQQTPKKFQRSETGLCQQLPRK*EDL*MQL -VTYVVSLKISPN*QGHSRTNPLDLKIALSF*RTNRFNHGKVSN*RLQHHQL*KNLIGDFP -SYWKLTLPKSSWVQSYSNRTCDAPTIPIVQCCIP*LTSQEN*TIPSSVIQHKRGNYLGFY -CHYNIGVTG*KAAT*R**LTMNLYELFRPKPSSPSEWSVF*ML*SILISGLSTVAEKQMF -SLIFSPVPVMFYFSLGKKGKGM*LLTTTKTLESKVVQKENLRWRK*STHTNSTASTCSAS -PNF*P*ERHFP*I*LPLGSEIILRCTIPNCISSKRTRRNK*AMHLVHLAPQPY*KSWNMR -I*YRRP*MFMRAKAMRQSAILCGN*GVGFGTPN*SSRLTKLSENASPVSS*NLQTRYWEA -*LL*YQHLL*HGGV*IILK*DPKSCSMQLSTQQAGWNPA*FPMQTSLTLCLCSRILSRTL -ESQSRLSVTMLAASEA*KHNDFKLANNCRLSIPHQLGQEEMAKSNRQMAF*KPYWSEFSW -ILLKLH*LALSHSR**ISIEESHPAGIALTSYSSALSPRRRKILIQYIPVKPQNQRSASG -PKNSEGNTPHQ*HAPTLVV*KQLGIKYGLTSRKKRHLYVLTPPETGYCEYASEDTRWSPT -MTGHGP*QLVIIIIPTP*YHRVDTN*ATSTTAQTYSRHMYVKDTQFVVYGMVAAVCWSRI -ERHSKIQQGFSLSDTIIKFLINL*FK*AVDS*F*EGG*FVDPN*WKPDRANCALLIGSRG -AGEYLNKLAILYYRXKFTFY*SQALLALYC*LVGATRHLREIIVIIN*STRSH ->blumeria_Grouper_14770_3_1 -G*TDTVSLV*SCGRKN*LETSVLRCMVLSKTELIRVRLRVRISYQLRFLTSIYQSPWIIS -YDPCRCKSIYVQIYEPEI*S*IHVCR**IRETFNLHLIHNHLMEC*CEINANVR*TFREE -CADDNDIGR*I**PN*PDLQMSYPWHSRIYNISTPLLTLHRG*IHK*KTVSIFIVISHLM -LVW*TRQWLY*YQKLKCINRCALVSVSLLYIYLRDF*LKEHVIV*ASRLQFFPL*NDKRC -RYV*KHHLVLDCEQVQWQPYCQSRLLLGCCLQGIGEVRAKSRYIVWMRALLPCTQLRRLN ->blumeria_Grouper_14770_3_2 -VRPIQ*VSYEVVEGRIDWKQVY*DVWF*VKLS**E*DCVCAYLIN*GF*PVFINLHGS*V -MIPVDVNLYTYRYMSQKYKAKYMCVGNRSEKPLTCI*YIII*WNASVK*MPMYVKLSVRN -VLMTMI*EGEFDNLISRTYK*VILGIPGYTIFQHPSSLCIEDRYISEKLLVYLLSFLI*C -WYGRHASGCTSTKN*SA*IGVPWSR*AFCTYICEIFS*RNM**CKRAVFNSFPCKMISDV -DMFRSII*FWIVSKFNGSRIVSRDCCWDAVSKESVKSAQNPDILFGCERYCHVLSFAG*M ->blumeria_Grouper_14770_3_3 -LDRYSKSRMKLWKEELTGNKCIEMYGSE*N*ADKSEIACAHILSTEVFDQYLSISMDHKL -*SL*M*IYIRTDI*ARNIKLNTCVSVIDPRNL*PAFDT*SSDGMLV*NKCQCTLNFP*GM -C**Q*YRKVNLIT*LAGLTNELSLAFQDIQYFNTPPHFASRIDT*VKNC*YIYCHFSSNA -GMVDTPVVVLVPKTEVHKSVCLGLGKPFVHISARFLAEGTCNSVSEPSSILSLVK**AMS -ICLEASFSFGL*ASSMAAVLSVEIAAGMLSPRNR*SPRKIQIYCLDASAIAMYSASQVE ->blumeria_Grouper_14770_3_4 -HSTCEAEYMAIALASKQYIWILRGLHRFLGDSIPAAISTDNTAAIELAHNPKLNDASKHI -DIAYHFTRERIEDGSLTLLHVPSAKNLADICTKGLPRPRHTDLCTSVFGTSTTTGVSTIP -ALDEK*Q*IY*QFFTYVSILDAK*GGVLKYCISWNAKDNSFVSPAN*VIKFTFLYHCHQH -IPHGKFNVHWHLFHTSIPSDDYVSNAG*RFLGSITDTHVFSFIFLAHISVRI*IYIYRDH -NL*SMEIDKYWSKTSVDKICAHAISLLSAQFYSEPYISIHLFPVNSSFHNFIRDLLYRSN ->blumeria_Grouper_14770_3_5 -IQPAKLSTWQ*RSHPNNISGFCADFTDSLETASQQQSRLTIRLPLNLLTIQN*MMLLNIS -TSLIILQGKELKTARLHYYMFLQLKISQIYVQKAYRDQGTPIYALQFLVLVQPLACLPYQ -H*MRNDNKYTNSFSLMYLSSMQSEEGC*NIVYPGMPRITHL*VRLIRLSNSPSYIIVIST -FLTESLTYIGIYFTLAFHQMIMYQMQVKGFSDLLPTHMYLALYFWLIYLYVYRFTSTGII -TYDPWRLINTGQKPQLIRYAHTQSHSYQLSFTQNHTSQYTCFQSILPSTTSYETYCIGLT ->blumeria_Grouper_14770_3_6 -FNLRS*VHGNSARIQTIYLDFARTSPIPWRQHPSSNLD*QYGCH*TCSQSKTK*CF*TYR -HRLSFYKGKN*RRLAYTITCSFS*KSRRYMYKRLTETKAHRFMHFSFWY*YNHWRVYHTS -IR*EMTINILTVFHLCIYPRCKVRRGVEILYILECQG*LICKSG*LGYQIHLPISLSSAH -SSRKV*RTLAFISH*HSIR*LCIKCRLKVSRIYYRHTCI*LYISGSYICTYIDLHLQGS* -LMIHGD**ILVKNLS**DMRTRNLTLISSVLLRTIHLNTLVSSQFFLPQLHTRLTVSV* ->blumeria_Grouper_1717_12_1 -ISSILP*RASKS*SNSFRSLSSVTGSNSLQNPMMKRSACAERVWNILPCSARNLVATI*G -DGVCWCGELR*LAS*IGSTNCCVGCCDGGCGPLRTISTS*RVEH*VGRGGQEPASAEDWG -GMSE*GLWQCEIVDGIRRA*R ->blumeria_Grouper_1717_12_2 -FPVSCPEGPVSPDRIVFEVSRQ*LVPTACRTQ**SALLVRSASGISCPVRRGIWSRRFEA -TEFVGAVSFDDSPRRLALQIVVWVVVMAVVAR*GPFRRLDASNIELGGGAKSQPLRRTGA -A*VSEVCGSVRS*MVYGALEG ->blumeria_Grouper_1717_12_3 -FQYLALKGQ*VLIE*FSKSLVSDWFQQLAEPNDEALCLCGARLEYPALFGEEFGRDDLRR -RSLLVR*ASMTRLVDWLYKLLCGLL*WRLWPVKDHFDVLTRRTLSWEGGPRASLCGGLGR -HE*VRFVAV*DRRWYTARLK ->blumeria_Grouper_1717_12_4 -PFKRAVYHLRSHTATNLTHSCRPSPPQRLALGPPSQLNVRRVKTSKWSLTGHNRHHNNPH -NNL*SQSTRRVIEAHRTNKLRRLKSSRPNSSPNRAGYSRRAPHKQSASSLGSASCWNQSL -TRDFENYSIRTYWPFRARYWK ->blumeria_Grouper_1717_12_5 -PSSAPYTIYDLTLPQTSLTHAAPVLRRGWLLAPPPNSMFDASRRRNGP*RATTAITTTHT -TICRANLRGESSKLTAPTNSVASNRRDQIPRRTGQDIPDALRTSRALHHWVLQAVGTSH* -RETSKTIRSGLTGPSGQDTGN ->blumeria_Grouper_1717_12_6 -LQARRIPSTISHCHKPHSLMPPQSSAEAGSWPPLPTQCSTRQDVEMVLNGPQPPSQQPTQ -QFVEPIYEASHRSSPHQQTPSPQIVATKFLAEQGRIFQTRSAQAERFIIGFCKLLEPVTD -ERLRKLFDQDLLALQGKILE diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/hmmer/tests/datas/test_input_nt.fa --- a/commons/pyRepetUnit/hmmer/tests/datas/test_input_nt.fa Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,124 +0,0 @@ ->blumeria_Grouper_28830_3 -TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC -CGACTAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTNATTC -TATAATACAGGATCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACA -GCGCACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACAAACTATCCCCCTTCTC -AAAACTAGCTGTCCACAGCTTATTTAAATTACAAGTTAATTAGAAATTTTATTATGGTAT -CACTCAAACTAAATCCTTGCTGAATTTTTGAGTGTCTTTCTATCCTGCTCCAGCATACGG -CGGCTACCATACCATAGACTACGAACTGGGTGTCCTTCACGTACATATGCCGGGAATAGG -TTTGTGCCGTTGTACTTGTTGCCTAATTTGTATCCACCCGGTGATATTAAGGAGTAGGTA -TTATTATTATGACAAGCTGCTACGGCCCATGGCCCGTCATAGTAGGGCTCCATCTTGTGT -CTTCGCTGGCGTACTCGCAGTACCCAGTCTCCGGGGGCGTAAGTACGTATAAGTGCCTTT -TCTTCCTGGAGGTAAGCCCGTATTTTATCCCTAGTTGCTTTCATACTACTAACGTAGGAG -CGTGCTATTGGTGCGGGGTGTTTCCTTCCGAGTTCTTCGGCCCAGAGGCGCTCCTCTGAT -TCTGTGGCTTCACGGGTATATACTGGATAAGAATTTTCCTCCTCCGGGGGCTGAGTGCCG -AAGAGTAAGAAGTAAGGGCTATACCCGCTGGGTGAGACTCTTCGATTGAAATTCATTACC -GCGAGTGAGAGAGCGCCAGCTAGTGTAATTTTAGGAGAATCCAGGAGAACTCTGACCAGT -ATGGCTTTCAGAACGCCATTTGCCTGTTCGACTTTGCCATTTCCTCTTGGCCTAGCTGGT -GTGGTATGGACAACCTGCAGTTGTTGGCTAGCTTGAAATCGTTGTGCTTCTATGCCTCCG -AAGCAGCCAGCATTGTCACTGATAATCTGCTTTGGCTTTCCAAAGTTCTGGATAATATAC -GTGAGCAGAGGCACAGTGTTAGCGAAGTCTGCATTGGGAACTAAGCGGGATTCCAGCCAG -CCTGTTGCGTACTCAATTGCATTGAGCAAGACTTGGGGTCCTACTTGAGTATGATCTATA -CCCCACCGTGTCAGAGGAGGTGCTGGTACTATAGGAGTTAAGCTTCCCAGTAACGGGTCT -GGAGGTTTCATGAGCTGACAGGACTTGCATTTTCGGACAGCTTCGTGAGCCGCGAGGATC -AGTTCGGGGTGCCAAAACCTACGCCCTAATTCCCGCATAGTATTGCCGATTGACGCATGG -CCTTGGCCCTCATGAACATTTACGGCCGTCGATACTAGATCCTCATATTCCAAGATTTCT -AGTAGGGTTGCGGCGCCAGATGGACCAGGTGCATCGCCTACTTGTTGCGACGGGTTCTTT -TTGATGAGATGCAATTTGGAATTGTACATCGCAAAATTATCTCGGACCCAAGTGGCAGCT -ATATTTAGGGGAAGTGCCTCTCCTAAGGTTAGAAATTCGGTGATGCACTGCAGGTCGATG -CGGTTGAGTTCGTGTGGGTGCTTTATTTCCTCCATCTCAAGTTCTCTTTCTGCACCACTT -TGGATTCTAGAGTTTTCGTTGTCGTCAGTAGCTACATTCCCTTCCCCTTCTTCCCTAGAG -AGAAATAGAACATCACAGGGACGGGAGAGAAAATCAGCGAGAACATTTGCTTTTCCGCGA -CGGTAGATAATCCTGATATTAAAATGCTCTATAGCATCTAAAAAACGGACCATTCTGACG -GGCTGCTCGGCTTTGGTCTGAATAGTTCGTAGAGATTCATGGTCAGTTATCACCGTTACG -TCGCCGCCTTCTACCCAGTGACGCCAATGTTGTAGTGACAGTAAAATCCCAAGTAATTCC -CTCTCTTGTGCTGAATAACGCTGCTGGGTATCGTTTAGTTTTCTTGAGAAGTAAGCTATG -GGATGCAGCACTGAACGATCGGAATTGTTGGAGCATCGCATGTACGGTTGGAGTATGACT -GCACCCACGAACTTTTGGGAAGCGTCAGTTTCCAATATGACGGGAAGTCTCCAATCAAAT -TTTTTTACAACTGGTGATGTTGTAAGCGCTAGTTTGATACTTTTCCATGATTGAATCGAT -TGGTCCGTCAGAATGACAGGGCAATTTTTAGGTCCAGAGGATTGGTCCGTGAGTGGCCCT -GCTAGTTGGGAGAAATTTTTAATGAGACAACGTAGGTAACCAGCTGCATTTACAAATCCT -CTTATTTCCGAGGTAGTTGTTGGCATAGGCCTGTCTCTGATCGCTGAAACTTTTTCGGGG -TCTGCTGCAATGCCATGTTTAGAAATATGGAAACCAAGGAAGATTCCCTCTGAAACAAAT -AGCCTGCACTTTGAAGCATTGAGGAGGAGACCATAGGAAGCGAATCTAGAAAAAATAAGT -ATCAACCGTGAGTGCAATTCTGCCATTGAGTCTGCCCAGACAGCTACATCGTCCAGGAGC -CCTGCGACAAATGGACGGAATGGCTCTAGAACTTCTTCCATAAAACACTGGAAAGTAGCT -GGTGCGTTGCATAGGCCGAAAGGCATAACTAGCCATTCATAGACACCGAAAGGAGTCACA -AATGCTGTTTTCTCTGAAGAGTCTTTGTGCATACGTATCTGCCAAAATCCGTTTTCCAGG -TCGAGGAATGCATAGAAGTTATGTCCTGCTGCGCGCTGAATTTCATCTTGAGCATTTGGT -AGGGGATGGGCGTGTTTCTTCGTAATCTTGTTAAGCTCTCTATAGTCAACACAAATACGC -CAAACGGTTTGGTTAGTCTGGGTTAGCGTCTTTTTTTGGTGTTAATAACAGAGGTGCAGC -CCATGGTCCCTTACATTTGCGTATGAATTGAGCCGGTCATGTGTTGCACAAGAAAGTCCC -CGGATGGCTTGTTGTTGCGCCGGGGCTATATCGCCTCGGAGGGGAGTTTTAAATTGGGTT -GACAATTACCCCGTTTCTATGCGGGTGTTTCTGTCTTGGGAGAGTTTTATCCCATTTGGC -GGGAGAGATTTATCGAAAAGTTGAAGGGGAATTTAACTTTGATATTGTAGGGAAAAACTG -TAATGCGGAATGAAGGGTGGGCTGGGTGCCATTTGACCATTGGAATATTTGAAGTAGTGA -AGACTTTTCGGTTTGGGAGAGTATTAATTATAGGATTAAGAATTGGTTGGTCAATTAAGT -TGAGAAGTTGCAGTTTGCCATTTGATAAACATCGTAGCCCCAGTTCATGGAATAAAGTTT -GTCCAAGTGTCACATCTGCTGGGAATGTGCCATCTGGGACAACTCCTAGAGACACTGTGA -ATTCCTGAGTCCAGAATGATTCAAGGTGATTCGAGCAAAGAAACTGTGCAGTTAAAATTG -CATCCTTAGAAATTGTTGGGCCAGGGCCACCAATGCCTGACATTTTAGAAATAATAGATG -TATTATAAGAAGTCAAATATTTAGAGAAAGACTGTGAAACATAACATGCTGAAGAGCCGT -AGTCAAAAAAAACTGAAAATTGGACATAGGGAAAATGAGTTATTCGTGCAAAAAACATTC -TGTGTGGCTTGCCATATCCTTCCCGTAGAGGTTGTCCTTTTGGGGGTGGCTCAAATTTGC -CCTTTCCTACGGCCACAAAGTAGGTATTCGGGCTGTCCTATTCATAAATTTCTTCATTTC -GCATTCGATATAGAATGGCTTCAATTTCGTCATCGAGCTGCTCATCTTCTATTTGGCCTT -CAGGGCTTATTTGCTCTTGATCCAAATCTTCTGGCTCAACAAGGAAAGTAGAAGTGACAG -GCTTTGATGAACGATCGTGTGGTGTTACAGGTTTTACATATTTTTTATTTTTCATTGATT -GGTAAGTTTTCCTGAATTTATCGCTGAAACGCGACGAGGTGTATTTAGCGTTTGGTGCAT -ATTCCCTTTGTTCTTTTGATTCCACCGGCGCTGTTTTCATCAACCGGCAGTCTTTCGCCC -AGTGGCCTGTCTTTCCGCAATTGAAGCATTCGTAACGCTTGTCGTGAATTGGGTATGATT -TATCTGTTTCTGCAATGTCTTGTGACGCAAAGACGTCTTGCCCATACGACCTTGGATCAG -CTATGGATGCGTCAAATGCTGGAAGCTTTTCGCCTTTTGACGCTGAGATCGGAATTGGTG -CATTGGACTCGGAATGTTTGAATACATCATCCTCAAGTGTCCACCTTGTAATACCGCGTG -TGACTTGAACCACTCGATCCGCAAGCTCCGCGCTGGTGAGTTTGGGGAGATTATTGGAAA -TGATGGTCCAGGTACGTGGAAGTGAGAGTCGAATATGCTGCCTCAGTATATCTCTAGTCT -GAGGCCCTACCATGACATCCGAAGGTAGGCTAAAGAAAGCTTTCCGGAGTCGTCGCGCAA -ATTGTAATTGAGTCTCGTCGTTTCTTGCAGTTATTCGTGCAAATGTTGTCAAAGGCGACC -CGAGTACATCATTGTCGAACAGTATTTTAAGGATACAGTCTACAGCTCCTGCCCAATCGA -GGTGTTGACTGATGATTGTTCTTCGCGCCGAGATGAAATCTTCATCCATTTCCATTGCAA -TTCTGATAGCCCAAGCAGAATATGGAAGCATATGTTGAATCATCAATGATTGCATGTGGT -ATAATATATTCATTATGTTCTCATCAGCAAAGTGCAATTTCCATTGTGGTGGGAATACCG -CGCGTGTTTTTCTATTTGCCTCTTTTAAAGGGCCGTGCGGATTTTCAGCTTCGGAACGCG -AAAAGAAATCTGGGAAGTACCGCTTTATTTTTCGCTCTTGTTCAGTAACATTCAATGGTT -CGTTAACTGACTGGCGGTATAAATTAATAGTCCCATCTTTGTTTTGCTCATCATTGCTTA -GGTTGGGCGTTGTTTCATAGAATTGCGCCGAGGTAAAGGGTCTTTTCTTAGGCTGAAACA -CGATTGGCCTGGTTGCGGGTCGCGAGGCGCTGCCTGCTGAAAAGTCAAATAGCTCCTCCC -GGTATGGTTTTTTATTTTCAGATGGCCCTGCTTCCGAAAGTTGAAAGGGGACTGAATTTT -TCGAAGAAGTTTTTGTTTCCACGTCTTCATTTCTACTTACTAGTTTGGAAATTAAGTCGT -TCATTGCAGACATTTGTTTGACTAGAAGAGAAATTTGTGATTGGGTCTCTTCAAACCTTT -GATCGATTCTCTTGGAGAGATCTTTTGTCACTGCCTTTGCAGCTTCATTAGCTTCGGAAA -AATTTTCGTTGGCTTTGGTTTGCCCGGCAATGTGATCCTTCATCAAGCTTTCCAACTGAG -CATTATTCAGGCCGACCATGATGATTGAATAGGTGGTGAAATGCGTAAAAAATTTGGAGA -CGTCTTAAATTGGGATGACCTAGAATTGTGAGGTTCTCTCAACAAAAATATATAATTTTG -TGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCG -ACAAATCAACAATATAATGCGAGTAGAGCTTGAGACTAATAAAACGTGAATTTCATTCTA -TAATACAGGACCGCCAACTTATTTAAATATTCCCCCGCACCACGTGAGCCAATCAACAGC -ACACAATTTGCACGGTCGGGTTTCCATCAATTGGGATCCACA ->blumeria_Grouper_14770_3 -GGTTAGACCGATACAGTAAGTCTCGTATGAAGTTGTGGAAGGAAGAATTGACTGGAAACA -AGTGTATTGAGATGTATGGTTCTGAGTAAAACTGAGCTGATAAGAGTGAGATTGCGTGTG -CGCATATCTTATCAACTGAGGTTTTTGACCAGTATTTATCAATCTCCATGGATCATAAGT -TATGATCCCTGTAGATGTAAATCTATATACGTACAGATATATGAGCCAGAAATATAAAGC -TAAATACATGTGTGTCGGTAATAGATCCGAGAAACCTTTAACCTGCATTTGATACATAAT -CATCTGATGGAATGCTAGTGTGAAATAAATGCCAATGTACGTTAAACTTTCCGTGAGGAA -TGTGCTGATGACAATGATATAGGAAGGTGAATTTGATAACCTAATTAGCCGGACTTACAA -ATGAGTTATCCTTGGCATTCCAGGATATACAATATTTCAACACCCCTCCTCACTTTGCAT -CGAGGATAGATACATAAGTGAAAAACTGTTAGTATATTTATTGTCATTTCTCATCTAATG -CTGGTATGGTAGACACGCCAGTGGTTGTACTAGTACCAAAAACTGAAGTGCATAAATCGG -TGTGCCTTGGTCTCGGTAAGCCTTTTGTACATATATCTGCGAGATTTTTAGCTGAAGGAA -CATGTAATAGTGTAAGCGAGCCGTCTTCAATTCTTTCCCTTGTAAAATGATAAGCGATGT -CGATATGTTTAGAAGCATCATTTAGTTTTGGATTGTGAGCAAGTTCAATGGCAGCCGTAT -TGTCAGTCGAGATTGCTGCTGGGATGCTGTCTCCAAGGAATCGGTGAAGTCCGCGCAAAA -TCCAGATATATTGTTTGGATGCGAGCGCTATTGCCATGTACTCAGCTTCGCAGGTTGAAT -G ->blumeria_Grouper_1717_12 -ATTTCCAGTATCTTGCCCTGAAGGGCCAGTAAGTCCTGATCGAATAGTTTTCGAAGTCTC -TCGTCAGTGACTGGTTCCAACAGCTTGCAGAACCCAATGATGAAGCGCTCTGCTTGTGCG -GAGCGCGTCTGGAATATCCTGCCCTGTTCGGCGAGGAATTTGGTCGCGACGATTTGAGGC -GACGGAGTTTGTTGGTGCGGTGAGCTTCGATGACTCGCCTCGTAGATTGGCTCTACAAAT -TGTTGTGTGGGTTGTTGTGATGGCGGTTGTGGCCCGTTAAGGACCATTTCGACGTCTTGA -CGCGTCGAACATTGAGTTGGGAGGGGGGGCCAAGAGCCAGCCTCTGCGGAGGACTGGGGC -GGCATGAGTGAGTGAGGTTTGTGGCAGTGTGAGATCGTAGATGGTATACGGCGCGCTTGA -AGGG - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.py --- a/commons/pyRepetUnit/profilesDB/CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ -from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils -import re -import sys - - -class CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber(object): - ''' - Check if profiles from a profiles list are present in profiles DB, if not you can generate the getz command to add them. - By default the profiles list is a list of profiles names - ''' - - def __init__(self): - ''' - Constructor - ''' - self.profilesDBUtils = ProfilesDatabankUtils() - self.profilesToAddNotInDB = [] - self._pfamAccNumber = False - - def setProfilesDBFile ( self, profilesDBFile ): - self._profilesDBFile = profilesDBFile - - def setProfilesToAdd ( self, profilesFile ): - self._profilesToAdd = profilesFile - - def setPfamAccNumberKeys ( self ): - self._pfamAccNumber = True - - def _IsProfilInDB(self, pfamDBList, profil): - IsProfilInDB = False - for profilInstance in pfamDBList.getList(): - if (self._pfamAccNumber == False and profilInstance.name == profil) or (self._pfamAccNumber == True and re.match(profil + "\.\d+", profilInstance.accNumber)): - IsProfilInDB = True - break - return IsProfilInDB - - def _generateProfilesList(self): - f = open(self._profilesToAdd) - profilesToAddList = f.readlines() - return profilesToAddList - - def generateNotExistingProfilesList ( self ): - ''' - generate the profiles list of profiles not in profiles DB among profiles in a list of name or accession number - ''' - self.profilesToAddNotInDB = [] - profilesToAddList = self._generateProfilesList() - pfamDBList = self.profilesDBUtils.read( self._profilesDBFile ) - if pfamDBList.getList( ) != []: - for profil in profilesToAddList: - if profil != "\n": - sys.stdout.flush() - profil = profil.rstrip( ) - IsProfilInDB = self._IsProfilInDB(pfamDBList, profil) - if ( IsProfilInDB == False): - self.profilesToAddNotInDB.append( profil ) - return ( self.profilesToAddNotInDB ) - - def generateGetzCmdProfilesList ( self, profilesList ): - ''' - generate the getz command to retrieve profiles list of name or accession number - ''' - getzCmd = "getz -e \'" - if (self._pfamAccNumber == False): - for profileName in profilesList: - getzCmd += "[pfamhmm-Id:\"" + profileName + "*\"] | " - else: - for profileAccNumber in profilesList: - getzCmd += "[pfamhmm-AccNumber:\"" + profileAccNumber + "\"] | " - getzCmd = getzCmd[ 0:len( getzCmd )-3 ] - getzCmd += "\'" - return getzCmd - - def CmdToCompleteProfileDB (self): - ''' - generate the getz command to retrieve profiles list of name or accession number if the profile is not yet in profiles DB - ''' - profilesList2Add = self.generateNotExistingProfilesList() - return self.generateGetzCmdProfilesList ( profilesList2Add ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/InsertProfilesMapFileInDB.py --- a/commons/pyRepetUnit/profilesDB/InsertProfilesMapFileInDB.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -from commons.core.coord.Map import Map -from pyRepet.sql.TableAdaptator import TableMapAdaptator - -class InsertProfilesMapFileInDB(object): - ''' - Insert a map File in a database - You have to specified the input file name, the table name and the repetDB object when you create the object - ''' - - def __init__(self, inputFileName, tableName, db): - ''' - Constructor - ''' - self.inputFileName = inputFileName - self.tableName = tableName - self.db = db - - def createAndLoadTable(self): - ''' - Create the table and load the map data from input table - ''' - self.db.createTable(self.tableName, "map", overwrite = True) - f = open (self.inputFileName, "r") - iMap = Map() - lMap = [] - while iMap.read( f ): - lMap.append(iMap) - iMap = Map() - f.close() - self._tMapA = TableMapAdaptator( self.db, self.tableName ) - self._tMapA.insMapList( lMap ) - - -if __name__ == "__main__": - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/Profiles.py --- a/commons/pyRepetUnit/profilesDB/Profiles.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ -import re - -#------------------------------------------------------------------------------ - -class Profiles: - ''' - Hmm profile Class - Attributes are name, desc, length, accNumber, GA_cut_off and retrieve - ''' - - #-------------------------------------------------------------------------- - - def __init__( self, name="", desc="", length=0, accNumber = "", GA_cut_off = 0, retrieve = False ): - self.name = name - self.desc = desc - self.length = length - self.accNumber = accNumber - self.GA_cut_off = GA_cut_off - self.retrieve = retrieve - self.tab_profile = [] - - #-------------------------------------------------------------------------- - - def _noProfileInFile(self): - self.name = None - self.desc = None - self.length = None - self.accNumber = None - self.GA_cut_off = None - - #-------------------------------------------------------------------------- - - def _initialisation(self): - self.name = "" - self.desc = "" - self.length = 0 - self.accNumber = "" - GA_cut_off = 0 - self.tab_profile = [] - - #-------------------------------------------------------------------------- - - def read( self, hmmFile ): - ''' - Read a profile and characterize the object profile - attributes name, length, desc, accNumber and GA_cut_off are specified - ''' - line = hmmFile.readline() - if line == "": - self._noProfileInFile() - return - self._initialisation() - if self.retrieve: - self.tab_profile.append(line) - while not re.match("\/\/.*", line): - line = hmmFile.readline() - if self.retrieve: - self.tab_profile.append(line) - name = re.match("NAME\s*(.*)", line) - if name: - self.name = name.group(1) - desc = re.match("DESC\s*(.*)", line) - if desc: - self.desc = desc.group(1) - length = re.match("LENG\s*(.*)", line) - if length: - self.length = int(length.group(1)) - accNumber = re.match("ACC\s*(.*)", line) - if accNumber: - self.accNumber = accNumber.group(1) - GA_cut_off = re.match("GA\s*\d*\.\d*\s*(.*);", line) - if GA_cut_off: - self.GA_cut_off = float(GA_cut_off.group(1)) - else : - if (self.GA_cut_off == 0): - self.GA_cut_off = "NA" - if self.retrieve: - return self.tab_profile - else: - return 1 - - #-------------------------------------------------------------------------- - - def readAndRetrieve( self, hmmFile ): - ''' - Read a profile and characterize the object profile - attributes name, length, desc, accNumber and GA_cut_off are specified - And a list of each line of profile is returned - ''' - self.retrieve = True - return self.read(hmmFile) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/ProfilesDB2Map.py --- a/commons/pyRepetUnit/profilesDB/ProfilesDB2Map.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils - - -class ProfilesDB2Map ( object ): - """ - write a file in map format from a ProfilDatabank object - You have to set an input File and an Output File names - """ - - def __init__(self): - self.profilesDBUtils = ProfilesDatabankUtils() - self._inputFile = "" - self._outputFile = "" - - def setInputFile(self, input): - self._inputFile = input - - def setOutputFile(self, output): - self._outputFile = output - - def _readProfilesDB( self ): - pfamDB = self.profilesDBUtils.read( self._inputFile ) - return pfamDB - - def _writeMapFile( self, pfamDBList ): - """ - write a file in map format from a ProfilDatabank object - """ - if pfamDBList.getList() != []: - f = open( self._outputFile , "w") - for ProfilInstance in pfamDBList.getList(): - f.write(ProfilInstance.name + "\t" + ProfilInstance.desc + "\t1\t" + str(ProfilInstance.length) + "\n") - f.close() - - def run( self ): - """ - read a profiles DB file, parse it and, write the corresponding .map file - """ - pfamDBList = self._readProfilesDB() - self._writeMapFile(pfamDBList) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/ProfilesDB4Repet.py --- a/commons/pyRepetUnit/profilesDB/ProfilesDB4Repet.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,226 +0,0 @@ -#!/usr/bin/env python - -import re -import getopt -import sys -from commons.pyRepetUnit.profilesDB.Profiles import Profiles -from commons.core.LoggerFactory import LoggerFactory - -LOG_DEPTH = "commons.pyRepetUnit.profiles" - -## Format a profiles DB for pipelines in REPET -# -class ProfilesDB4Repet( object ): - - def __init__(self): - self.profile = Profiles() - self._inputFile = "" - self._outputFile = "" - self._verbosity = 2 - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - - def _help( self ): - print - print "usage: %s.py [ options ]" % ( type(self).__name__ ) - print "options:" - print " -h: this help" - print " -i: name of the profiles DB to format for Repet" - print " -o: name of the output profiles DB for Repet" - print - - - def _setAttributesFromCmdLine( self ): - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:o:") - except getopt.GetoptError, err: - print str(err); self._help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self._help(); sys.exit(0) - elif o == "-i": - self.setInputFile( a ) - elif o == "-o": - self.setOutputFile( a ) - - #TDOD: add nb of each domain in log file, verbose... - def _searchCurrentDomain(self, profile): - currentDomain = "" - #TODO: pattern GAGA and GAGE should be excluded ! - #TODO: add new tag like "ORF1_LTR" for ATHILA as key word in Pfam - #TODO: add new tags from GypsyDB (MOV etc...) - if (re.search("[gG][aA][Gg]", profile[1]) or re.search("[gG][aA][Gg]", profile[3])): - currentDomain = "GAG" - elif (re.search("Zinc knuckle", profile[1]) or re.search("Zinc knuckle", profile[3])): - currentDomain = "GAG" - elif (re.search("PF02813", profile[2]) or re.search("PF01021", profile[2])): - currentDomain = "GAG" - elif (re.search("GAG_", profile[1])): - currentDomain = "GAG" - elif (re.search("GAGCOAT_", profile[1])): - currentDomain = "GAG" - - elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]aspartic", profile[3])) and (re.search("[pP]roteinase", profile[1]) or re.search("[pP]roteinase", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]spartic", profile[3])) and (re.search("[pP]rotease", profile[1]) or re.search("[pP]rotease", profile[3]))): - currentDomain = "AP" - elif ((re.search("[rR]etrotransposon", profile[1]) or re.search("[rR]etrotransposon", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]spartic", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartic", profile[1]) or re.search("[aA]spartic", profile[3])) and (re.search("[eE]ndopeptidase", profile[1]) or re.search("[eE]ndopeptidase", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[pP]roteinase", profile[1]) or re.search("[pP]roteinase", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[pP]rotease", profile[1]) or re.search("[pP]rotease", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))): - currentDomain = "AP" - elif ((re.search("[aA]spartyl", profile[1]) or re.search("[aA]spartyl", profile[3])) and (re.search("[eE]ndopeptidase", profile[1]) or re.search("[eE]ndopeptidase", profile[3]))): - currentDomain = "AP" - elif ((re.search("AP_", profile[1])) and not (re.search("[eE]ndonuclease", profile[3]))): - currentDomain = "AP" - - elif ((re.search("[iI]ntegrase", profile[1]) or re.search("[iI]ntegrase", profile[3])) and not (re.search(" C ", profile[1])) and not (re.search(" C ", profile[3]))): - currentDomain = "INT" - elif (re.search(".*[Cc]hromo.*", profile[1]) or re.search(".*[Cc]hromo.*", profile[3])): - currentDomain = "INT" - elif (re.search("INT_", profile[1])): - currentDomain = "INT" - - - elif ((re.search("[rR]everse", profile[1]) or re.search("[Rr]everse", profile[3])) and (re.search("[tT]ranscriptase", profile[1]) or re.search("[tT]ranscriptase", profile[3]))): - currentDomain = "RT" - elif (re.search("RT_", profile[1])): - currentDomain = "RT" - - - elif ((re.search("R[nN]ase", profile[1]) or re.search("R[nN]ase", profile[3])) and (re.search("H", profile[1]) or re.search("H", profile[3]))): - currentDomain = "RH" - elif ((re.search("R[nN]ase", profile[1]) or re.search("R[nN]ase", profile[3])) and (re.search("H ", profile[1]) or re.search("H ", profile[3]))): - currentDomain = "RH" - elif (re.search("RNaseH_", profile[1])): - currentDomain = "RH" - - - elif ((re.search("[eE]nvelope", profile[1]) or re.search("[eE]nvelope", profile[3])) and (re.search("[pP]rotein", profile[1]) or re.search("[pP]rotein", profile[3]))): - currentDomain = "ENV" - elif ((re.search("ENV", profile[1]) or re.search("ENV", profile[3])) and (re.search("[pP]olyprotein", profile[1]) or re.search("[pP]olyprotein", profile[3]))): - currentDomain = "ENV" - elif ((re.search("[eE]nvelope", profile[1]) or re.search("[eE]nvelope", profile[3])) and (re.search("[pP]olyprotein", profile[1]) or re.search("[pP]olyprotein", profile[3]))): - currentDomain = "ENV" - elif ((re.search("[eE]nvelope", profile[1]) or re.search("[eE]nvelope", profile[3])) and (re.search("[gG]lycoprotein", profile[1]) or re.search("[gG]lycoprotein", profile[3]))): - currentDomain = "ENV" - elif (re.search("PF07253", profile[2]) or re.search("PF03811", profile[2])): - currentDomain = "ENV" - elif (re.search("ENV_", profile[1])): - currentDomain = "ENV" - - elif ((re.search("[tT]yrosine", profile[1]) or re.search("[tT]yrosine", profile[3])) and (re.search("[rR]ecombinase", profile[1]) or re.search("[rR]ecombinase", profile[3]))): - currentDomain = "YR" - - elif ((re.search("[eE]ndonuclease", profile[1]) or re.search("[eE]ndonuclease", profile[3])) and not (re.search("AP ", profile[1]) or re.search("AP ", profile[3])) and not (re.search("[aA]purinic", profile[1]) or re.search("[aA]purinic", profile[3]))): - currentDomain = "EN" - - elif ((re.search("[eE]ndonuclease", profile[1]) or re.search("[eE]ndonuclease", profile[3])) and (re.search("AP ", profile[1]) or re.search("AP ", profile[3]))): - currentDomain = "APE" - elif ((re.search("[eE]ndonuclease", profile[1]) or re.search("[eE]ndonuclease", profile[3])) and (re.search("[aA]purinic", profile[1]) or re.search("[aA]purinic", profile[3]))): - currentDomain = "APE" - - elif ((re.search("[tT]ransposase", profile[1]) or re.search("[tT]ransposase", profile[3])) and not (re.search("DDE ", profile[1]) or re.search("DDE ", profile[3]))): - currentDomain = "Tase" - elif (re.search("DUF659", profile[1])): - currentDomain = "Tase" - elif (re.search("PF01695", profile[2])) or (re.search("PF02316", profile[2])) or (re.search("PF09039", profile[2])) or (re.search("PF04827", profile[2])) or (re.search("PF05699", profile[2])): - currentDomain = "Tase" - - elif ((re.search("[tT]ransposase", profile[1]) or re.search("[tT]ransposase", profile[3])) and (re.search("DDE ", profile[1]) or re.search("DDE ", profile[3]))): - currentDomain = "Tase*" - - elif ((re.search("[rR]eplication", profile[1]) or re.search("[rR]eplication", profile[3])) and (re.search("[pP]rotein", profile[1]) or re.search("[pP]rotein", profile[3])) and (re.search("A ", profile[1]) or re.search("A ", profile[3]))): - currentDomain = "RPA" - elif (re.search("[rR]epA ", profile[1]) or re.search("[rR]epA ", profile[3])): - currentDomain = "RPA" - elif (re.search("RPA", profile[1]) or re.search("RPA", profile[3])): - currentDomain = "RPA" - - elif (re.search("[cC]-integrase", profile[1]) or re.search("[cC]-integrase", profile[3])): - currentDomain = "C-INT" - - elif ((re.search("[pP]ackaging", profile[1]) or re.search("[pP]ackaging", profile[3])) and (re.search("ATPase", profile[1]) or re.search("ATPase", profile[3]))): - currentDomain = "ATP" - - elif ((re.search("[cC]ysteine", profile[1]) or re.search("[cC]ysteine", profile[3])) and (re.search("[pP]rotease", profile[1]) or re.search("[pP]rotease", profile[3]))): - currentDomain = "CYP" - elif ((re.search("[cC]ysteine", profile[1]) or re.search("[cC]ysteine", profile[3])) and (re.search("[pP]eptidase", profile[1]) or re.search("[pP]eptidase", profile[3]))): - currentDomain = "CYP" - elif (re.search("[pP]eptidase_C", profile[1]) or re.search("[pP]eptidase_C", profile[3])): - currentDomain = "CYP" - elif (re.search("PF00559", profile[2])): - currentDomain = "CYP" - - elif (re.search("[pP]ol\S*_*B", profile[1]) or re.search("[pP]ol\S*_*B", profile[3])): - currentDomain = "POLB" - elif ((re.search("[pP]olymerase", profile[1]) or re.search("[pP]olymerase", profile[3])) and (re.search("B ", profile[1]) or re.search("B ", profile[3]))): - currentDomain = "POLB" - - elif (re.search("[hH]elicase", profile[1]) or re.search("[hH]elicase", profile[3])): - currentDomain = "HEL" - - else : - currentDomain = "OTHER" - return currentDomain - - - ## Replace the old profile name by accession number, name, domain and gather cut off - # - # @param fout file handle - # @param profile Profiles instance - # @param currentDomain string - # - def _writeModifiedProfile(self, fout, profile, currentDomain): - for i in xrange(0, len(profile), 1): - if i != 1: - fout.write(profile[i]) - else: - fout.write("NAME " + self.profile.accNumber + "_"\ - + self.profile.name + "_"\ - + currentDomain + "_"\ - + str(self.profile.GA_cut_off) + "\n") - - - ## Set input file name - # - # @param inputFileName string - # - def setInputFile(self, inputFileName): - self._inputFile = inputFileName - - - ## Set output file name - # - # @param outputFileName string - # - def setOutputFile(self, outputFileName): - self._outputFile = outputFileName - - - ## Read a profiles DB file, parse it and, write a new profiles DB with TE domain information and GA score cut_off placed side by side of the name - # - def run( self ): - LoggerFactory.setLevel(self._log, self._verbosity) - fileIn = open( self._inputFile ) - fout = open( self._outputFile, "w" ) - profile = self.profile.readAndRetrieve( fileIn ) - while profile != None: - currentDomain = self._searchCurrentDomain(profile) - if currentDomain == "OTHER": - self._log.warning(self.profile.accNumber + " " + self.profile.name + " has no associated domain") - self._writeModifiedProfile(fout, profile, currentDomain) - profile = self.profile.read( fileIn ) - - -if __name__ == "__main__": - i = ProfilesDB4Repet() - i._setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/ProfilesDatabank.py --- a/commons/pyRepetUnit/profilesDB/ProfilesDatabank.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -class ProfilesDatabank: - - """ - List of profiles objects. - """ - - list; - - def __init__( self ): - self._profilesDatabank = [] - - def append( self, list ): - self._profilesDatabank.append(list) - - def len (self): - return len(self._profilesDatabank) - - def get(self, index): - return self._profilesDatabank[index] - - def getList(self): - return self._profilesDatabank \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py --- a/commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -""" -Utility to handle a databank of HMM profiles. -""" - -import sys -from commons.pyRepetUnit.profilesDB.Profiles import Profiles -from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank -from commons.core.utils.FileUtils import FileUtils - -class ProfilesDatabankUtils: - """ - Utility to handle a databank of HMM profiles. - """ - - def read( inFileName, verbose=0 ): - """ - Read a file in Pfam format and return a L[ProfilesDatabank} instance. - @param inFileName: name of the input file - @type inFileName: string - @param verbose: verbosity level - @type verbose: integer - """ - if verbose > 0: print "reading file '%s'..." % ( inFileName ); sys.stdout.flush() - - - if FileUtils.isEmpty(inFileName): - return (None) - profilesInstance = Profiles() - profilesDBInstance = ProfilesDatabank() - f = open( inFileName , "r") - while profilesInstance.read( f ): - profilesDBInstance.append( profilesInstance ) - profilesInstance = Profiles() - f.close() - if verbose > 0: print "file '%s' is loaded" % ( inFileName ); sys.stdout.flush() - return (profilesDBInstance) - - read = staticmethod( read ) diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/InsertProfilesMapFileInDBTestRessources.py --- a/commons/pyRepetUnit/profilesDB/tests/InsertProfilesMapFileInDBTestRessources.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -''' -Created on 24 juin 2009 - -@author: choede -''' - -class InsertProfilesMapFileInDBTestRessources(object): - ''' - Put here ressources not present in config file - ''' - REPET_DB_USER = "ochoede" - REPET_DB_HOST = "pisano" - REPET_DB_PW = "ochoede" - REPET_DB_NAME = "repet_ochoede" \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/TestCompleteProfilesDBFromProfilesNameListOrAccNumber.py --- a/commons/pyRepetUnit/profilesDB/tests/TestCompleteProfilesDBFromProfilesNameListOrAccNumber.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -''' -Created on 18 mai 2009 - -@author: choede -''' -import unittest -import commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber - - -class TestCompleteProfilesDBFromProfilesNameListOrAccNumber(unittest.TestCase): - - - def setUp(self): - self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt" - self._filePfamList = "./datas/ListpfamAccNumber.txt" - self._profilesDB = "./datas/profilesDBTest.hmm" - self.CompleteProfilesDB = commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber() - self.CompleteProfilesDB.setProfilesDBFile ( self._profilesDB ) - self._expectedList = ["zf-CCHC", "InvE", "Chromo", "TLV_coat"] - self._expectedList2 = ["PF00075", "PF00424", "PF00469"] - self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'" - self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'" - - - def tearDown(self): - pass - - - def testListNotExistingProfiles(self): - #with name - self.CompleteProfilesDB.setProfilesToAdd ( self._fileProfilesList ) - profilesNotInDBList = self.CompleteProfilesDB.generateNotExistingProfilesList( ) - i = 0 - if profilesNotInDBList != []: - for profil in profilesNotInDBList: - self.assertEquals(profil, self._expectedList[i]) - i = i + 1 - #with pfam accession number - self.CompleteProfilesDB.setProfilesToAdd ( self._filePfamList ) - self.CompleteProfilesDB.setPfamAccNumberKeys () - profilesNotInDBList = self.CompleteProfilesDB.generateNotExistingProfilesList( ) - i = 0 - if profilesNotInDBList != []: - for profil in profilesNotInDBList: - self.assertEquals(profil, self._expectedList2[i]) - i = i + 1 - - def testCreateGetzCommand(self): - getzCmd = self.CompleteProfilesDB.generateGetzCmdProfilesList( self._expectedList ) - # pour le moment je cherche dans les fs ou les ls si je ne veux que les fs specifier type = fs ce sera surement le cas a terme - self.assertEqual (getzCmd, self._expectedGetzCmd) - - def testCmdToCompleteProfileDBFromList(self): - #names list - self.CompleteProfilesDB.setProfilesToAdd ( self._fileProfilesList ) - getzCmd = self.CompleteProfilesDB.CmdToCompleteProfileDB() - self.assertEqual (getzCmd, self._expectedGetzCmd) - #pfam accession Number list - self.CompleteProfilesDB.setPfamAccNumberKeys () - self.CompleteProfilesDB.setProfilesToAdd ( self._filePfamList ) - getzCmd = self.CompleteProfilesDB.CmdToCompleteProfileDB() - self.assertEqual (getzCmd, self._expectedGetzCmd2) - - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/TestInsertProfilesMapFileInDB.py --- a/commons/pyRepetUnit/profilesDB/tests/TestInsertProfilesMapFileInDB.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -import unittest -import time -import os -from commons.core.sql.TableMapAdaptator import TableMapAdaptator -from commons.core.coord.Map import Map -#from commons.pyRepetUnit.profilesDB.tests.InsertProfilesMapFileInDBTestRessources import InsertProfilesMapFileInDBTestRessources -from commons.pyRepetUnit.profilesDB.InsertProfilesMapFileInDB import InsertProfilesMapFileInDB -from commons.core.sql.DbMySql import DbMySql - - -class TestInsertProfilesMapFileInDB(unittest.TestCase): - - def setUp(self): - self._inputFileName = "./datas/profiles.map" - self._createProfilesMapFile() -# self._host = InsertProfilesMapFileInDBTestRessources.REPET_DB_HOST -# self._user = InsertProfilesMapFileInDBTestRessources.REPET_DB_USER -# self._passwd = InsertProfilesMapFileInDBTestRessources.REPET_DB_PW -# self._dbname = InsertProfilesMapFileInDBTestRessources.REPET_DB_NAME -# self._db = DbMySql( self._user, self._host, self._passwd, self._dbname ) - self._db = DbMySql( os.environ["REPET_USER"], - os.environ["REPET_HOST"], - os.environ["REPET_PW"], - os.environ["REPET_DB"] ) - self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) - self._table = "dummyMapTable_%s" % ( self._uniqId ) - - def tearDown(self): - os.remove(self._inputFileName) - self._deleteDBtables() - self._db.close() - - def testInsertProfilesMapFileInDB(self): - resultFromFileMapUtils = self._readMapResultsFromFileAndFillList() - InsertProfilesMapFileInDBinstance = InsertProfilesMapFileInDB(self._inputFileName, self._table, self._db) - InsertProfilesMapFileInDBinstance.createAndLoadTable() - resultFromTableMapUtils = self._readMapResultsFromTableAndFillList() - self.assertEquals(resultFromFileMapUtils, resultFromTableMapUtils) - - def _createProfilesMapFile(self): - f = open(self._inputFileName, "w") - f.write("rrm\t\t1\t77\n") - f.write("fn3\tFibronectin type III domain\t1\t84\n") - f.write("pkinase\tProtein kinase domain\t1\t294\n") - f.close() - - def _readMapResultsFromTableAndFillList(self): - tableMapAdaptatorInstance = TableMapAdaptator (self._db, self._table) - return tableMapAdaptatorInstance.getListOfAllMaps() - - def _readMapResultsFromFileAndFillList(self): - mapInstance = Map() - lMap = [] - f = open( self._inputFileName , "r") - while mapInstance.read( f ): - lMap.append (mapInstance) - mapInstance = Map() - f.close() - return lMap - - def _deleteDBtables(self): - self._db.dropTable(self._table) - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/TestProfiles.py --- a/commons/pyRepetUnit/profilesDB/tests/TestProfiles.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,151 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.profilesDB.Profiles import Profiles -from commons.core.utils.FileUtils import FileUtils - - -class TestProfiles(unittest.TestCase): - - def createInputDBFile(self): - f = open(self._inputDBFile, "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME fn3\n") - f.write("ACC PF00041\n") - f.write("DESC Fibronectin type III domain\n") - f.write("LENG 84\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 2.0;\n") - f.write("TC 7.9 2.1;\n") - f.write("NC 7.0 1.1;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME truc\n") - f.write("ACC PF00042.012\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0;\n") - f.write("TC 7.9 0.1;\n") - f.write("NC 7.8 0.1;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.close() - - - def setUp(self): - self.profiles = Profiles() - self._inputDBFile = "dummy.hmm" - - - def testRead(self): - # atomic profiles file - self.createInputDBFile() - file = open( self._inputDBFile ) - profile = self.profiles - profile.read(file) - self.assertEqual("fn3",profile.name) - self.assertEqual("Fibronectin type III domain", profile.desc) - self.assertEqual(84, profile.length) - self.assertEqual("PF00041", profile.accNumber) - self.assertEqual(2.0, profile.GA_cut_off) - profile.read(file) - self.assertEqual("truc",profile.name) - self.assertEqual("", profile.desc) - self.assertEqual(123, profile.length) - self.assertEqual("PF00042.012", profile.accNumber) - self.assertEqual(-1.0, profile.GA_cut_off) - os.system("rm " + self._inputDBFile) - # empty file - f = open(self._inputDBFile, "w") - f.close() - file = open( self._inputDBFile ) - profile = self.profiles - profile.read(file) - self.assertEqual(None, profile.name) - self.assertEqual(None, profile.desc) - self.assertEqual(None, profile.length) - self.assertEqual(None, profile.accNumber) - self.assertEqual(None, profile.GA_cut_off) - os.system("rm " + self._inputDBFile) - - - def testReadAndRetrieve(self): - # atomic profiles file - self.createInputDBFile() - file = open( self._inputDBFile ) - profile = self.profiles - myProfile = profile.readAndRetrieve(file) - self.assertEqual("fn3",profile.name) - self.assertEqual("Fibronectin type III domain", profile.desc) - self.assertEqual(84, profile.length) - self.assertEqual("PF00041", profile.accNumber) - self.assertEqual(2.0, profile.GA_cut_off) - myProfile2 = profile.readAndRetrieve(file) - self.assertEqual("truc",profile.name) - self.assertEqual("", profile.desc) - self.assertEqual(123, profile.length) - self.assertEqual("PF00042.012", profile.accNumber) - self.assertEqual(-1.0, profile.GA_cut_off) - #I check if retrieve work like I want - f = open("retrieveResult", "w") - for item in myProfile: - f.write(item) - for item in myProfile2: - f.write(item) - f.close() - self.assertTrue(FileUtils.are2FilesIdentical("retrieveResult", self._inputDBFile)) - os.system("rm " + self._inputDBFile) - os.system("rm retrieveResult") - # empty file - f = open(self._inputDBFile, "w") - f.close() - file = open( self._inputDBFile ) - profile = self.profiles - myProfile3 = profile.readAndRetrieve(file) - self.assertEqual(None, profile.name) - self.assertEqual(None, profile.desc) - self.assertEqual(None, profile.length) - self.assertEqual(None, profile.accNumber) - self.assertEqual(None, profile.GA_cut_off) - self.assertEqual(None, myProfile3) - os.system("rm " + self._inputDBFile) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/TestProfilesDB2Map.py --- a/commons/pyRepetUnit/profilesDB/tests/TestProfilesDB2Map.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,199 +0,0 @@ -import os -import unittest -from commons.pyRepetUnit.profilesDB.Profiles import Profiles -from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank -import commons.pyRepetUnit.profilesDB.ProfilesDB2Map -from commons.core.utils.FileUtils import FileUtils - - -class TestProfilesDB2Map(unittest.TestCase): - - def setUp(self): - self.profilesDB2Map = commons.pyRepetUnit.profilesDB.ProfilesDB2Map.ProfilesDB2Map() - - - def testWriteProfilesDB(self): - # atomic hmmerpfam file - profilesDB = ProfilesDatabank() - profiles1 = Profiles() - profiles1.name = "fn3" - profiles1.desc = "Fibronectin type III domain" - profiles1.length = 84 - profilesDB.append( profiles1 ) - profiles2 = Profiles() - profiles2.name = "truc" - profiles2.desc = "" - profiles2.length = 123 - profilesDB.append( profiles2 ) - file = open( "expectedFile", "w" ) - file.write( "fn3\tFibronectin type III domain\t1\t84\n" ) - file.write( "truc\t\t1\t123\n" ) - file.close() - self.profilesDB2Map.setOutputFile("testOutput.map") - self.profilesDB2Map._writeMapFile(profilesDB) - self.assertTrue(FileUtils.are2FilesIdentical("expectedFile", "testOutput.map")) - os.remove("expectedFile") - os.remove("testOutput.map") - #empty profileDB object - profilesDB = ProfilesDatabank() - self.profilesDB2Map._writeMapFile(profilesDB) - self.assertFalse(FileUtils.isRessourceExists("testOutput.map")) - - def testReadProfilesDB(self): - # atomic hmmerpfam file - f = open("dummy.hmm", "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME fn3\n") - f.write("ACC PF00041\n") - f.write("DESC Fibronectin type III domain\n") - f.write("LENG 84\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0\n") - f.write("TC 7.9 0.1\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME truc\n") - f.write("ACC PF00041\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0\n") - f.write("TC 7.9 0.1\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.close() - self.profilesDB2Map.setInputFile("dummy.hmm") - pfamDB = self.profilesDB2Map._readProfilesDB() - expectedProfiles1 = Profiles() - expectedProfiles1.name = "fn3" - expectedProfiles1.desc = "Fibronectin type III domain" - expectedProfiles1.length = 84 - expectedProfiles2 = Profiles() - expectedProfiles2.name = "truc" - expectedProfiles2.desc = "" - expectedProfiles2.length = 123 - self.assertEqual(expectedProfiles1.name, pfamDB.get(0).name) - self.assertEqual(expectedProfiles1.desc, pfamDB.get(0).desc) - self.assertEqual(expectedProfiles1.length, pfamDB.get(0).length) - self.assertEqual(expectedProfiles2.name, pfamDB.get(1).name) - self.assertEqual(expectedProfiles2.desc, pfamDB.get(1).desc) - self.assertEqual(expectedProfiles2.length, pfamDB.get(1).length) - os.remove("dummy.hmm") - #empty pfamDB file - file = open( "pfamDBEmpty", "w" ) - file.close() - self.profilesDB2Map.setInputFile("pfamDBEmpty") - pfamDB2 = self.profilesDB2Map._readProfilesDB() - self.assertEquals(None, pfamDB2) - os.system("rm pfamDBEmpty") - - def testRun(self): - f = open("dummy.hmm", "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME fn3\n") - f.write("ACC PF00041\n") - f.write("DESC Fibronectin type III domain\n") - f.write("LENG 84\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0\n") - f.write("TC 7.9 0.1\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME truc\n") - f.write("ACC PF00041\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0\n") - f.write("TC 7.9 0.1\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.close() - self.profilesDB2Map.setInputFile("dummy.hmm") - self.profilesDB2Map.setOutputFile("testOutput.map") - self.profilesDB2Map.run() - file = open( "expectedFile", "w" ) - file.write( "fn3\tFibronectin type III domain\t1\t84\n" ) - file.write( "truc\t\t1\t123\n" ) - file.close() - self.assertTrue(FileUtils.are2FilesIdentical("expectedFile", "testOutput.map")) - os.remove("expectedFile") - os.remove("testOutput.map") - os.remove("dummy.hmm") - - -if __name__ == "__main__": - unittest.main() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/TestProfilesDatabankUtils.py --- a/commons/pyRepetUnit/profilesDB/tests/TestProfilesDatabankUtils.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -import unittest -import os -from commons.pyRepetUnit.profilesDB.Profiles import Profiles -from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils - - -class TestProfilesDatabankUtils( unittest.TestCase ): - - def setUp( self ): - self.profilesDBUtils = ProfilesDatabankUtils() - - - def test_read_emptyFile( self ): - file = open( "pfamDBEmpty", "w" ) - file.close() - pfamDB2 = self.profilesDBUtils.read( "pfamDBEmpty" ) - self.assertEquals( None, pfamDB2 ) - os.remove( "pfamDBEmpty" ) - - - def test_read( self ): - f = open("dummy.hmm", "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME fn3\n") - f.write("ACC PF00041\n") - f.write("DESC Fibronectin type III domain\n") - f.write("LENG 84\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0\n") - f.write("TC 7.9 0.1\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME truc\n") - f.write("ACC PF00041\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 7.8 -1.0\n") - f.write("TC 7.9 0.1\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.close() - pfamDB = self.profilesDBUtils.read("dummy.hmm") - expectedProfiles1 = Profiles() - expectedProfiles1.name = "fn3" - expectedProfiles1.desc = "Fibronectin type III domain" - expectedProfiles1.length = 84 - expectedProfiles2 = Profiles() - expectedProfiles2.name = "truc" - expectedProfiles2.desc = "" - expectedProfiles2.length = 123 - - self.assertEqual( expectedProfiles1.name, pfamDB.get(0).name ) - self.assertEqual( expectedProfiles1.desc, pfamDB.get(0).desc ) - self.assertEqual( expectedProfiles1.length, pfamDB.get(0).length ) - self.assertEqual( expectedProfiles2.name, pfamDB.get(1).name ) - self.assertEqual( expectedProfiles2.desc, pfamDB.get(1).desc ) - self.assertEqual( expectedProfiles2.length, pfamDB.get(1).length ) - - os.remove("dummy.hmm") - - -if __name__ == "__main__": - unittest.main() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/Test_F_CompleteProfilDB.py --- a/commons/pyRepetUnit/profilesDB/tests/Test_F_CompleteProfilDB.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils - -class Test_F_CompleteProfilDB(unittest.TestCase): - - def setUp(self): - self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt" - self._filePfamList = "./datas/ListpfamAccNumber.txt" - self._profilesDB = "./datas/profilesDBTest.hmm" - self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'" - self._expectedFile(self._expectedGetzCmd) - self._outputFileName = "./datas/outputFile" - self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'" - - def tearDown(self): - os.remove(self._outputFileName) - os.remove(self._expectedGetzCmdFile) - - def testCompleteProfilesDBScriptByName(self): - Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._fileProfilesList + " -o " + self._outputFileName + "\n" - os.system (Cmd) - self.assertTrue (FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile)) - - def testCompleteProfilesDBScriptByAccession(self): - self._expectedFile(self._expectedGetzCmd2) - Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._filePfamList + " -o " + self._outputFileName + " -n\n" - os.system(Cmd) - self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile)) - - def _expectedFile(self, expectedGetzCmd): - self._expectedGetzCmdFile = "./datas/expectedCmdFile" - f = open(self._expectedGetzCmdFile, 'w') - f.write(expectedGetzCmd) - f.close - - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/Test_F_ProfilesDB2Map.py --- a/commons/pyRepetUnit/profilesDB/tests/Test_F_ProfilesDB2Map.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -import os -import unittest -from commons.core.utils.FileUtils import FileUtils -from commons.pyRepetUnit.profilesDB.ProfilesDB2Map import ProfilesDB2Map - -class Test_F_ProfilesDB2Map(unittest.TestCase): - - def setUp(self): - self.profilesDB2Map = ProfilesDB2Map() - self._inputFile = "./datas/myhmms" - self._outputFile = "./datas/outputFile.map" - self._expectedFile = "./datas/profiles.map" - self._createProfilesMapFile() - - def tearDown(self): - os.remove(self._outputFile) - os.remove(self._expectedFile) - - def testRun(self): - self.profilesDB2Map.setInputFile(self._inputFile) - self.profilesDB2Map.setOutputFile(self._outputFile) - pfamDB = self.profilesDB2Map.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile)) - - def _createProfilesMapFile(self): - f = open(self._expectedFile, "w") - f.write("rrm\t\t1\t77\n") - f.write("fn3\tFibronectin type III domain\t1\t84\n") - f.write("pkinase\tProtein kinase domain\t1\t294\n") - f.close() - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/Test_F_ProfilesDB4Repet.py --- a/commons/pyRepetUnit/profilesDB/tests/Test_F_ProfilesDB4Repet.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils - -class Test_F_ProfilesDB4Repet(unittest.TestCase): - - def setUp(self): - self._inputDBFile = "%s/Tools/ProfilesDB4Repet_v2.hmm" % os.environ["REPET_DATA"] - self._outputDBFile = "output.hmm" - - def tearDown(self): - os.remove(self._outputDBFile) - - def test_run_as_script(self): - cmd = "python ../ProfilesDB4Repet.py -i " + self._inputDBFile + " -o " + self._outputDBFile - os.system(cmd) - self.assertEqual(FileUtils.getNbLinesInSingleFile(self._outputDBFile), 375854) - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/Test_ProfilesDB4Repet.py --- a/commons/pyRepetUnit/profilesDB/tests/Test_ProfilesDB4Repet.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,442 +0,0 @@ -import unittest -import os -from commons.pyRepetUnit.profilesDB.ProfilesDB4Repet import ProfilesDB4Repet -from commons.core.utils.FileUtils import FileUtils - - -class Test_ProfilesDB4Repet(unittest.TestCase): - - def setUp(self): - self._inputDBFile = "./datas/dummy.hmm" - self._expectedDBFile = "./datas/expected.hmm" - self._outputDBFile = "./datas/output.hmm" - self._profilesDB4Repet = ProfilesDB4Repet() - - def tearDown(self): - os.remove(self._expectedDBFile) - os.remove(self._outputDBFile) - os.remove(self._inputDBFile) - - def testFormateProfilesDB4Repet(self): - self._createHmmFile() - self._createExpectedHmmFile() - self._profilesDB4Repet.setInputFile(self._inputDBFile) - self._profilesDB4Repet.setOutputFile(self._outputDBFile) - self._profilesDB4Repet.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile)) - - def test_formateProfilesDB4Repet_GypsyDB(self): - self._createHmmFile_GypsyDB() - self._createExpectedHmmFile_GypsyDB() - self._profilesDB4Repet.setInputFile(self._inputDBFile) - self._profilesDB4Repet.setOutputFile(self._outputDBFile) - self._profilesDB4Repet.run() - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile)) - - def _createExpectedHmmFile(self): - f = open(self._expectedDBFile, "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME PF07582.4_AP_endonuc_2_N_APE_20.9\n") - f.write("ACC PF07582.4\n") - f.write("DESC AP endonuclease family 2 C terminus\n") - f.write("LENG 84\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 20.9000 20.9000;\n") - f.write("TC 21.2000 21.2000;\n") - f.write("NC 20.8000 20.8000;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME PF01606.8_Arteri_env_ENV_25.0\n") - f.write("ACC PF01606.8\n") - f.write("DESC DESC Arterivirus envelope protein\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 21.0000 25.0000;\n") - f.write("TC 306.0000 406.0000;\n") - f.write("NC 10.3000 11.3000;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME PF01606.8_Dummy_name_OTHER_25.0\n") - f.write("ACC PF01606.8\n") - f.write("DESC Dummy Description\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 21.0000 25.0000;\n") - f.write("TC 306.0000 406.0000;\n") - f.write("NC 10.3000 11.3000;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.close() - - def _createHmmFile(self): - f = open(self._inputDBFile, "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME AP_endonuc_2_N\n") - f.write("ACC PF07582.4\n") - f.write("DESC AP endonuclease family 2 C terminus\n") - f.write("LENG 84\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 20.9000 20.9000;\n") - f.write("TC 21.2000 21.2000;\n") - f.write("NC 20.8000 20.8000;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME Arteri_env\n") - f.write("ACC PF01606.8\n") - f.write("DESC DESC Arterivirus envelope protein\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 21.0000 25.0000;\n") - f.write("TC 306.0000 406.0000;\n") - f.write("NC 10.3000 11.3000;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME Dummy_name\n") - f.write("ACC PF01606.8\n") - f.write("DESC Dummy Description\n") - f.write("LENG 123\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS yes\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -A myhmms fn3.sto\n") - f.write("COM hmmcalibrate myhmms\n") - f.write("NSEQ 108\n") - f.write("DATE Thu Jan 8 17:50:26 2009\n") - f.write("CKSUM 6130\n") - f.write("GA 21.0000 25.0000;\n") - f.write("TC 306.0000 406.0000;\n") - f.write("NC 10.3000 11.3000;\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") - f.write("EVD -45.973442 0.237545\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write("COM hmmcalibrate myhmms\n") - f.write(" -13 * -6756\n") - f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") - f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") - f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") - f.write("//\n") - f.close() - - def _createExpectedHmmFile_GypsyDB(self): - f = open(self._expectedDBFile, "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME _AP_17_6_AP_NA\n") - f.write("LENG 97\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n") - f.write("COM hmmcalibrate output/AP_17_6.hmm\n") - f.write("NSEQ 7\n") - f.write("DATE Tue Nov 3 12:11:06 2009\n") - f.write("CKSUM 7992\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -62.517647 0.206604\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -193 * -2999\n") - f.write("1 -2855 -2358 -5336 -4935 -1676 -5061 -4339 3600 -4729 809 -490 -4773 -4645 -4163 -4574 -4431 -2811 -4 -3348 -3185 1\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n") - f.write("2 -3852 -3208 -4863 -4900 -13 -4670 -1533 -2120 -4409 1711 -1558 -3673 -4546 -3569 -4004 -4001 -3768 -2552 -797 4153 97\n") - f.write("- * * * * * * * * * * * * * * * * * * * *\n") - f.write("- * * * * * * * * 0 \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME _ENV_athila_ENV_NA\n") - f.write("LENG 647\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") - f.write("COM hmmcalibrate ENV_athila.hmm\n") - f.write("NSEQ 3\n") - f.write("DATE Fri Sep 9 13:24:44 2005\n") - f.write("CKSUM 3522\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -12.496953 0.641902\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -576 * -1603\n") - f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") - f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME _ENVathila_OTHER_NA\n") - f.write("LENG 647\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") - f.write("COM hmmcalibrate ENV_athila.hmm\n") - f.write("NSEQ 3\n") - f.write("DATE Fri Sep 9 13:24:44 2005\n") - f.write("CKSUM 3522\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -12.496953 0.641902\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -576 * -1603\n") - f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") - f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME _MOV_cavemovirus_OTHER_NA\n") - f.write("LENG 302\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n") - f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n") - f.write("NSEQ 2\n") - f.write("DATE Tue Nov 3 11:25:12 2009\n") - f.write("CKSUM 1918\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -135.876633 0.154850\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -585 * -1585\n") - f.write("1 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 5\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n") - f.write("2 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 6\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") - f.write("3 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 7\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") - f.write("//\n") - f.close() - - def _createHmmFile_GypsyDB(self): - f = open(self._inputDBFile, "w") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME AP_17_6\n") - f.write("LENG 97\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n") - f.write("COM hmmcalibrate output/AP_17_6.hmm\n") - f.write("NSEQ 7\n") - f.write("DATE Tue Nov 3 12:11:06 2009\n") - f.write("CKSUM 7992\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -62.517647 0.206604\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -193 * -2999\n") - f.write("1 -2855 -2358 -5336 -4935 -1676 -5061 -4339 3600 -4729 809 -490 -4773 -4645 -4163 -4574 -4431 -2811 -4 -3348 -3185 1\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n") - f.write("2 -3852 -3208 -4863 -4900 -13 -4670 -1533 -2120 -4409 1711 -1558 -3673 -4546 -3569 -4004 -4001 -3768 -2552 -797 4153 97\n") - f.write("- * * * * * * * * * * * * * * * * * * * *\n") - f.write("- * * * * * * * * 0 \n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME ENV_athila\n") - f.write("LENG 647\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") - f.write("COM hmmcalibrate ENV_athila.hmm\n") - f.write("NSEQ 3\n") - f.write("DATE Fri Sep 9 13:24:44 2005\n") - f.write("CKSUM 3522\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -12.496953 0.641902\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -576 * -1603\n") - f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") - f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME ENVathila\n") - f.write("LENG 647\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") - f.write("COM hmmcalibrate ENV_athila.hmm\n") - f.write("NSEQ 3\n") - f.write("DATE Fri Sep 9 13:24:44 2005\n") - f.write("CKSUM 3522\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -12.496953 0.641902\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -576 * -1603\n") - f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") - f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") - f.write("//\n") - f.write("HMMER2.0 [2.3.2]\n") - f.write("NAME MOV_cavemovirus\n") - f.write("LENG 302\n") - f.write("ALPH Amino\n") - f.write("RF no\n") - f.write("CS no\n") - f.write("MAP yes\n") - f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n") - f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n") - f.write("NSEQ 2\n") - f.write("DATE Tue Nov 3 11:25:12 2009\n") - f.write("CKSUM 1918\n") - f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") - f.write("NULT -4 -8455\n") - f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") - f.write("EVD -135.876633 0.154850\n") - f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") - f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") - f.write(" -585 * -1585\n") - f.write("1 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 5\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n") - f.write("2 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 6\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") - f.write("3 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 7\n") - f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") - f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") - f.write("//\n") - f.close() - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/completeProfilesDBFromAFileWithProfilesList_script.py --- a/commons/pyRepetUnit/profilesDB/tests/completeProfilesDBFromAFileWithProfilesList_script.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ -#!/usr/bin/env python -''' -Created on 19 mai 2009 - -@author: choede -''' - -import commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber -import user, os, sys, getopt, exceptions -from pyRepet.util.file.FileUtils import * - -#------------------------------------------------------------------------------ - -def help(): - - """ - Give the command-line parameters. - """ - - print "" - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -d: name of profiles databank (format='pfam')" - print " -l: name of the profiles list file (name or accession number, default=profiles name)" - print " -o: name of the output file (default=profiles list file+'.getz')" - print " -v: verbose (default=0/1/2)" - print " -n: pfam accession number (default=Not set)" - print "" - -#------------------------------------------------------------------------------ - -def main(): - - DBFileName = "" - outFileName = "" - verbose = 0 - listFileName = "" - accNumber = False - - try: - opts,args=getopt.getopt(sys.argv[1:],"hd:l:o:v:n") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-d": - DBFileName = a - elif o == "-l": - listFileName = a - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - elif o == "-n": - accNumber = True - - - if DBFileName == "" or listFileName == "": - print "*** Error: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "beginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s.getz" % ( listFileName ) - - CompleteProfilesDB = commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber() - CompleteProfilesDB.setProfilesDBFile ( DBFileName ) - CompleteProfilesDB.setProfilesToAdd ( listFileName ) - if accNumber == True: - CompleteProfilesDB.setPfamAccNumberKeys () - if verbose > 0: - print "The profiles list is in Accession number" - sys.stdout.flush() - getzCmd = CompleteProfilesDB.CmdToCompleteProfileDB() - f = open( outFileName , 'w') - f.write ( getzCmd ) - f.close() - - if verbose > 0: - fileUtils = FileUtils( ) - if fileUtils.isRessourceExists( outFileName ) and not(fileUtils.isFileEmpty( outFileName )): - print "%s finished successfully" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - else: - print "warning %s execution failed" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#------------------------------------------------------------------------------ - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/datas/ListPfamProfilsInRepbase.txt --- a/commons/pyRepetUnit/profilesDB/tests/datas/ListPfamProfilsInRepbase.txt Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -RVT_1 -RVT_2 -rve -zf-CCHC -DDE -hATC -Hermes_DBD -MULE -Exo_endo_phos -Peptidase_C27 -Transposase_mut -InvE -Retrotrans_gag -Chromo -TLV_coat - - diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/datas/ListpfamAccNumber.txt --- a/commons/pyRepetUnit/profilesDB/tests/datas/ListpfamAccNumber.txt Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -PF00075 -PF00077 -PF00078 -PF00424 -PF05407 -PF00469 diff -r 9bcfa7936eec -r c265f13066d8 commons/pyRepetUnit/profilesDB/tests/datas/myhmms --- a/commons/pyRepetUnit/profilesDB/tests/datas/myhmms Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1433 +0,0 @@ -HMMER2.0 [2.3.2] -NAME rrm -LENG 77 -ALPH Amino -RF no -CS no -MAP yes -COM hmmbuild -A myhmms rrm.sto -COM hmmcalibrate myhmms -NSEQ 90 -DATE Thu Jan 8 17:50:18 2009 -CKSUM 8325 -XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 -NULT -4 -8455 -NULE 595 -1558 85 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TestAcceptanceProfilesDB4Repet -import TestInsertProfilesMapFileInDB - -def main(): - - profilesDBTestSuite = unittest.TestSuite() - profilesDBTestSuite.addTest(unittest.makeSuite(TestProfilesDB2Map.TestProfilesDB2Map,'test')) - profilesDBTestSuite.addTest(unittest.makeSuite(TestAcceptanceProfilesDB2Map.TestAcceptanceProfilesDB2Map,'test')) - profilesDBTestSuite.addTest(unittest.makeSuite(TestCompleteProfilesDBFromProfilesNameListOrAccNumber.TestCompleteProfilesDBFromProfilesNameListOrAccNumber, 'test')) - profilesDBTestSuite.addTest(unittest.makeSuite(TestAcceptanceCompleteProfilDB_script.TestAcceptanceCompleteProfilDB_script, 'test')) - profilesDBTestSuite.addTest(unittest.makeSuite(TestProfilesDB4Repet.TestProfilesDB4Repet, 'test')) - profilesDBTestSuite.addTest(unittest.makeSuite(TestAcceptanceProfilesDB4Repet.TestAcceptanceProfilesDB4Repet, 'test')) - profilesDBTestSuite.addTest(unittest.makeSuite(TestInsertProfilesMapFileInDB.TestInsertProfilesMapFileInDB, 'test')) - - runner = unittest.TextTestRunner(sys.stderr, 2, 2) - runner.run(profilesDBTestSuite) - - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/AlignTEOnGenomeAccordingToAnnotation.py --- a/commons/tools/AlignTEOnGenomeAccordingToAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,282 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import re -import os -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker -import subprocess -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.core.coord.PathUtils import PathUtils -from commons.core.coord.SetUtils import SetUtils -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.coord.Set import Set -from commons.core.sql.DbFactory import DbFactory - -## Align a TE on genome according to annotation - -LOG_DEPTH = "repet.tools" - -class AlignTEOnGenomeAccordingToAnnotation(object): - - def __init__(self, pathTableName = "", queryTableName = "", subjectTableName = "", mergeSamePathId = False, outTableName = "", matchPenality=10, mism=8, gapo=16, gape=4, gapl=20, configFileName = "", doClean = False, verbosity = 0): - self._pathTableName = pathTableName - self._queryTableName = queryTableName - self._subjectTableName = subjectTableName - self._mergeSamePathId = mergeSamePathId - self.setOutTableName(outTableName) - self._matchPenality = matchPenality - self._mismatch = mism - self._gapOpening = gapo - self._gapExtend = gape - self._gapLength = gapl - self._configFileName = configFileName - self._doClean = doClean - self._verbosity = verbosity - self._iDb = None - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "Align a TE on genome according to annotation." - epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python AlignTEOnGenomeAccordingToAnnotation.py -p DmelChr4_chr_allTEs_nr_noSSR_join_path -q DmelChr4_chr_seq -s DmelChr4_refTEs_seq -v 0" - epilog += "\n" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-p", "--path", dest = "pathTableName", action = "store", type = "string", help = "path table name [compulsory] [format: path]", default = "") - parser.add_option("-q", "--query", dest = "queryTableName", action = "store", type = "string", help = "query table name [compulsory] [format: seq]", default = "") - parser.add_option("-s", "--subject", dest = "subjectTableName", action = "store", type = "string", help = "subject table name [compulsory] [format: seq]", default = "") - parser.add_option("-m", "--merge", dest = "mergeSamePathId", action = "store_true", help = "merge joined matchs [optional] [default: False]", default = False) - parser.add_option("-o", "--out", dest = "outTableName", action = "store", type = "string", help = "output table name [default: _align]", default = "") - #TODO: add options for : matchPenality=10, mism=8, gapo=16, gape=4, gapl=20 - parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "configuration file name (e.g. TEannot.cfg)", default = "") - #NOTE: doClean unused -# parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setPathTableName(options.pathTableName) - self.setQueryTableName(options.queryTableName) - self.setSubjectTableName(options.subjectTableName) - self.setMergeSamePathId(options.mergeSamePathId) - self.setOutTableName(options.outTableName) - self.setConfigFileName(options.configFileName) -# self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def _checkConfig(self): - iConfigRules = ConfigRules() - iConfigRules.addRuleSection(section="", mandatory=True) - iConfigRules.addRuleOption(section="", option ="fasta_name", mandatory=True, type="string") - iConfigRules.addRuleOption(section="", option ="clean", mandatory=True, type="bool") - iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) - iConfig = iConfigChecker.getConfig() - self._setAttributesFromConfig(iConfig) - - def _setAttributesFromConfig(self, iConfig): - self.setOutTableName(self._outTableName) - self.setDoClean(iConfig.get("", "clean")) - - def setPathTableName(self, pathTableName): - self._pathTableName = pathTableName - - def setQueryTableName(self, queryTableName): - self._queryTableName = queryTableName - - def setSubjectTableName(self, subjectTableName): - self._subjectTableName = subjectTableName - - def setMergeSamePathId(self, mergeSamePathId): - self._mergeSamePathId = mergeSamePathId - - def setOutTableName(self, outTableName): - if outTableName == "": - self._outTableName = "%s_align" % self._pathTableName - else: - self._outTableName = outTableName - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def setDbInstance(self, iDb): - self._iDb = iDb - - def _checkOptions(self): - if self._pathTableName == "" or not self._iDb.doesTableExist(self._pathTableName): - self._logAndRaise("ERROR: Missing path table") - if self._queryTableName == "" or not self._iDb.doesTableExist(self._queryTableName): - self._logAndRaise("ERROR: Missing query table") - if self._subjectTableName == "" or not self._iDb.doesTableExist(self._subjectTableName): - self._logAndRaise("ERROR: Missing subject table") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def alignBioseqWithNWalign(self, iBioseq1, iBioseq2): - fastaFileName1 = "seqtoalign1.tmp" - iBioseq1.save(fastaFileName1) - fastaFileName2 = "seqtoalign2.tmp" - iBioseq2.save(fastaFileName2) - alignBioseqDBFileName = "aligned.tmp" - cmd = "NWalign" - cmd += " %s" % fastaFileName1 - cmd += " %s" % fastaFileName2 - cmd += " -m %s" % self._matchPenality - cmd += " -d %s" % self._mismatch - cmd += " -g %s" % self._gapOpening - cmd += " -e %s" % self._gapExtend - cmd += " -l %s" % self._gapLength - cmd += " -D" - cmd += " -o %s" % alignBioseqDBFileName - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - iAlignedBioseqDB = AlignedBioseqDB() - iAlignedBioseqDB.load(alignBioseqDBFileName) - os.remove(fastaFileName1) - os.remove(fastaFileName2) - os.remove(alignBioseqDBFileName) - return iAlignedBioseqDB - - def alignSeqAccordingToPathAndBuildAlignedSeqTable(self): - if self._iDb.doesTableExist(self._outTableName): - self._logAndRaise("ERROR: out table %s already exists" % self._outTableName) - - #TODO: create alignedSeq table in DbMySql... - sqlCmd="CREATE TABLE %s (path int unsigned, query_aligned_seq longtext, subject_aligned_seq longtext, score int unsigned, identity float unsigned)" % self._outTableName - self._iDb.execute(sqlCmd) - - iQueryTSA = TableSeqAdaptator(self._iDb, self._queryTableName) - iSubjectTSA = TableSeqAdaptator(self._iDb, self._subjectTableName) - iTPA = TablePathAdaptator(self._iDb, self._pathTableName) - - if self._mergeSamePathId: - lPathId = iTPA.getIdList() - pathNb = len(lPathId) - count = 0 - for pathNum in lPathId: - self._log.debug(count,"/",pathNb,"=>path",pathNum,"...") - lPaths = iTPA.getPathListFromId(pathNum) - #TODO: getSetListFromQueries() call getSubjectAsSetOfQuery() => "reverse complement" the query (coordinates are inversed, so getBioseq() will take the reverse-comp.) : is it correct ? - lQuerySets = PathUtils.getSetListFromQueries(lPaths) - #NOTE: merge sets if overlap - lQueryMergedSets = SetUtils.mergeSetsInList(lQuerySets) - #TODO: getBioseqFromSetList() build a sequence that does not exist : is it correct ? - iQueryBioseq = iQueryTSA.getBioseqFromSetList(lQueryMergedSets) - lSubjectSets = PathUtils.getSetListFromSubjects(lPaths) - #TODO: no merge for subjects : is it correct ? matcher allow overlap on query and not on subject ? - iSubjectBioseq = iSubjectTSA.getBioseqFromSetList(lSubjectSets) - iAlignedBioseqDB = self.alignBioseqWithNWalign(iQueryBioseq, iSubjectBioseq) - self._insertAlignedBioseqDBWithScoreAndIdentityInTable(pathNum, iAlignedBioseqDB) - else: - lPathId = iTPA.getIdList() - pathNb = len(lPathId) - count = 0 - for pathNum in lPathId: - self._log.debug(count,"/",pathNb,"=>path",pathNum,"...") - lPaths = iTPA.getPathListFromId(pathNum) - queryName = lPaths[0].getQueryName() - subjectName = lPaths[0].getSubjectName() - lQueryStart = [] - lQueryEnd = [] - lSubjectStart = [] - lSubjectEnd = [] - isReversed = not lPaths[0].isSubjectOnDirectStrand() - for iPath in lPaths: - lQueryStart.append(iPath.getQueryStart()) - lQueryEnd.append(iPath.getQueryEnd()) - lSubjectStart.append(iPath.getSubjectStart()) - lSubjectEnd.append(iPath.getSubjectEnd()) - queryStart = min(lQueryStart) - queryEnd = max(lQueryEnd) - if isReversed: - subjectStart = max(lSubjectStart) - subjectEnd = min(lSubjectEnd) - else: - subjectStart = min(lSubjectStart) - subjectEnd = max(lSubjectEnd) - lQuerySets = [Set(pathNum,subjectName, queryName,queryStart,queryEnd)] - lSubjectSets = [Set(pathNum,queryName, subjectName,subjectStart,subjectEnd)] - - iQueryBioseq = iQueryTSA.getBioseqFromSetList(lQuerySets) - iSubjectBioseq = iSubjectTSA.getBioseqFromSetList(lSubjectSets) - iAlignedBioseqDB = self.alignBioseqWithNWalign(iQueryBioseq, iSubjectBioseq) - self._insertAlignedBioseqDBWithScoreAndIdentityInTable(pathNum, iAlignedBioseqDB) - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - if self._configFileName: - self._checkConfig() - self._iDb = DbFactory.createInstance() - self._checkOptions() - self._log.info("START AlignTEOnGenomeAccordingToAnnotation") - self._log.debug("path table name: %s" % self._pathTableName) - self._log.debug("query table name: %s" % self._queryTableName) - self._log.debug("subject table name: %s" % self._subjectTableName) - self.alignSeqAccordingToPathAndBuildAlignedSeqTable() - self._iDb.close() - self._log.info("END AlignTEOnGenomeAccordingToAnnotation") - - def _insertAlignedBioseqDBWithScoreAndIdentityInTable(self, pathNum, iAlignedBioseqDB): - scoreWithEndLine = re.split("Score=", iAlignedBioseqDB.db[0].header)[1] - score = int(scoreWithEndLine.split()[0]) - - identity = re.split("Identity=", scoreWithEndLine)[1] - if identity == "nan": - identity = "0.0" - identity = float(identity)*100.0 - - #TODO: create TableAlignedSeqAdaptator (to use insert...) - sqlCmd = 'INSERT INTO %s VALUES (%d,"%s","%s", %d,%f);' % (self._outTableName, pathNum, iAlignedBioseqDB.db[0].sequence, iAlignedBioseqDB.db[1].sequence, score, identity) - self._iDb.execute(sqlCmd) - - self._log.debug("header:", iAlignedBioseqDB.db[0].header) - self._log.debug("path", pathNum, "Score=", score, "Identity=", identity, "ok") - self._log.debug(iAlignedBioseqDB.db[0].sequence[:80]) - self._log.debug(iAlignedBioseqDB.db[1].sequence[:80]) - -if __name__ == "__main__": - iLaunch = AlignTEOnGenomeAccordingToAnnotation() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/AnnotationStats.py --- a/commons/tools/AnnotationStats.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,374 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -##@file -# Give summary information on a TE annotation table. -# options: -# -h: this help -# -t: analysis type (default = 1, 1: per transposable element (TE), 2: per cluster, 3: per classification, 4: with map input file) -# -p: name of the table (_path) or file (.path) with the annotated TE copies -# -s: name of the table (_seq) or file (.fasta or .fa) with the TE reference sequences -# -g: length of the genome (in bp) -# -m: name of the file with the group and the corresponding TE names (format = 'map') -# -o: name of the output file (default = pathTableName + '_stats.txt') -# -C: name of the configuration file to access MySQL (e.g. 'TEannot.cfg') -# -c: remove map files and blastclust file (if analysis type is 2 or 3) -# -I: identity coverage threshold (default = 0) -# -L: length coverage threshold (default=0.8) -# -v: verbosity level (default = 0) - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.stat.Stat import Stat -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.tools.getCumulLengthFromTEannot import getCumulLengthFromTEannot - -LOG_DEPTH = "repet.tools" - -#TODO: use templating engine instead of raw strings for AnnotationStatsWriter -class AnnotationStats( object ): - - def __init__(self, analysisName="TE", clusterFileName="",seqTableName="", pathTableName="", genomeLength=0, statsFileName="", globalStatsFileName="", verbosity=3): - self._analysisName = analysisName - self._clusterFileName = clusterFileName - self._seqTableName = seqTableName - self._pathTableName = pathTableName - self._genomeLength = genomeLength - self._statsFileName = statsFileName - self._globalStatsFileName = globalStatsFileName - self._iDb = None - self._iTablePathAdaptator = None - self._iTableSeqAdaptator = None - self._save = False - self._clean = False - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def setCoverageThreshold( self, lengthThresh ): - self._coverageThreshold = float(lengthThresh) - - def setIdentityThreshold( self, identityThresh ): - self._identityThreshold = int(identityThresh) - - def setAnalyseType(self, analyseType): - self._analyseType = str(analyseType) - - def setPathTableName(self, pathTableName): - self._pathTableName = pathTableName - - def setDBInstance(self, iDb): - self._iDb = iDb - - def setTablePathAdaptator(self, iTablePathAdaptator): - self._iTablePathAdaptator = iTablePathAdaptator - - def setTableSeqAdaptator(self, iTableSeqAdaptator): - self._iTableSeqAdaptator = iTableSeqAdaptator - - ## Get the coverage of TE copies for a given family (using 'mapOp') - # - # @param consensus string name of a TE family ('subject_name' in the 'path' table) - # @return cumulCoverage integer cumulative coverage - # - def getCumulCoverage( self, consensus = "" ): - gclft = getCumulLengthFromTEannot() - gclft.setInputTable( self._pathTableName ) - gclft.setTErefseq( consensus ) - gclft.setClean() - gclft._db = self._iDb - gclft._tpA = self._iTablePathAdaptator - mapFileName = gclft.getAllSubjectsAsMapOfQueries() - mergeFileName = gclft.mergeRanges( mapFileName ) - cumulCoverage = gclft.getCumulLength( mergeFileName ) #self._iTablePathAdaptator.getCumulPathLength_from_subject( consensus ) - return cumulCoverage - - ## Get the number of full-lengths (95% <= L =< 105%) - # - # @param consensusLength integer - # @param lLengths list of integers - # @return fullLengthConsensusNb integer - # - def getNbFullLengths( self, consensusLength, lLengths ): - fullLengthConsensusNb = 0 - for i in lLengths: - if i / float(consensusLength ) >= 0.95 and i / float(consensusLength ) <= 1.05: - fullLengthConsensusNb += 1 - return fullLengthConsensusNb - - def getStatPerTE(self, consensusName): - dConsensusStats = {} - lLengthPerFragment = self._iTablePathAdaptator.getPathLengthListFromSubject(consensusName) - lLengthPerCopy = self._iTablePathAdaptator.getChainLengthListFromSubject(consensusName) - lIdentityPerCopy = self._iTablePathAdaptator.getChainIdentityListFromSubject(consensusName) - dConsensusStats["length"] = self._iTableSeqAdaptator.getSeqLengthFromAccession(consensusName) - dConsensusStats["cumulCoverage"] = self.getCumulCoverage(consensusName) - dConsensusStats["nbFragments"] = len(lLengthPerFragment) - dConsensusStats["nbFullLengthFragments"] = self.getNbFullLengths(dConsensusStats["length"], lLengthPerFragment) - dConsensusStats["nbCopies"] = len(lLengthPerCopy) - dConsensusStats["nbFullLengthCopies"] = self.getNbFullLengths(dConsensusStats["length"], lLengthPerCopy) - dConsensusStats["statsIdentityPerChain"] = Stat() - dConsensusStats["statsLengthPerChain"] = Stat() - dConsensusStats["statsLengthPerChainPerc"] = Stat() - self._statsForIdentityAndLength(dConsensusStats, lLengthPerCopy, lIdentityPerCopy) - return dConsensusStats - - def getStatPerCluster(self, lConsensusNames): - dConsensusClusterStats = {} - lLengthPerFragment = [] - lLengthPerCopy = [] - cumulCoverageLength = 0 - for consensusName in lConsensusNames: - cumulCoverageLength += self.getCumulCoverage(consensusName) - lLengthPerFragment.extend(self._iTablePathAdaptator.getPathLengthListFromSubject(consensusName)) - lLengthPerCopy.extend(self._iTablePathAdaptator.getChainLengthListFromSubject(consensusName)) - dConsensusClusterStats["cumulCoverage"] = cumulCoverageLength - dConsensusClusterStats["nbFragments"] = len(lLengthPerFragment) - dConsensusClusterStats["nbCopies"] = len(lLengthPerCopy) - return dConsensusClusterStats - - def getClusterListFromFile(self): - lClusters = [] - with open(self._clusterFileName) as fCluster: - for line in fCluster: - lConsensusNames = line.rstrip().split("\t") - lClusters.append(lConsensusNames) - return lClusters - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._iDb = DbFactory.createInstance() - self._iTablePathAdaptator = TablePathAdaptator(self._iDb, self._pathTableName) - self._iTableSeqAdaptator = TableSeqAdaptator(self._iDb, self._seqTableName) - - iASW = AnnotationStatsWriter() - if self._analysisName == "TE": - with open(self._statsFileName, "w") as fStats: - string = "%s\tlength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tmeanLgth\tmeanLgthPerc\n" % self._analysisName - fStats.write(string) - - lNamesTErefseq = self._iTableSeqAdaptator.getAccessionsList() - lDistinctSubjects = self._iTablePathAdaptator.getSubjectList() - totalCumulCoverage = self.getCumulCoverage() - - with open(self._globalStatsFileName, "w") as fG: - fG.write("%s\n" % iASW.printResume(lNamesTErefseq, lDistinctSubjects, totalCumulCoverage, self._genomeLength)) - for consensusName in lNamesTErefseq: - self._log.debug("processing '%s'..." % consensusName) - dStatForOneConsensus = self.getStatPerTE(consensusName) - iASW.addCalculsOfOneTE(dStatForOneConsensus) - fStats.write("%s\n" % iASW.getStatAsString(consensusName, dStatForOneConsensus)) - fG.write(iASW.printStatsForAllTEs(len(lNamesTErefseq))) - - elif self._analysisName == "Cluster": - lClusters = self.getClusterListFromFile() - lClusters.sort(key=lambda k: len(k), reverse=True) - with open(self._statsFileName, "w") as fStats: - string = "%s\tcovg\tfrags\tcopies\n" % self._analysisName - #TODO: add fullLgthFrags and fullLgthCopies ? Is addition of previous results significant ? - fStats.write(string) - for index, lConsensus in enumerate(lClusters): - self._log.debug("processing '%s'..." % lConsensus) - dStatForOneCluster = self.getStatPerCluster(lConsensus) - fStats.write("%s\n" % iASW.getStatAsStringForCluster(str(index + 1), dStatForOneCluster)) - - if self._save: - outTableName = "%s_statsPer%s" % (self._pathTableName, self._analysisName) - self._iDb.createTable(outTableName, "pathstat", self._statsFileName) - - self._iDb.close() - self._log.info("END %s" % type(self).__name__) - - def _statsForIdentityAndLength(self, dStat, lLengthPerCopy, lIdentityPerCopy): - for i in lIdentityPerCopy: - dStat["statsIdentityPerChain"].add(i) - lLengthPercPerCopy = [] - for i in lLengthPerCopy: - dStat["statsLengthPerChain"].add(i) - lperc = 100 * i / float(dStat["length"]) - lLengthPercPerCopy.append(lperc) - dStat["statsLengthPerChainPerc"].add(lperc) - -class AnnotationStatsWriter(object): - - def __init__(self): - self._dAllTErefseqs = { "sumCumulCoverage": 0, - "totalNbFragments": 0, - "totalNbFullLengthFragments": 0, - "totalNbCopies": 0, - "totalNbFullLengthCopies": 0, - "nbFamWithFullLengthFragments": 0, - "nbFamWithOneFullLengthFragment": 0, - "nbFamWithTwoFullLengthFragments": 0, - "nbFamWithThreeFullLengthFragments": 0, - "nbFamWithMoreThanThreeFullLengthFragments": 0, - "nbFamWithFullLengthCopies": 0, - "nbFamWithOneFullLengthCopy": 0, - "nbFamWithTwoFullLengthCopies": 0, - "nbFamWithThreeFullLengthCopies": 0, - "nbFamWithMoreThanThreeFullLengthCopies": 0, - "statsAllCopiesMedIdentity": Stat(), - "statsAllCopiesMedLengthPerc": Stat() - } - - def getAllTEsRefSeqDict(self): - return self._dAllTErefseqs - - def getStatAsString( self, name, d ): - """ - Return a string with all data properly formatted. - """ - string = "" - string += "%s" % name - string += "\t%i" % d["length"] - string += "\t%i" % d["cumulCoverage"] - string += "\t%i" % d["nbFragments"] - string += "\t%i" % d["nbFullLengthFragments"] - string += "\t%i" % d["nbCopies"] - string += "\t%i" % d["nbFullLengthCopies"] - - if d["statsIdentityPerChain"].getValuesNumber() != 0: - string += "\t%.2f" % d["statsIdentityPerChain"].mean() - else: - string += "\tNA" - - if d["statsLengthPerChain"].getValuesNumber() != 0: - string += "\t%.2f" % d["statsLengthPerChain"].mean() - else: - string += "\tNA" - - if d["statsLengthPerChainPerc"].getValuesNumber() != 0: - string += "\t%.2f" % d["statsLengthPerChainPerc"].mean() - else: - string += "\tNA" - - return string - - def getStatAsStringForCluster( self, name, d ): - """ - Return a string with all data properly formatted. - """ - string = "" - string += "%s" % name - string += "\t%i" % d["cumulCoverage"] - string += "\t%i" % d["nbFragments"] - string += "\t%i" % d["nbCopies"] - - return string - - def addCalculsOfOneTE(self, dOneTErefseq): - self._dAllTErefseqs[ "sumCumulCoverage" ] += dOneTErefseq[ "cumulCoverage" ] - - self._dAllTErefseqs[ "totalNbFragments" ] += dOneTErefseq[ "nbFragments" ] - self._dAllTErefseqs[ "totalNbFullLengthFragments" ] += dOneTErefseq[ "nbFullLengthFragments" ] - if dOneTErefseq[ "nbFullLengthFragments" ] > 0: - self._dAllTErefseqs[ "nbFamWithFullLengthFragments" ] += 1 - if dOneTErefseq[ "nbFullLengthFragments" ] == 1: - self._dAllTErefseqs[ "nbFamWithOneFullLengthFragment" ] += 1 - elif dOneTErefseq[ "nbFullLengthFragments" ] == 2: - self._dAllTErefseqs[ "nbFamWithTwoFullLengthFragments" ] += 1 - elif dOneTErefseq[ "nbFullLengthFragments" ] == 3: - self._dAllTErefseqs[ "nbFamWithThreeFullLengthFragments" ] += 1 - elif dOneTErefseq[ "nbFullLengthFragments" ] > 3: - self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthFragments" ] += 1 - - self._dAllTErefseqs[ "totalNbCopies" ] += dOneTErefseq[ "nbCopies" ] - self._dAllTErefseqs[ "totalNbFullLengthCopies" ] += dOneTErefseq[ "nbFullLengthCopies" ] - if dOneTErefseq[ "nbFullLengthCopies" ] > 0: - self._dAllTErefseqs[ "nbFamWithFullLengthCopies" ] += 1 - if dOneTErefseq[ "nbFullLengthCopies" ] == 1: - self._dAllTErefseqs[ "nbFamWithOneFullLengthCopy" ] += 1 - elif dOneTErefseq[ "nbFullLengthCopies" ] == 2: - self._dAllTErefseqs[ "nbFamWithTwoFullLengthCopies" ] += 1 - elif dOneTErefseq[ "nbFullLengthCopies" ] == 3: - self._dAllTErefseqs[ "nbFamWithThreeFullLengthCopies" ] += 1 - elif dOneTErefseq[ "nbFullLengthCopies" ] > 3: - self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthCopies" ] += 1 - - if dOneTErefseq[ "statsIdentityPerChain" ].getValuesNumber() != 0: - self._dAllTErefseqs[ "statsAllCopiesMedIdentity" ].add( dOneTErefseq[ "statsIdentityPerChain" ].median() ) - - if dOneTErefseq[ "statsLengthPerChainPerc" ].getValuesNumber() != 0: - self._dAllTErefseqs[ "statsAllCopiesMedLengthPerc" ].add( dOneTErefseq[ "statsLengthPerChainPerc" ].median() ) - - def printStatsForAllTEs(self, TEnb): -# statString += "(sum of cumulative coverages: %i bp)" % ( self._dAllTErefseqs[ "sumCumulCoverage" ] ) - statString = "total nb of TE fragments: %i\n" % ( self._dAllTErefseqs[ "totalNbFragments" ] ) - - if self._dAllTErefseqs[ "totalNbFragments" ] != 0: - - statString += "total nb full-length fragments: %i (%.2f%%)\n" % \ - ( self._dAllTErefseqs[ "totalNbFullLengthFragments" ], \ - 100*self._dAllTErefseqs[ "totalNbFullLengthFragments" ] / float(self._dAllTErefseqs[ "totalNbFragments" ]) ) - - statString += "total nb of TE copies: %i\n" % ( self._dAllTErefseqs[ "totalNbCopies" ] ) - - statString += "total nb full-length copies: %i (%.2f%%)\n" % \ - ( self._dAllTErefseqs[ "totalNbFullLengthCopies" ], \ - 100*self._dAllTErefseqs[ "totalNbFullLengthCopies" ] / float(self._dAllTErefseqs[ "totalNbCopies" ]) ) - - statString += "families with full-length fragments: %i (%.2f%%)\n" % \ - ( self._dAllTErefseqs[ "nbFamWithFullLengthFragments" ], \ - 100*self._dAllTErefseqs[ "nbFamWithFullLengthFragments" ] / float(TEnb) ) - statString += " with only one full-length fragment: %i\n" % ( self._dAllTErefseqs[ "nbFamWithOneFullLengthFragment" ] ) - statString += " with only two full-length fragments: %i\n" % ( self._dAllTErefseqs[ "nbFamWithTwoFullLengthFragments" ] ) - statString += " with only three full-length fragments: %i\n" % ( self._dAllTErefseqs[ "nbFamWithThreeFullLengthFragments" ] ) - statString += " with more than three full-length fragments: %i\n" % ( self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthFragments" ] ) - - statString += "families with full-length copies: %i (%.2f%%)\n" % \ - ( self._dAllTErefseqs[ "nbFamWithFullLengthCopies" ], \ - 100*self._dAllTErefseqs[ "nbFamWithFullLengthCopies" ] / float(TEnb) ) - statString += " with only one full-length copy: %i\n" % ( self._dAllTErefseqs[ "nbFamWithOneFullLengthCopy" ] ) - statString += " with only two full-length copies: %i\n" % ( self._dAllTErefseqs[ "nbFamWithTwoFullLengthCopies" ] ) - statString += " with only three full-length copies: %i\n" % ( self._dAllTErefseqs[ "nbFamWithThreeFullLengthCopies" ] ) - statString += " with more than three full-length copies: %i\n" % ( self._dAllTErefseqs[ "nbFamWithMoreThanThreeFullLengthCopies" ] ) - - statString += "mean of median identity of all families: %.2f +- %.2f\n" % \ - ( self._dAllTErefseqs[ "statsAllCopiesMedIdentity" ].mean(), \ - self._dAllTErefseqs[ "statsAllCopiesMedIdentity" ].sd() ) - - statString += "mean of median length percentage of all families: %.2f +- %.2f\n" % \ - ( self._dAllTErefseqs[ "statsAllCopiesMedLengthPerc" ].mean(), \ - self._dAllTErefseqs[ "statsAllCopiesMedLengthPerc" ].sd() ) - return statString - - def printResume(self, lNamesTErefseq, lDistinctSubjects, totalCumulCoverage, genomeLength): - statString = "nb of sequences: %i\n" % len(lNamesTErefseq) - statString += "nb of matched sequences: %i\n" % len(lDistinctSubjects) - statString += "cumulative coverage: %i bp\n" % totalCumulCoverage - statString += "coverage percentage: %.2f%%\n" % ( 100 * totalCumulCoverage / float(genomeLength) ) -# statString += "processing the %i TE families..." % len(lNamesTErefseq) - return statString diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/BenchmarkTEconsensus.py --- a/commons/tools/BenchmarkTEconsensus.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,567 +0,0 @@ -#!/usr/bin/env python - -##@file -# Compare two fasta files of TEs to assess how reference sequences are recovered by de novo consensus. - - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -import os -import sys -import getopt -import shutil -import glob - - -import pyRepet.launcher.programLauncher -from commons.core.coord.AlignUtils import AlignUtils -from commons.core.coord.MatchUtils import MatchUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.core.seq.FastaUtils import FastaUtils -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -class BenchmarkTEconsensus( object ): - - def __init__( self ): - self._qryFile = "" - self._sbjFile = "" - self._method = 1 - self._keepConflictSbj = False - self._thresholdCoverage = 95 - self._thresholdIdentity = 80 - self._thresholdEvalue = 1e-10 - self._thresholdCoverageMatch = 90 - self._useCluster = False - self._queue = "" - self._configFileName = "" - self._clean = False - self._verbose = 0 - self._pL = pyRepet.launcher.programLauncher.programLauncher() - - - def help( self ): - print - print "usage: BenchmarkTEconsensus.py [ options ]" - print "options:" - print " -h: this help" - print " -q: name of the query file (de novo consensus, format='fasta')" - print " -s: name of the subject file (reference sequences, format='fasta')" - print " -m: method" - print " 1: Blaster + Matcher (default)" - print " 2: Blaster + merge + Matcher (not with '-Q')" - print " 3: Orienter + Mafft + Matcher" - print " 4: Yass + Matcher" - print " -a: keep all conflicting subjects in Matcher" - print " -t: coverage threshold over which the match is 'complete' (in %% of the seq length, default=%i)" % self._thresholdCoverage - print " -I: identity threshold for 'CC' matches (default=%i)" % self._thresholdIdentity - print " -E: E-value threshold for 'CC' matches (default=1e-10)" - print " -T: coverage threshold for match length on query compare to subject length (default=%i)" % self._thresholdCoverageMatch - print " -Q: queue name to run in parallel" - print " -C: name of the configuration file (compulsory with '-Q')" - print " -c: clean" - print " -v: verbosity level (default=0/1/2)" - print - - - def setAttributesFromCmdLine( self ): - try: - opts, args = getopt.getopt( sys.argv[1:], "hq:s:m:at:I:E:T:Q:C:cv:" ) - except getopt.GetoptError, err: - sys.stderr.write( "%s\n" % ( str(err) ) ) - self.help() - sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); - sys.exit(0) - elif o == "-q": - self._qryFile = a - elif o == "-s": - self._sbjFile = a - elif o == "-m": - self._method = int(a) - elif o == "-a": - self._keepConflictSbj = True - elif o == "-t": - self._thresholdCoverage = int(a) - elif o == "-I": - self._thresholdIdentity = int(a) - elif o == "-E": - self._thresholdEvalue = float(a) - elif o == "-T": - self._thresholdCoverageMatch = int(a) - elif o == "-Q": - self._useCluster = True - self._queue = a - elif o == "-C": - self._configFile = a - elif o == "-c": - self._clean = True - elif o == "-v": - self._verbose = int(a) - - - def checkAttributes( self ): - if self._qryFile == "": - msg = "ERROR: missing query file (-q)" - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - if not os.path.exists( self._qryFile ): - msg = "ERROR: can't find file '%s'" % ( self._qryFile ) - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - if self._sbjFile == "": - msg = "ERROR: missing subject file (-s)" - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - if not os.path.exists( self._sbjFile ): - msg = "ERROR: can't find file '%s'" % ( self._sbjFile ) - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - if self._useCluster: - if self._configFile == "": - msg = "ERROR: missing configuration file (-C)" - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - if not os.path.exists( self._configFile ): - msg = "ERROR: can't find file '%s'" % ( self._configFile ) - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - if self._method == 2: - msg = "ERROR: can't launch method 2 in parallel" - sys.stderr.write( "%s\n" % ( msg ) ) - self.help() - sys.exit(1) - nbSeqQry = FastaUtils.dbSize( self._qryFile ) - if nbSeqQry == 0: - print "WARNING: query file is empty" - sys.exit(0) - nbSeqSbj = FastaUtils.dbSize( self._sbjFile ) - if nbSeqSbj == 0: - print "WARNING: subject file is empty" - sys.exit(0) - - - def preprocess( self ): - tmpDir = "tmp%s_t%i_m%i_I%i" % ( os.getpid(), - self._thresholdCoverage, - self._method, - self._thresholdIdentity ) - if os.path.exists( tmpDir ): - shutil.rmtree( tmpDir ) - os.mkdir( tmpDir ) - os.chdir( tmpDir ) - - os.symlink( "../%s" % self._qryFile, self._qryFile ) - csh = ChangeSequenceHeaders() - csh.setInputFile( self._qryFile ) - csh.setFormat( "fasta" ) - csh.setStep( 1 ) - csh.setPrefix( "query" ) - csh.setOutputFile( "%s.newH" % ( self._qryFile ) ) - csh.setVerbosityLevel( self._verbose ) - csh.run() - self._qryFile += ".newH" - - if not os.path.exists( self._sbjFile ): - os.symlink( "../%s" % self._sbjFile, self._sbjFile ) - - - def compareFastaViaBlasterMatcher( self, merged=False ): - """ - Blaster (+ merged) + Matcher - """ - if self._keepConflictSbj: - s = "match" - else: - s = "clean_match" - matchFile = "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - pathFile = "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - if merged: - matchFile += ".merged" - pathFile += ".merged" - matchFile += ".%s.tab" % ( s ) - pathFile += ".%s.path" % ( s ) - - if not self._useCluster: - prg = "blaster" - cmd = prg - cmd += " -q %s" % ( self._qryFile ) - cmd += " -s %s" % ( self._sbjFile ) - cmd += " -B %s_vs_%s.m%i" % ( self._qryFile, - self._sbjFile, - self._method ) - cmd += " -v %i" % ( self._verbose ) - self._pL.launch( prg, cmd ) - - if merged: - tmpFile = "%s_vs_%s.m%i.align.merged" % ( self._qryFile, - self._sbjFile, - self._method ) - AlignUtils.mergeFile( "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ), - tmpFile ) - else: - tmpFile = "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - - prg = "matcher" - cmd = prg - cmd += " -m %s" % ( tmpFile ) - cmd += " -q %s" % ( self._qryFile ) - cmd += " -s %s" % ( self._sbjFile ) - cmd += " -j" - if self._keepConflictSbj: - cmd += " -a" - cmd += " -v %i" % ( self._verbose ) - self._pL.launch( prg, cmd ) - - else: - os.symlink( "../%s" % self._configFile, self._configFileName ) - - prg = os.environ["REPET_PATH"] + "/bin/launchBlasterMatcherPerQuery.py" - cmd = prg - cmd += " -q %s" % ( self._qryFile ) - cmd += " -s %s" % ( self._sbjFile ) - cmd += " -Q %s" % ( self._queue ) - cmd += " -C %s" % ( self._configFile ) - cmd += " -n %i" % ( 10 ) - if self._keepConflictSbj: - cmd += " -M \"%s\"" % ( "-j -a" ) - else: - cmd += " -M \"%s\"" % ( "-j" ) - cmd += " -Z tab" - if self._clean: - cmd += " -c" - cmd += " -v %i" % ( self._verbose - 1 ) - self._pL.launch( prg, cmd ) - - csh = ChangeSequenceHeaders() - csh.setInputFile( matchFile ) - csh.setFormat( "tab" ) - csh.setStep( 2 ) - csh.setLinkFile( "%slink" % ( self._qryFile ) ) - csh.setOutputFile( matchFile.replace(".newH","") ) - csh.run() - - csh.setInputFile( pathFile ) - csh.setFormat( "path" ) - csh.setStep( 2 ) - csh.setOutputFile( pathFile.replace(".newH","") ) - csh.run() - - return matchFile.replace(".newH",""), pathFile.replace(".newH","") - - - def compareFastaViaMafft( self ): - """ - Orienter, Mafft, Matcher - """ - FastaUtils.dbSplit( self._qryFile, 1, False, False, "query" ) - FastaUtils.dbSplit( self._sbjFile, 1, False, False, "subject" ) - lQueries = glob.glob( "query_*.fa" ) - lSubjects = glob.glob( "subject_*.fa" ) - - if self._keepConflictSbj: - s = "match" - else: - s = "clean_match" - matchFile = "%s_vs_%s.m%i.align.%s.tab" % ( self._qryFile, - self._sbjFile, - self._method, - s ) - os.system( "touch %s" % matchFile ) - pathFile = "%s_vs_%s.m%i.align.%s.path" % ( self._qryFile, - self._sbjFile, - self._method, - s ) - os.system( "touch %s" % pathFile ) - - countQueries = 0 - for query in lQueries: - countQueries += 1 - queryHeader = FastaUtils.dbHeaders( query )[0] - queryLength = FastaUtils.dbLengths( query )[0] - countSubjects = 0 - for subject in lSubjects: - countSubjects += 1 - subjectHeader = FastaUtils.dbHeaders( subject )[0] - subjectLength = FastaUtils.dbLengths( subject )[0] - if self._verbose > 0: - print "compare '%s' (%i bp, %i/%i) and '%s' (%i bp, %i/%i)" % ( queryHeader, queryLength, - countQueries, len(lQueries), - subjectHeader, subjectLength, - countSubjects, len(lSubjects) ) - sys.stdout.flush() - qsLengthRatio = 100 * queryLength / float(subjectLength) - if qsLengthRatio < self._thresholdCoverage - 2 or qsLengthRatio > 100 + (100-self._thresholdCoverage) + 2: - if self._verbose > 0: - print "skip (q/s=%.2f%%)" % ( qsLengthRatio ) - continue - - tmpFile = "%s_vs_%s" % ( query, subject ) - FileUtils.catFilesFromList( [ query, subject ], - tmpFile ) - prg = "OrientSequences.py" - cmd = prg - cmd += " -i %s" % ( tmpFile ) - cmd += " -p mummer" - cmd += " -c" - cmd += " -v %i" % ( self._verbose - 1 ) - self._pL.launch( prg, cmd ) - prg = "MafftProgramLauncher.py" - cmd = prg - cmd += " -i %s.oriented" % ( tmpFile ) - cmd += " -c" - cmd += " -v %i" % ( self._verbose - 1 ) - self._pL.launch( prg, cmd ) - - absDB = AlignedBioseqDB( "%s.oriented.fa_aln" % tmpFile ) - lHeaders = absDB.getHeaderList() - lAligns = absDB.getAlignList( lHeaders[0], lHeaders[1] ) - for i in lAligns: - if "re-oriented" in i.getQueryName(): - i.setQueryName( queryHeader ) - start = i.getQueryStart() - end = i.getQueryEnd() - i.setQueryStart( queryLength - end + 1 ) - i.setQueryEnd( queryLength - start + 1 ) - if "re-oriented" in i.getSubjectName(): - i.setSubjectName( subjectHeader ) - start = i.getSubjectStart() - end = i.getSubjectEnd() - i.setSubjectEnd( subjectLength - end + 1 ) - i.setSubjectStart( subjectLength - start + 1 ) - if not i.isQueryOnDirectStrand(): - i.reverse() - AlignUtils.writeListInFile( lAligns, - "%s.oriented.fa_aln.align" % tmpFile ) - - prg = os.environ["REPET_PATH"] + "/bin/matcher" - cmd = prg - cmd += " -m %s.oriented.fa_aln.align" % ( tmpFile ) - cmd += " -q %s" % ( query ) - cmd += " -s %s" % ( subject ) - cmd += " -j" - if self._keepConflictSbj: - cmd += " -a" - cmd += " -v %i" % ( self._verbose - 1 ) - self._pL.launch( prg, cmd ) - - FileUtils.appendFileContent( "%s.oriented.fa_aln.align.%s.path" % ( tmpFile, s ), pathFile ) - lMatches = MatchUtils.getMatchListFromFile( "%s.oriented.fa_aln.align.%s.tab" % ( tmpFile, s ) ) - MatchUtils.writeListInFile( lMatches, matchFile, "a" ) - - for f in [ tmpFile, - "%s.oriented" % ( tmpFile ), -# "%s.oriented.fa_aln" % ( tmpFile ), - "%s.oriented.fa_aln.align" % ( tmpFile ), - "%s.oriented.fa_aln.align.match.fa" % ( tmpFile ), - "%s.oriented.fa_aln.align.match.map" % ( tmpFile ), - "%s.oriented.fa_aln.align.match.param" % ( tmpFile ), - "%s.oriented.fa_aln.align.match.path" % ( tmpFile ), - "%s.oriented.fa_aln.align.match.tab" % ( tmpFile ), - ]: - os.remove( f ) - - if not FileUtils.isEmpty( matchFile ): - csh = ChangeSequenceHeaders() - csh.setInputFile( matchFile ) - csh.setFormat( "tab" ) - csh.setStep( 2 ) - csh.setLinkFile( "%slink" % ( self._qryFile ) ) - csh.setOutputFile( matchFile.replace(".newH","") ) - csh.run() - csh.setInputFile( pathFile ) - csh.setFormat( "path" ) - csh.setStep( 2 ) - csh.setOutputFile( pathFile.replace(".newH","") ) - csh.run() - return matchFile.replace(".newH",""), pathFile.replace(".newH","") - else: - return "", "" - - - def compareFastaViaYassMatcher( self, merged=False ): - """ - Yass + Matcher - """ - if self._keepConflictSbj: - s = "match" - else: - s = "clean_match" - matchFile = "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - pathFile = "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - if merged: - matchFile += ".merged" - pathFile += ".merged" - matchFile += ".%s.tab" % ( s ) - pathFile += ".%s.path" % ( s ) - - if not self._useCluster: - prg = os.environ["REPET_PATH"] + "/bin/YassProgramLauncher.py" - cmd = prg - cmd += " -i %s" % ( self._qryFile ) - cmd += " -s %s" % ( self._sbjFile ) - cmd += " -c" -# cmd += " -p '-i 12'" - cmd += " -o %s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - cmd += " -v %i" % ( self._verbose ) - self._pL.launch( prg, cmd ) - - if merged: - tmpFile = "%s_vs_%s.m%i.align.merged" % ( self._qryFile, - self._sbjFile, - self._method ) - AlignUtils.mergeFile( "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ), - tmpFile ) - else: - tmpFile = "%s_vs_%s.m%i.align" % ( self._qryFile, - self._sbjFile, - self._method ) - - prg = os.environ["REPET_PATH"] + "/bin/matcher" - cmd = prg - cmd += " -m %s" % ( tmpFile ) - cmd += " -q %s" % ( self._qryFile ) - cmd += " -s %s" % ( self._sbjFile ) - cmd += " -j" - if self._keepConflictSbj: - cmd += " -a" - cmd += " -v %i" % ( self._verbose ) - self._pL.launch( prg, cmd ) - - csh = ChangeSequenceHeaders() - csh.setInputFile( matchFile ) - csh.setFormat( "tab" ) - csh.setStep( 2 ) - csh.setLinkFile( "%slink" % ( self._qryFile ) ) - csh.setOutputFile( matchFile.replace(".newH","") ) - csh.run() - - csh.setInputFile( pathFile ) - csh.setFormat( "path" ) - csh.setStep( 2 ) - csh.setOutputFile( pathFile.replace(".newH","") ) - csh.run() - - return matchFile.replace(".newH",""), pathFile.replace(".newH","") - - - def analyzeMatchFile( self, matchFile, pathFile ): - if matchFile != "": - if self._verbose > 0: - print "analyze the 'tab' file..." - sys.stdout.flush() - prg = os.environ["REPET_PATH"] + "/bin/tabFileReader.py" - cmd = prg - cmd += " -m %s" % ( matchFile ) - cmd += " -q %s" % ( self._qryFile.replace(".newH","") ) - cmd += " -s %s" % ( self._sbjFile.replace(".newH","") ) - cmd += " -t %i" % ( self._thresholdCoverage ) - cmd += " -I %i" % ( self._thresholdIdentity ) - cmd += " -E %g" % ( self._thresholdEvalue ) - cmd += " -T %i" % ( self._thresholdCoverageMatch ) - cmd += " -v %i" % ( self._verbose - 1 ) - self._pL.launch( prg, cmd ) - for f in [ matchFile, pathFile, - "%s_tabFileReader.txt" % matchFile, - "%s_qryCategories.txt" % matchFile, - "%s_sbjCategories.txt" % matchFile ]: - shutil.copy( f, ".." ) - os.chdir( ".." ) - - - def start( self ): - self.checkAttributes() - if self._verbose > 0: - print "START BenchmarkTEconsensus.py" - sys.stdout.flush() - - - def end( self ): - if self._clean: - tmpDir = "tmp%s_t%i_m%i_I%i" % ( os.getpid(), - self._thresholdCoverage, - self._method, - self._thresholdIdentity ) - shutil.rmtree( tmpDir ) - if self._verbose > 0: - print "END BenchmarkTEconsensus.py" - sys.stdout.flush() - - - def run( self ): - self.start() - - self.preprocess() - - if self._method == 1: - matchFile, pathFile = self.compareFastaViaBlasterMatcher() - elif self._method == 2: - matchFile, pathFile = self.compareFastaViaBlasterMatcher( merged=True ) - elif self._method == 3: - matchFile, pathFile = self.compareFastaViaMafft() - elif self._method == 4: - matchFile, pathFile = self.compareFastaViaYassMatcher() - - self.analyzeMatchFile( matchFile, pathFile ) - - self.end() - - -if __name__ == "__main__": - i = BenchmarkTEconsensus() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/CalcCoordCumulLength.py --- a/commons/tools/CalcCoordCumulLength.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,186 +0,0 @@ -#!/usr/bin/env python - -""" -Calculate the cumulative length of coordinates data in the L{Map} format. -""" - -import os -import sys -import getopt -from pyRepet.launcher.programLauncher import programLauncher -from pyRepet.util.Stat import Stat -from commons.core.checker.CheckerUtils import CheckerUtils - - -class CalcCoordCumulLength( object ): - """ - Compute the coverage of coordinates data in the L{Map 0: - print "merge the coordinates with mapOp..."; sys.stdout.flush() - if not CheckerUtils.isExecutableInUserPath( "mapOp" ): - msg = "ERROR: 'mapOp' is not in your PATH" - sys.stderr.write( "%s\n" % msg ) - sys.exit(1) - pL = programLauncher() - prg = os.environ["REPET_PATH"] + "/bin/mapOp" - cmd = prg - cmd += " -q %s" % ( self._inFileName ) - cmd += " -m" - cmd += " > /dev/null" - pL.launch( prg, cmd, self._verbose - 1 ) - if self._verbose > 0: - print "coordinates merged !"; sys.stdout.flush() - mergeFileName = "%s.merge" % ( self._inFileName ) - inPath, inName = os.path.split( self._inFileName ) - if inPath != "": - os.system( "mv %s.merge %s" % ( inName, inPath ) ) - return mergeFileName - - - def getStatsPerChr( self, mergeFileName ): - """ - Return summary statistics on the coordinates, per chromosome. - @param mergeFileName: L{Map} instances - """ - dChr2Stats = {} - if self._verbose > 0: - print "compute the coverage of the coordinates..."; sys.stdout.flush() - mergeF = open( mergeFileName, "r" ) - line = mergeF.readline() - while True: - if line == "": break - tokens = line[:-1].split("\t") - if int(tokens[2]) < int(tokens[3]): - matchLength = int(tokens[3]) - int(tokens[2]) + 1 - elif int(tokens[2]) > int(tokens[3]): - matchLength = int(tokens[2]) - int(tokens[3]) + 1 - if not dChr2Stats.has_key( tokens[1] ): - dChr2Stats[ tokens[1] ] = Stat() - dChr2Stats[ tokens[1] ].add( matchLength ) - line = mergeF.readline() - mergeF.close() - os.remove( mergeFileName ) - return dChr2Stats - - - def saveCumulLength( self, dChr2Stats ): - """ - Write the stats in the output file. - """ - outF = open( self._outFileName, "w" ) - totalLength = 0 - for i in dChr2Stats.keys(): - totalLength += dChr2Stats[i].sum - string = "cumulative length (in bp) on '%s': %i" % ( i, dChr2Stats[i].sum ) - outF.write( "%s\n" % ( string ) ) - if self._verbose > 0: print string - string = "total cumulative length (in bp): %i" % ( totalLength ) - outF.write( "%s\n" % ( string ) ) - if self._verbose > 0: print string - outF.close() - sys.stdout.flush() - - - def start( self ): - """ - Useful commands before running the program. - """ - if self._verbose > 0: - print "beginning of %s" % (sys.argv[0].split("/")[-1]); sys.stdout.flush() - self.checkAttributes() - if self._verbose > 0: - print "input file : '%s'" % ( self._inFileName ) - sys.stdout.flush() - - - def end( self ): - """ - Useful commands before ending the program. - """ - if self._verbose > 0: - print "%s finished successfully" % (sys.argv[0].split("/")[-1]); sys.stdout.flush() - - - def run( self ): - """ - Run the program. - """ - self.start() - mergeFileName = self.mergeCoordinates() - dChr2Stats = self.getStatsPerChr( mergeFileName ) - self.saveCumulLength( dChr2Stats ) - self.end() - - -if __name__ == '__main__': - i = CalcCoordCumulLength() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/ChangeSequenceHeaders.py --- a/commons/tools/ChangeSequenceHeaders.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,524 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -import os -import sys -import getopt -from commons.core.coord.Align import Align -from commons.core.coord.Path import Path -from commons.core.coord.Match import Match - - - -class ChangeSequenceHeaders( object ): - - def __init__( self, name="ChangeSequenceHeaders", inFile="", format="", step=0, prefix="seq", outFile="",linkFile="", whichCluster = "", replace_query=True, replace_subject=True, verbosity=0): - self._name = name - self._inFile = inFile - self._format = format - self._step = step - self._prefix = prefix - self._linkFile = linkFile - self._whichCluster = whichCluster - self._outFile = outFile - self.replace_query = replace_query - self.replace_subject = replace_subject - self._verbose = verbosity - - - def help( self ): - print - print "usage: %s.py [ options ]" % ( self._name ) - print "options:" - print " -h: this help" - print " -i: name of the input file" - print " -f: format of the input file (fasta/newick/align/path/tab)" - print " -s: step (1: shorten headers / 2: retrieve initial headers)" - print " -p: prefix of new headers (with '-s 1', default='seq')" - print " -l: name of the 'link' file (with '-s 2', format=map)" - print " -w: header formatting type (A: after LTRharvest, B: for ClusterConsensus, not specified: no change)" - print " -o: name of the output file (default=inFile+'.newH'/'.initH')" - print - - - def setAttributesFromCmdLine( self ): - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:f:s:p:l:w:o:v:") - except getopt.GetoptError, err: - sys.stderr.write( "%s\n" % ( str(err) ) ) - self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-i": - self.setInputFile( a ) - elif o == "-f": - self.setFormat( a ) - elif o == "-s": - self.setStep( a ) - elif o == "-p": - self.setPrefix( a ) - elif o == "-l": - self.setLinkFile( a ) - elif o == "-w": - self.setWhichcluster( a ) - elif o == "-o": - self.setOutputFile( a ) - elif o == "-v": - self.setVerbosityLevel( a ) - - - def setInputFile( self, inFile ): - self._inFile = inFile - - def setFormat( self, format ): - self._format = format - - def setPrefix( self, prefix ): - self._prefix = prefix - - def setStep( self, step ): - self._step = int(step) - - def setLinkFile( self, linkFile ): - self._linkFile = linkFile - - def setWhichcluster( self, whichCluster ): - self._whichCluster = whichCluster - - def setOutputFile( self, outFile ): - self._outFile = outFile - - def setVerbosityLevel( self, verbose ): - self._verbose = int(verbose) - - - def checkAttributes( self ): - if self._inFile == "": - sys.stderr.write( "ERROR: missing input file name (-i)\n" ) - self.help(); sys.exit(1) - if not os.path.exists( self._inFile ): - sys.stderr.write( "ERROR: input file doesn't exist (-i)\n" ) - self.help(); sys.exit(1) - if self._format not in ["fasta","newick","align","path","tab","axt","lastz", "psl","chain"]: - sys.stderr.write( "ERROR: unrecognized format '%s' (-f)\n" ) - self.help(); sys.exit(1) - if self._step not in [1,2]: - sys.stderr.write( "ERROR: missing step (-s)\n" ) - self.help(); sys.exit(1) - if self._step == 1 and self._prefix == "": - sys.stderr.write( "ERROR: missing prefix (-p)\n" ) - self.help(); sys.exit(1) - if self._step == 2: - if self._linkFile == "": - sys.stderr.write( "ERROR: missing link file name (-l)\n" ) - self.help(); sys.exit(1) - if not os.path.exists( self._linkFile ): - sys.stderr.write( "ERROR: link file doesn't exist (-l)\n" ) - self.help(); sys.exit(1) - if self._whichCluster not in ["A", "B", ""]: - sys.stderr.write( "ERROR: formatting type not available (-w option): %s\n" % self._whichCluster) - self.help(); sys.exit(1) - if self._outFile == "": - if self._step == 1: - self._outFile = "%s.newH" % ( self._inFile ) - elif self._step == 2: - self._outFile = "%s.initH" % ( self._inFile ) - - - def shortenSequenceHeadersForFastaFile( self ): - if self._verbose > 0: - print "shorten sequence headers for fasta file..." - sys.stdout.flush() - if self._verbose > 1: - print "save sequences in '%s'" %( self._outFile ) - inFileHandler = open( self._inFile, "r" ) - linkFileHandler = open( self._linkFile, "w" ) - outFileHandler = open( self._outFile, "w" ) - countSeq = 0 - lengthSeq = 0 - while True: - line = inFileHandler.readline() - if line == "": - break - if line[0] == ">": - countSeq += 1 - newHeader = "%s%i" % ( self._prefix, countSeq ) - if self._verbose > 1: - print "initial '%s' -> new '%s'" % ( line[1:-1], newHeader ) - outFileHandler.write( ">%s\n" % ( newHeader ) ) - if lengthSeq != 0: - linkFileHandler.write( "\t%i\t%i\n" % ( 1, lengthSeq ) ) - lengthSeq = 0 - linkFileHandler.write( "%s\t%s" % ( newHeader, line[1:-1] ) ) - else: - lengthSeq += len( line.replace("\n","") ) - outFileHandler.write( line ) - linkFileHandler.write( "\t%i\t%i\n" % ( 1, lengthSeq ) ) - inFileHandler.close() - linkFileHandler.close() - outFileHandler.close() - if self._verbose > 0: - print "nb of sequences: %i" % ( countSeq ) - - - def getLinksNewToInitialHeaders( self ): - if self._verbose > 0: - print "retrieve the links new->initial headers" - sys.stdout.flush() - dNew2Init = {} - linkFileHandler = open( self._linkFile,"r" ) - while True: - line = linkFileHandler.readline() - if line == "": - break - tokens = line.split("\t") - if len(tokens) == 4: - dNew2Init[ tokens[0] ] = tokens[1] - elif len(tokens) == 2: - dNew2Init[ tokens[0] ] = tokens[1].split("\n")[0] - else: - sys.stderr.write( "ERROR: link file is badly formatted\n" ) - sys.exit(1) - linkFileHandler.close() - if self._verbose > 0: print "nb of links: %i" % ( len(dNew2Init.keys()) ); sys.stdout.flush() - return dNew2Init - - - def retrieveInitialSequenceHeadersForFastaFile( self, dNew2Init ): - if self._verbose > 0: - print "retrieve initial headers for fasta file" - sys.stdout.flush() - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - countSeq = 0 - while True: - line = inFileHandler.readline() - if line == "": - break - if line[0] == ">": - if self._whichCluster == "": - initHeader = line[1:-1] - newHeader = dNew2Init[initHeader] - else: - tokens = line[1:-1].split("_") - initHeader = dNew2Init[tokens[1]] - - pattern = "" - if "BlastclustCluster" in tokens[0]: - pattern = "Blc" - if "MCLCluster" in tokens[0]: - pattern = "MCL" - - if self._whichCluster == "A": - newHeader = "%s_%s" % (tokens[0], initHeader) - elif self._whichCluster == "B": - classif = initHeader.split("_")[0] - consensusName = "_".join(initHeader.split("_")[1:]) - clusterId = tokens[0].split("Cluster")[1].split("Mb")[0] - newHeader = "%s_%s%s_%s" % (classif, pattern, clusterId, consensusName) - - outFileHandler.write( ">%s\n" % newHeader ) - else: - outFileHandler.write( line ) - inFileHandler.close() - outFileHandler.close() - if self._verbose > 0: - print "nb of sequences: %i" % ( countSeq ) - - - def retrieveInitialSequenceHeadersForNewickFile( self, dNew2Init ): - inF = open( self._inFile, "r" ) - lines = inF.readlines() - inF.close() - line = "".join(lines) #.replace(";","").replace("\n","") - outF = open( self._outFile, "w" ) - for newH in dNew2Init.keys(): - line = line.replace( newH+":", dNew2Init[newH].replace(" ","_").replace("::","-").replace(":","-").replace(",","-")+":" ) - outF.write( line ) - outF.close() - - - def retrieveInitialSequenceHeadersForAlignFile( self, dNew2Init ): - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - a = Align() - while True: - line = inFileHandler.readline() - if line == "": - break - a.setFromTuple( line.split("\t") ) - nameToBeReplaced = a.range_query.seqname - if dNew2Init.has_key( nameToBeReplaced ): - a.range_query.seqname = dNew2Init[ nameToBeReplaced ] - nameToBeReplaced = a.range_subject.seqname - if dNew2Init.has_key( nameToBeReplaced ): - a.range_subject.seqname = dNew2Init[ nameToBeReplaced ] - a.write( outFileHandler ) - inFileHandler.close() - outFileHandler.close() - - - def retrieveInitialSequenceHeadersForPathFile( self, dNew2Init ): - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - p = Path() - while True: - line = inFileHandler.readline() - if line == "": - break - p.setFromTuple( line.split("\t") ) - nameToBeReplaced = p.range_query.seqname - if dNew2Init.has_key( nameToBeReplaced ): - p.range_query.seqname = dNew2Init[ nameToBeReplaced ] - nameToBeReplaced = p.range_subject.seqname - if dNew2Init.has_key( nameToBeReplaced ): - p.range_subject.seqname = dNew2Init[ nameToBeReplaced ] - p.write( outFileHandler ) - inFileHandler.close() - outFileHandler.close() - - - def retrieveInitialSequenceHeadersForMatchFile( self, dNew2Init ): - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - m = Match() - while True: - line = inFileHandler.readline() - if line == "": - break - if line[0:10] == "query.name": - continue - m.setFromTuple( line.split("\t") ) - nameToBeReplaced = m.range_query.seqname - if dNew2Init.has_key( nameToBeReplaced ): - m.range_query.seqname = dNew2Init[ nameToBeReplaced ] - nameToBeReplaced = m.range_subject.seqname - if dNew2Init.has_key( nameToBeReplaced ): - m.range_subject.seqname = dNew2Init[ nameToBeReplaced ] - m.write( outFileHandler ) - inFileHandler.close() - outFileHandler.close() - - def retrieveInitialSequenceHeadersForAxtFile( self, dNew2Init): - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - while True: - try: - line = inFileHandler.next() - except StopIteration: - break - - if line == "" or not "seq" in line: - outFileHandler.write(line) - else : - elems = line.split(" ") - try: - subject_seqname = elems[1] - if self.replace_subject : - nameToBeReplaced = elems[1] - if dNew2Init.has_key( nameToBeReplaced ): - subject_seqname = dNew2Init[nameToBeReplaced] - subject_seqname = subject_seqname.strip('\n').strip('\r') - - query_seqname = elems[4] - if self.replace_query: - nameToBeReplaced = elems[4] - if dNew2Init.has_key( nameToBeReplaced ): - query_seqname = dNew2Init[nameToBeReplaced] - query_seqname = query_seqname.strip('\n').strip('\r') - - modedelems = [ elems[0], subject_seqname, elems[2], elems[3], query_seqname, elems[5], elems[6], elems[7], elems[8]] - newLine = " ".join(modedelems) - outFileHandler.write("%s\n" % newLine) - if self._verbose >0 : - print("query", query_seqname, "subject", subject_seqname) - print("Output axt_line : line %s " % newLine) - except: pass - inFileHandler.close() - outFileHandler.close() - - def retrieveInitialSequenceHeadersForPslFile( self, dNew2Init): - - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - while True: - try: - line = inFileHandler.next() - except StopIteration: - break - - if line == "" or not "seq" in line: - outFileHandler.write(line) - else : - elems = line.split() - try: - subject_seqname = elems[13] - if self.replace_subject : - nameToBeReplaced = elems[13] - if dNew2Init.has_key( nameToBeReplaced ): - subject_seqname = dNew2Init[nameToBeReplaced] - subject_seqname = subject_seqname.strip('\n').strip('\r') - - query_seqname = elems[9] - if self.replace_query: - nameToBeReplaced = elems[9] - if dNew2Init.has_key( nameToBeReplaced ): - query_seqname = dNew2Init[nameToBeReplaced] - query_seqname = query_seqname.strip('\n').strip('\r') - - modedelems =elems[0:9]+[query_seqname]+elems[10:13]+[subject_seqname]+elems[14:21] - #modedelems = [ elems[0], elems[1], elems[2], elems[3], elems[4], elems[5], elems[6], elems[7], elems[8], query_seqname, ] - #modedelems = [ elems[0], subject_seqname, elems[2], elems[3], query_seqname, elems[5], elems[6], elems[7], elems[8]] - newLine = "\t".join(modedelems) - outFileHandler.write("%s\n" % newLine) - if self._verbose >0 : - print("query", query_seqname, "subject", subject_seqname) - print("Output psl_line : line %s " % newLine) - except: pass - sys.stdout.flush() - inFileHandler.close() - outFileHandler.close() - - - def retrieveInitialSequenceHeadersForLastZFile( self, dNew2Init): - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - while True: - try: - line = inFileHandler.next() - except StopIteration: - break - #score, name1, strand1, size1, zstart1, end1, name2, strand2, size2, zstart2, end2, identity, coverage - - if line == "" or not "seq" in line: - outFileHandler.write(line) - else : - elems = line.split("\t") - try: - subject_seqname = elems[1] - if self.replace_subject : - nameToBeReplaced = elems[1] - if dNew2Init.has_key( nameToBeReplaced ): - subject_seqname = dNew2Init[nameToBeReplaced] - subject_seqname = subject_seqname.strip('\n').strip('\r') - - query_seqname = elems[6] - if self.replace_query: - nameToBeReplaced = elems[6] - if dNew2Init.has_key( nameToBeReplaced ): - query_seqname = dNew2Init[nameToBeReplaced] - query_seqname = query_seqname.strip('\n').strip('\r') - - modedelems = [ elems[0], subject_seqname, elems[2], elems[3], elems[4], elems[5], query_seqname, elems[7], elems[8],elems[9],elems[10], elems[11], elems[12],elems[13],elems[14].strip('\n').strip('\r')] - newLine = "\t".join(modedelems) - outFileHandler.write("%s\n" % newLine) - if self._verbose >0 : - print("query", query_seqname, "subject", subject_seqname) - print("Output lastz_line : line %s " % newLine) - except: pass - inFileHandler.close() - outFileHandler.close() - - def retrieveInitialSequenceHeadersForChainFile( self, dNew2Init): - #format: chain score tName tSize tStrand tStart tEnd qName qSize qStrand qStart qEnd id - inFileHandler = open( self._inFile, "r" ) - outFileHandler = open( self._outFile, "w" ) - while True: - try: - line = inFileHandler.next() - except StopIteration: - break - if line == "" or not "seq" in line: - outFileHandler.write(line) - else : - elems = line.split(" ") - try: - subject_seqname = elems[2] - if self.replace_subject : - nameToBeReplaced = elems[2] - if dNew2Init.has_key( nameToBeReplaced ): - subject_seqname = dNew2Init[nameToBeReplaced] - subject_seqname = subject_seqname.strip('\n').strip('\r') - - query_seqname = elems[7] - if self.replace_query: - nameToBeReplaced = elems[7] - if dNew2Init.has_key( nameToBeReplaced ): - query_seqname = dNew2Init[nameToBeReplaced] - query_seqname = query_seqname.strip('\n').strip('\r') - - modedelems = elems[:] - modedelems[2] = subject_seqname - modedelems[7] = query_seqname - newLine = " ".join(modedelems) - outFileHandler.write("%s\n" % newLine) - except: pass - - inFileHandler.close() - outFileHandler.close() - - - def run( self ): - self.checkAttributes() - if self._step == 1: - if self._linkFile == "": - self._linkFile = "%s.newHlink" % ( self._inFile ) - if self._format == "fasta": - self.shortenSequenceHeadersForFastaFile() - if self._step == 2: - dNew2Init = self.getLinksNewToInitialHeaders() - if self._format == "fasta": - self.retrieveInitialSequenceHeadersForFastaFile( dNew2Init ) - elif self._format == "newick": - self.retrieveInitialSequenceHeadersForNewickFile( dNew2Init ) - elif self._format == "align": - self.retrieveInitialSequenceHeadersForAlignFile( dNew2Init ) - elif self._format == "path": - self.retrieveInitialSequenceHeadersForPathFile( dNew2Init ) - elif self._format == "axt": - self.retrieveInitialSequenceHeadersForAxtFile( dNew2Init) - elif self._format == "psl": - self.retrieveInitialSequenceHeadersForPslFile( dNew2Init) - elif self._format == "lastz": - self.retrieveInitialSequenceHeadersForLastZFile(dNew2Init) - elif self._format == "chain": - self.retrieveInitialSequenceHeadersForChainFile(dNew2Init) - elif self._format in [ "tab", "match" ]: - self.retrieveInitialSequenceHeadersForMatchFile( dNew2Init ) - - -if __name__ == "__main__": - i = ChangeSequenceHeaders() - i.setAttributesFromCmdLine() - i.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/CheckMysqlConnect.py --- a/commons/tools/CheckMysqlConnect.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,86 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import sys -import os -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.RepetException import RepetException -from commons.tools.CleanClusterNodesAfterRepet import CleanClusterNodesAfterRepet - -REPET_PATH = os.environ.get("REPET_PATH") - -def main(): - - description = "Check MySQL connection on each node" - usage = "CheckMysqlConnect.py [options]" - examples = "\nExample 1: check MySQL connection from every node of a SGE cluster using environment variables:\n" - examples += "\t$ python CheckMysqlConnect.py" - examples += "\n\t" - examples += "\nExample 2: check MySQL connection from every node of a SGE cluster using configuration file:\n" - examples += "\t$ python CheckMysqlConnect.py -C configFileName" - examples += "\n\t" - examples += "\nExample 3: check MySQL connection from every node of a SGE cluster using environment variables and using a different python executable than the one in the PATH:\n" - examples += "\t$ python CheckMysqlConnect.py -p /path/to/python" - examples += "\n\n" - - parser = RepetOptionParser(description = description, usage = usage, version = "v1.0", epilog = examples) - parser.add_option( "-p", "--path", dest = "pythonPath", type = "string", help = "path to python executable ('python' included, without finishing '/')", default = "python") - parser.add_option( "-C", "--config", dest = "config", type = "string", help = "path to config file", default = "") - - options, args = parser.parse_args() - pythonPath = options.pythonPath - configFile = options.config - - iCleanClusterNodesAfterRepet = CleanClusterNodesAfterRepet() - nodesList = iCleanClusterNodesAfterRepet.getAllNodesList() - - nbNodes = len(nodesList) - nodeCount = 0 - configOption = "" - for node in nodesList: - try: - nodeCount += 1 - print "Connect to node '%s' (%i/%i)..." % (node, nodeCount, nbNodes) - sys.stdout.flush() - cmd = "ssh" - cmd += " -q %s " % ( node ) - if configFile != "": - configOption = " -C %s" % configFile - cmd += "'%s %s/bin/MysqlConnect.py -n %s %s'" % (pythonPath, REPET_PATH, node, configOption) - os.system(cmd) - except RepetException, e: - print e.getMessage() - - iCleanClusterNodesAfterRepet.clean() - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/CleanClusterNodesAfterRepet.py --- a/commons/tools/CleanClusterNodesAfterRepet.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,177 +0,0 @@ -#!/usr/bin/env python - -## @file -# Clean the cluster nodes after REPET was used. -# -# usage: CleanClusterNodesAfterRepet.py [ options ] -# options: -# -h: this help -# -n: node to clean (otherwise all nodes will be cleaned) -# -t: temporary directory (e.g. '/tmp') -# -p: pattern (e.g. 'DmelChr4*') -# -v: verbosity level (default=0/1/2) - -import os -import sys -import getopt - -class CleanClusterNodesAfterRepet( object ): - """ - Clean the cluster nodes after REPET was used. - """ - - def __init__( self ): - """ - Constructor. - """ - self._lNodes = [] - self._tmpDir = "" - self._pattern = "" - self._verbose = 0 - self._lNodesToExcept = ["compute-2-46", "compute-2-47"] - - def help( self ): - """ - Display the help on stdout. - """ - print - print "usage: %s.py [ options ]" % ( type(self).__name__ ) - print "options:" - print " -h: this help" - print " -n: node to clean (otherwise all nodes will be cleaned)" - print " -t: temporary directory (e.g. '/tmp')" - print " -p: pattern (e.g. 'DmelChr4*')" - print " -v: verbosity level (default=0/1/2)" - print - - def setAttributesFromCmdLine( self ): - """ - Set the attributes from the command-line. - """ - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:n:t:p:v:") - except getopt.GetoptError, err: - print str(err); self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-n": - self.setLNodes( a.split(" ") ) - elif o == "-t": - self.setTempDirectory( a ) - elif o == "-p": - self.setPattern( a ) - elif o == "-v": - self.setVerbosityLevel( a ) - - def setLNodes( self, a ): - self._lNodes = a - - def setTempDirectory( self, a ): - if a[-1] == "/": - self._tmpDir = a[:-1] - else: - self._tmpDir = a - - def setPattern( self, a ): - self._pattern = a - - def setVerbosityLevel( self, verbose ): - self._verbose = int(verbose) - - def checkAttributes( self ): - """ - Before running, check the required attributes are properly filled. - """ - if self._tmpDir == "": - print "ERROR: need a valid temporary directory" - self.help(); sys.exit(1) - - def getAllNodesList( self ): - """ - Return the list of the names of each node. - """ - lNodes = [] - log = os.system( "qhost > qhost.txt" ) - if log != 0: print "ERROR with qhost"; sys.exit(1) - inF = open( "qhost.txt", "r" ) - line = inF.readline() - line = inF.readline() - line = inF.readline() - while True: - if line == "": - break - tokens = line.split() - if tokens[3] == "-": - line = inF.readline() - continue - lNodes.append( tokens[0] ) - line = inF.readline() - inF.close() - #Remove nodes to avoid from the nodes list - for node in self._lNodesToExcept: - if node in lNodes: - lNodes.remove(node) - return lNodes - - def showNodeList( self, lNodes ): - print "nb of nodes: %i" % ( len(lNodes) ) - for i in range(0,len(lNodes)): - print " %i: %s" % ( i+1, lNodes[i] ) - - def cleanNodes( self): - """ - Connect to each job and clean the temporary directory. - """ - nbNodes = len(self._lNodes) - nodeCount = 0 - for node in self._lNodes: - nodeCount += 1 - if self._verbose > 0: - print "connect to node '%s' (%i/%i)..." % ( node, nodeCount, nbNodes ) - sys.stdout.flush() - cmd = "ssh" - cmd += " -q %s " % ( node ) - cmd += "'find %s" % ( self._tmpDir ) - cmd += " -user %s" % ( os.environ["USER"] ) - if self._pattern != "": - cmd += " -name '%s'" % ( self._pattern ) - cmd += " 2> /dev/null -exec rm -rf {} \; ; exit'" - if self._verbose > 0: print cmd; sys.stdout.flush() - os.system( cmd ) # warning, even if everything goes right, ssh returns an error code, i.e. different than 0 - - def clean( self ): - if os.path.exists( "qhost.txt" ): - os.remove( "qhost.txt" ) - - def start( self ): - """ - Useful commands before running the program. - """ - if self._verbose > 0: - print "START %s" % ( type(self).__name__ ); sys.stdout.flush() - self.checkAttributes() - - def end( self ): - """ - Useful commands before ending the program. - """ - self.clean() - if self._verbose > 0: - print "END %s" % ( type(self).__name__ ); sys.stdout.flush() - - def run( self ): - """ - Run the program. - """ - self.start() - if self._lNodes == []: - self._lNodes = self.getAllNodesList() - if self._verbose > 0: self.showNodeList( self._lNodes ) - self.cleanNodes() - self.end() - -if __name__ == "__main__": - i = CleanClusterNodesAfterRepet() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/CorrelateTEageWithGCcontent.py --- a/commons/tools/CorrelateTEageWithGCcontent.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,204 +0,0 @@ -#!/usr/bin/env python - -import sys -import os -import getopt -import math -from commons.core.sql.DbMySql import DbMySql -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.core.coord.PathUtils import PathUtils -from commons.core.coord.SetUtils import SetUtils -from commons.core.seq.BioseqUtils import BioseqUtils - - -class CorrelateTEageWithGCcontent( object ): - - def __init__( self ): - self._inputCoord = "" - self._inputGenome = "" - self._inputTErefseq = "" - self._configFile = "" - self._outFile = "" - self._verbose = 0 - self._db = None - self._tableCoord = "" - self._pathA = TablePathAdaptator() - self._tableGenome = "" - self._seqA = TableSeqAdaptator() - - - def help( self ): - print - print "usage: CorrelateTEageWithGCcontent.py [ options ]" - print "options:" - print " -h: this help" - print " -i: input TE coordinates (can be file or table)" - print " TEs as subjects in 'path' format" - print " -g: input genome sequences (can be fasta file or table)" - print " -r: input TE reference sequences (can be fasta file or table)" - print " -C: configuration file (if table as input)" - print " -o: output fasta file (default=inputCoord+'.gc')" - print " -v: verbosity level (default=0/1)" - print - - - def setAttributesFromCmdLine( self ): - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:g:r:C:o:v:") - except getopt.GetoptError, err: - msg = "%s" % str(err) - sys.stderr.write( "%s\n" % msg ) - self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-i": - self._inputCoord = a - elif o == "-g": - self._inputGenome = a - elif o == "-r": - self._inputTErefseq = a - elif o == "-C": - self._configFile = a - elif o =="-o": - self._outFile = a - elif o == "-v": - self._verbose = int(a) - - - def checkAttributes( self ): - if self._inputCoord == "": - msg = "ERROR: missing input TE coordinates (-i)" - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._inputCoord ): - if not os.path.exists( self._configFile ): - msg = "ERROR: neither input file '%s' nor configuration file '%s'" % ( self._inputCoord, self._configFile ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._configFile ): - msg = "ERROR: can't find configuration file '%s'" % ( self._configFile ) - sys.stderr.write( "%s\n" % msg ) - sys.exit(1) - self._db = DbMySql( cfgFileName=self._configFile ) - if not self._db.exist( self._inputCoord ): - msg = "ERROR: can't find table '%s'" % ( self._inputCoord ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - self._tableCoord = self._inputCoord - else: - self._tableCoord = self._inputCoord.replace(".","_") - if self._inputGenome == "": - msg = "ERROR: missing input genome sequences (-g)" - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._inputGenome ): - if not self._db.doesTableExist( self._inputGenome ): - msg = "ERROR: can't find table '%s'" % ( self._inputGenome ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - self._tableGenome = self._inputGenome - else: - self._tableGenome = self._inputGenome.replace(".","_") - if self._inputTErefseq == "": - msg = "ERROR: missing input TE reference sequences (-r)" - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._inputTErefseq ): - if not self._db.doesTableExist( self._inputTErefseq ): - msg = "ERROR: can't find table '%s'" % ( self._inputTErefseq ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if self._outFile == "": - self._outFile = "%s.gc" % ( self._inputCoord ) - - - def getLengthOfTErefseqs( self ): - if os.path.exists( self._inputTErefseq ): - return BioseqUtils.getLengthPerSeqFromFile( self._inputTErefseq ) - else: - dTErefseq2Length = {} - refseqA = TableSeqAdaptator( self._db, self._inputTErefseq ) - lAccessions = refseqA.getAccessionsList() - for acc in lAccessions: - dTErefseq2Length[ acc ] = refseqA.getSeqLengthFromAccession( acc ) - return dTErefseq2Length - - - def start( self ): - self.checkAttributes() - if self._verbose > 0: - print "START CorrelateTEageWithGCcontent.py" - sys.stdout.flush() - if os.path.exists( self._inputCoord ): - self._db = DbMySql( cfgFileName=self._configFile ) - self._db.createTable( self._tableCoord, "path", self._inputCoord, True ) - self._pathA = TablePathAdaptator( self._db, self._tableCoord ) - if os.path.exists( self._inputGenome ): - self._db.createTable( self._tableGenome, "seq", self._inputGenome, True ) - self._seqA = TableSeqAdaptator( self._db, self._tableGenome ) - if self._verbose > 0: - print "output fasta file: %s" % self._outFile - - - def end( self ): - if os.path.exists( self._inputCoord ): - self._db.dropTable( self._tableCoord ) - if os.path.exists( self._inputGenome ): - self._db.dropTable( self._tableGenome ) - self._db.close() - if self._verbose > 0: - print "END CorrelateTEageWithGCcontent.py" - sys.stdout.flush() - - - def run( self ): - self.start() - - dTErefseq2Length = self.getLengthOfTErefseqs() - - outFileHandler = open( self._outFile, "w" ) - outFileHandler.write( "copy\tTE\tchr\tlength\tid\tGC\tlengthPerc\n" ) - - lIdentifiers = self._pathA.getIdList() - nbTEcopies = len(lIdentifiers) - if self._verbose > 0: - print "nb of TE copies: %i" % ( nbTEcopies ) - sys.stdout.flush() - count = 0 - power10 = int( math.floor( math.log10( nbTEcopies ) ) ) - 1 - for id in lIdentifiers: - count += 1 - if self._verbose > 0 and power10 > 0 and count % math.pow(10,power10) == 0: - print "%s / %s" % ( str(count).zfill(power10+2), str(nbTEcopies).zfill(power10+2) ) - sys.stdout.flush() - lPaths = self._pathA.getPathListFromId( id ) - lSets = PathUtils.getSetListFromQueries( lPaths ) - lMergedSets = SetUtils.mergeSetsInList( lSets ) - bs = self._seqA.getBioseqFromSetList( lMergedSets ) - data = "%i" % id - data += "\t%s" % ( bs.header.split("::")[0] ) - data += "\t%s" % ( lPaths[0].getQueryName() ) - data += "\t%i" % ( bs.getLength() ) - data += "\t%.2f" % ( PathUtils.getIdentityFromPathList( lPaths ) ) - data += "\t%.2f" % ( bs.getGCpercentage() ) - data += "\t%.2f" % ( 100 * bs.getLength() / float( dTErefseq2Length[ bs.header.split("::")[0] ] ) ) - outFileHandler.write( "%s\n" % data ) - - outFileHandler.close() - - self.end() - - -if __name__ == "__main__": - i = CorrelateTEageWithGCcontent() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/FilterAlign.py --- a/commons/tools/FilterAlign.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,149 +0,0 @@ -#!/usr/bin/env python - -import sys -import getopt -import os - - -def help(): - print - print "usage: ",sys.argv[0].split("/")[-1],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='align')" - print " -E: maximum E-value (default=100)" - print " -S: minimum score (default=0)" - print " -I: minimum identity (default=0)" - print " -l: minimum length (default=0)" - print " -L: maximum length (default=1000000000)" - print " -o: name of the output file (default=inFileName+'.filtered')" - print " -v: verbose (default=0/1)" - print - - -def main(): - """ - This program filters the output from BLASTER ('align' file recording HSPs). - """ - - inFileName = "" - outFileName = "" - maxEValue = 100 - minIdentity = 0 - minLength = 0 - maxLength = 1000000000 - minScore = 0 - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:E:S:I:l:L:o:v:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit() - elif o == "-i": - inFileName = a - elif o == "-E": - maxEValue = float(a) - elif o == "-S": - minScore = int(float(a)) - elif o == "-I": - minIdentity = int(float(a)) - elif o == "-l": - minLength = int(a) - elif o == "-L": - maxLength = int(a) - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing input file name" - help() - sys.exit(1) - - if outFileName == "": - outFileName = "%s.filtered" % ( inFileName ) - - if os.path.exists( os.environ["REPET_PATH"] + "/bin/filterAlign" ): - prg = os.environ["REPET_PATH"] + "/bin/filterAlign" - cmd = prg - cmd += " -i %s" % ( inFileName ) - cmd += " -E %g" % ( maxEValue ) - cmd += " -S %i" % ( minScore ) - cmd += " -I %f" % ( minIdentity ) - cmd += " -l %i" % ( minLength ) - cmd += " -L %i" % ( maxLength ) - cmd += " -o %s" % ( outFileName ) - cmd += " -v %i" % ( verbose ) - return os.system( cmd ) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - inFile = open( inFileName, "r" ) - outFile = open( outFileName, "w" ) - - nbMatches = 0 - nbFiltered = 0 - - line = inFile.readline() - while True: - if line == "": - break - nbMatches += 1 - data = line.split("\t") - qryName = data[0] - qryStart = data[1] - qryEnd = data[2] - sbjName = data[3] - sbjStart = data[4] - sbjEnd = data[5] - Evalue = data[6] - score = data[7] - identity = data[8] - - if int(qryStart) < int(qryEnd): - matchLength = int(qryEnd) - int(qryStart) + 1 - elif int(qryStart) > int(qryEnd): - matchLength = int(qryStart) - int(qryEnd) + 1 - - if float(Evalue) <= maxEValue and matchLength >= minLength and \ - float(identity) >= minIdentity and matchLength <= maxLength and \ - int(score) >= minScore: - string = qryName + "\t" + qryStart + "\t" + qryEnd + "\t" +\ - sbjName + "\t" + sbjStart + "\t" + sbjEnd + "\t" +\ - Evalue + "\t" + score + "\t" + identity - outFile.write( string ) - else: - nbFiltered += 1 - string = "qry %s (%s-%s) vs subj %s (%s-%s): Eval=%s identity=%s matchLength=%s score=%s" %\ - ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Evalue, identity.split("\n")[0], matchLength, score ) - if verbose > 1: - print string; sys.stdout.flush() - - line = inFile.readline() - - inFile.close() - outFile.close() - - if verbose > 0: - msg = "total number of matches: %i" % ( nbMatches ) - msg += "\nnumber of filtered matches: %i" % ( nbFiltered ) - print msg; sys.stdout.flush() - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/GFF3Maker.py --- a/commons/tools/GFF3Maker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,498 +0,0 @@ -#!/usr/bin/env python - -##@file GFF3Maker.py - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -import sys -import os - -## GFF3Maker exports annotations from a 'path' table into a GFF3 file. -# -class GFF3Maker(object): - - def __init__(self, inFastaName = "", tablesFileName = "", classifTableName = "", isChado = False, isGFF3WithoutAnnotation = False, isWithSequence = False, areMatchPartsCompulsory = False, configFileName = "", verbose = 0, doMergeIdenticalMatches = False, doSplit = False): - self._inFastaName = inFastaName - self._tablesFileName = tablesFileName - self._classifTableName = classifTableName - self._isChado = isChado - self._isGFF3WithoutAnnotation = isGFF3WithoutAnnotation - self._isWithSequence = isWithSequence - self._areMatchPartsCompulsory = areMatchPartsCompulsory - self._configFileName = configFileName - self._doMergeIdenticalMatches = doMergeIdenticalMatches - self._doSplit = doSplit - self._iDB = None - self._verbose = verbose - - def setAttributesFromCmdLine(self): - description = "GFF3Maker exports annotations from 'path', 'set' and/or 'classif' tables into a GFF3 file\n" - parser = RepetOptionParser(description = description) - parser.add_option("-f", "--inseq", dest = "inFastaName", action = "store", type = "string", help = "'seq' table recording the input sequences", default = "") - parser.add_option("-t", "--tablesfile", dest = "tablesFileName", action = "store", type = "string", help = "tabulated file of table name to use to create the gff3 files (fields: tier name, format, table name)", default = "") - parser.add_option("-w", "--withSequence", dest = "isWithSequence", action = "store_true", help = "write the sequence at the end of GFF3 file", default = False) - parser.add_option("-a", "--withoutAnnotation", dest = "isGFF3WithoutAnnotation", action = "store_true", help = "write GFF3 files even if no annotation", default = False) - parser.add_option("-p", "--matchPart", dest = "areMatchPartsCompulsory", action = "store_true", help = "always associate a match_part to a match", default = False) - parser.add_option("-i", "--classifTable", dest = "classifTable", action = "store", type = "string", help = "name of the TE library classification table [optional]", default = "") - parser.add_option("-c", "--chado", dest = "isChado", action = "store_true", help = "Chado compliance", default = False) - parser.add_option("-m", "--doMergeIdenticalMatches", dest = "doMergeIdenticalMatches", action = "store_true", help = "merge identical matches based on query start, query end, score", default = False) - parser.add_option("-s", "--doSplit", dest = "doSplit", action = "store_true", help = "split each GFF3 per annotation type", default = False) - parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "configuration file for database connection", default = "") - parser.add_option("-v", "--verbose", dest = "verbose", action = "store", type = "int", help = "verbosity level (default=0, else 1 or 2)", default = 0) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - #TODO: write a "setAttributesFromConfig" - def _setAttributesFromOptions(self, options): - self.setInFastaName(options.inFastaName) - self.setTablesFileName(options.tablesFileName) - self.setClassifTable(options.classifTable) - self.setIsChado(options.isChado) - self.setDoMergeIdenticalMatches(options.doMergeIdenticalMatches) - self.setIsWithSequence(options.isWithSequence) - self.setIsGFF3WithoutAnnotation(options.isGFF3WithoutAnnotation) - self.setAreMatchPartCompulsory(options.areMatchPartsCompulsory) - self.setDoSplit(options.doSplit) - self.setConfigFileName(options.configFileName) - self.setVerbose(options.verbose) - - def setInFastaName(self, inFastaName): - self._inFastaName = inFastaName - - def setTablesFileName(self, tablesFileName): - self._tablesFileName = tablesFileName - - def setIsWithSequence(self, isWithSequence): - self._isWithSequence = isWithSequence - - def setIsGFF3WithoutAnnotation(self, isGFF3WithoutAnnotation): - self._isGFF3WithoutAnnotation = isGFF3WithoutAnnotation - - def setAreMatchPartCompulsory(self, areMatchPartsCompulsory): - self._areMatchPartsCompulsory = areMatchPartsCompulsory - - def setClassifTable(self, classifTable): - self._classifTableName = classifTable - - def setIsChado(self, isChado): - self._isChado = isChado - - def setDoMergeIdenticalMatches(self, doMergeIdenticalMatches): - self._doMergeIdenticalMatches = doMergeIdenticalMatches - - def setDoSplit(self, doSplit): - self._doSplit = doSplit - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def setVerbose(self, verbose): - self._verbose = verbose - - def checkOptions(self): - if self._inFastaName == "": - raise Exception("ERROR: options -f required") - - if self._configFileName != "": - if not FileUtils.isRessourceExists(self._configFileName): - raise Exception("ERROR: configuration file does not exist!") - - if self._classifTableName and not self._iDB.doesTableExist(self._classifTableName): - raise Exception("ERROR: classification table '%s' does not exist!" % self._classifTableName) - - ## Retrieve the features to write in the GFF3 file. - # - # @param pathTable string name of the table recording the annotations (i.e. the features) - # @param seqName string name of the sequence (the source feature) on which we want to visualize the matches (the features) - # @param source string the program that generated the feature (i.e. REPET) - # @param frame string "." by default (or "+", "-") - # @return pathString string which will be printed in path file - # - def _getPathFeatures(self, pathTable, seqTable, seqName, source, feature, frame): - pathString = "" - iTPA = TablePathAdaptator(self._iDB, pathTable) - lPaths = iTPA.getPathListSortedByQueryCoordAndScoreFromQuery(seqName) - # organise them into 'match' and 'match_part' - if lPaths: - dPathID2Data = self._gatherSamePathFeatures(lPaths) - # build the output string - for pathID in dPathID2Data: - pathString += self._organizeEachPathFeature(pathID, dPathID2Data[pathID], seqName, source, frame, seqTable) - return pathString - - ## Gather matches with the same path ID. - # - # @param data list of string lists results of a SQL request - # @return dPathID2Matchs dict whose keys are path IDs and values are matches data - # - def _gatherSamePathFeatures(self, lPaths): - dPathID2Matchs = {} - iPreviousPath = lPaths[0] - iPreviousPath.otherTargets = [] - for iPath in lPaths[1:]: - if self._doMergeIdenticalMatches and iPreviousPath.getQueryStart() == iPath.getQueryStart() and iPreviousPath.getQueryEnd() == iPath.getQueryEnd() and iPreviousPath.getScore() == iPath.getScore() and iPreviousPath.getSubjectName() != iPath.getSubjectName(): - iPreviousPath.otherTargets.append("%s %d %d" % (iPath.getSubjectName(), iPath.getSubjectStart(), iPath.getSubjectEnd())) - else: - self._addPathToMatchDict(dPathID2Matchs, iPreviousPath) - iPreviousPath = iPath - iPreviousPath.otherTargets = [] - self._addPathToMatchDict(dPathID2Matchs, iPreviousPath) - return dPathID2Matchs - - def _getClassifEvidenceBySeqName(self, seqName): - lseqName = seqName.split('_') - seqNameStructure = '%s_%%' % lseqName[0] - if lseqName[-1] == 'reversed': - seqNameStructure += '%s_%s' % (lseqName[-2],lseqName[-1]) - else: - seqNameStructure += lseqName[-1] - qry = "SELECT evidence FROM %s WHERE seq_name like \"%s\"" % (self._classifTableName, seqNameStructure) - self._iDB.execute(qry) - result = "" - try: - result = "".join(self._iDB.fetchall()[0]) - except: pass - return result - - def _addPathToMatchDict(self, dPathID2Matchs, iPreviousPath): - pathId = iPreviousPath.getIdentifier() - subjectStart = iPreviousPath.getSubjectStart() - subjectEnd = iPreviousPath.getSubjectEnd() - strand = iPreviousPath.getSubjectStrand() - if subjectStart > subjectEnd: - tmp = subjectStart - subjectStart = subjectEnd - subjectEnd = tmp - queryStart = iPreviousPath.getQueryStart() - queryEnd = iPreviousPath.getQueryEnd() - subjectName = iPreviousPath.getSubjectName() - eValue = iPreviousPath.getEvalue() - identity = iPreviousPath.getIdentity() - otherTargets = iPreviousPath.otherTargets - if dPathID2Matchs.has_key(pathId): - dPathID2Matchs[pathId].append([queryStart, queryEnd, strand, subjectName, subjectStart, subjectEnd, eValue, identity, otherTargets]) - else: - dPathID2Matchs[pathId] = [[queryStart, queryEnd, strand, subjectName, subjectStart, subjectEnd, eValue, identity, otherTargets]] - - def _getConsensusLengthByTargetName(self, targetName, seqTableName): - iTableSeqAdaptator = TableSeqAdaptator(self._iDB, seqTableName) - return iTableSeqAdaptator.getSeqLengthFromDescription(targetName) - - ## For a specific path ID, organize match data according to the GFF3 format. - # - # @param pathID string path ID - # @param lMatches match list - # @param seqName string name of the source feature - # @param source string 'source' field for GFF3 format - # @param frame string 'frame' field for GFF3 format - # @return lines string to write in the GFF3 file - # - def _organizeEachPathFeature(self, pathID, lMatches, seqName, source, frame, seqTable = ""): - lines = "" - minStart = lMatches[0][0] - maxEnd = lMatches[0][1] - minStartSubject = lMatches[0][4] - maxEndSubject = lMatches[0][5] - strand = lMatches[0][2] - - # for each match - for i in lMatches: - if i[0] < minStart: - minStart = i[0] - if i[1] > maxEnd: - maxEnd = i[1] - if i[4] < minStartSubject: - minStartSubject = i[4] - if i[5] > maxEndSubject: - maxEndSubject = i[5] - - target = lMatches[0][3] - - targetDescTag = "" - if self._classifTableName != "": - targetDescTag = self._getClassifEvidenceBySeqName(target) - if targetDescTag != "": - targetDescTag = ";TargetDescription=%s" % targetDescTag.replace('=', ':').replace(';', '').replace(',', ' |') - - targetLengthTag = "" - if seqTable != "": - targetLengthTag = self._getConsensusLengthByTargetName(target, seqTable) - targetLengthTag = ";TargetLength=%i" % targetLengthTag - - attributes = "ID=ms%s_%s_%s" % (pathID, seqName, target) - if self._isChado: - attributes += ";Target=%s+%s+%s" % (target, minStartSubject, maxEndSubject) - else: - attributes += ";Target=%s %s %s" % (target, minStartSubject, maxEndSubject) - - if lMatches[0][8]: - otherTargets = ", ".join(lMatches[0][8]) - attributes += ";OtherTargets=%s" % otherTargets - else: - attributes += targetLengthTag - attributes += targetDescTag - if len(lMatches) == 1: - attributes += ";Identity=%s" % lMatches[0][7] - - - lines += "%s\t%s\tmatch\t%s\t%s\t0.0\t%s\t%s\t%s\n" % (seqName, source, minStart, maxEnd, strand, frame, attributes) - - if len(lMatches) > 1 or self._areMatchPartsCompulsory: - count = 1 - for i in lMatches: - attributes = "ID=mp%s-%i_%s_%s" % (pathID, count, seqName, target) - attributes += ";Parent=ms%s%s%s%s%s" % (pathID, "_", seqName, "_", target) - if self._isChado: - attributes += ";Target=%s+%s+%s" % (target, i[4], i[5]) - else: - attributes += ";Target=%s %s %s" % (target, i[4], i[5]) - - if not i[8]: - attributes += ";Identity=%s" % i[7] - lines += "%s\t%s\tmatch_part\t%s\t%s\t%s\t%s\t%s\t%s\n" % (seqName, source, i[0], i[1], i[6], i[2], frame, attributes) - count += 1 - - return lines - - ## Retrieve the features to write in the GFF3 file. - # - # @param table string name of the table recording the annotations (i.e. the features) - # @param key string name of the sequence (the source feature) on which we want to visualize the matches (the features) - # @param source string the program that generated the feature (i.e. REPET) - # @param frame string "." by default (or "+", "-") - # @return setString string which will be printed in set file - # - def _getSetFeatures(self, table, key, source, feature, frame): - setString = "" - # retrieve all the data about the matches - qry = "SELECT DISTINCT path,name,start,end FROM %s WHERE chr=\"%s\"" % (table, key) - self._iDB.execute(qry) - data = self._iDB.fetchall() - # organise them into 'match' and 'match_part' - dPathID2Data = self._gatherSameSetFeatures(data) - # build the output string - for pathID in dPathID2Data: - setString += self._organizeEachSetFeature(pathID, dPathID2Data[pathID], key, source, frame) - return setString - - ## Gather matches with the same path ID. - # - # @param data list of string lists results of a SQL request - # @return dSetID2Matchs dict whose keys are set IDs and values are matches data - # - def _gatherSameSetFeatures(self, data): - dSetID2Matchs = {} - - for i in data: - setID = i[0] - name = i[1] - start = i[2] - end = i[3] - - matchStart = min(start, end) - matchEnd = max(start, end) - strand = self._getStrand(start, end) - - if dSetID2Matchs.has_key(setID): - dSetID2Matchs[setID].append([name, matchStart, matchEnd, strand]) - - else: - dSetID2Matchs[setID] = [[name, matchStart, matchEnd, strand]] - - return dSetID2Matchs - - ## For a specific set ID, organize match data according to the GFF3 format. - # - # @param setID string path ID - # @param lMatches match list - # @param seqName string name of the source feature - # @param source string 'source' field for GFF3 format - # @param frame string 'frame' field for GFF3 format - # @return lines string to write in the GFF3 file - # - def _organizeEachSetFeature(self, setID, lMatches, seqName, source, frame): - lines = "" - minStart = min(lMatches[0][1], lMatches[0][2]) - maxEnd = max(lMatches[0][1], lMatches[0][2]) - strand = lMatches[0][3] - - # for each match - for i in lMatches: - start = min(i[1],i[2]) - if start < minStart: - minStart = start - end = max(i[1],i[2]) - if end > maxEnd: - maxEnd = end - - target = lMatches[0][0].replace("(","").replace(")","").replace("#","") - - attributes = "ID=ms%s_%s_%s" % (setID, seqName, target) - if self._isChado: - attributes += ";Target=%s+%s+%s" % (target, "1", abs(minStart-maxEnd)+1) - else: - attributes += ";Target=%s %s %s" % (target, "1", abs(minStart-maxEnd)+1) - lines += "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (seqName, source, "match", minStart, maxEnd, "0.0", strand, frame, attributes) - - if len(lMatches) > 1 or self._areMatchPartsCompulsory: - count = 1 - for i in lMatches: - attributes = "ID=mp%s-%i_%s_%s" % (setID, count, seqName, target) - attributes += ";Parent=ms%s%s%s%s%s" % (setID, "_", seqName, "_", target) - if self._isChado: - attributes += ";Target=%s+%s+%s" % (target, "1", abs(i[1]-i[2])+1) - else: - attributes += ";Target=%s %s %s" % (target, "1", abs(i[1]-i[2])+1) - lines += "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (seqName, source, "match_part", i[1], i[2], "0.0", i[3], frame, attributes) - count += 1 - - return lines - - ## Return the strand ('+' if start < end, '-' otherwise). - # - # @param start integer start coordinate - # @param end integer end coordinate - # @return strand string "+" or "-" - # - def _getStrand(self, start, end): - if start < end: - return "+" - else: - return "-" - - def run(self): - #TODO: cat all gff in one gff file in option - if self._configFileName == "": - self._iDB = DbFactory.createInstance() - else: - self._iDB = DbFactory.createInstance(self._configFileName) - - self.checkOptions() - if self._verbose > 0: - print "START GFF3Maker" - sys.stdout.flush() - - tablesFile = open(self._tablesFileName, "r") - linesFromAnnotationTablesFile = tablesFile.readlines() - tablesFile.close() - feature = "region" - frame = "." - - iTSA = TableSeqAdaptator(self._iDB, self._inFastaName) - lTuples = iTSA.getAccessionAndLengthList() - for seqName, length in lTuples : - if not self._doSplit: - fileName = "%s.gff3" % seqName - outFile = open(fileName, "w") - outFile.write("##gff-version 3\n") - outFile.write("##sequence-region %s 1 %s\n" % (seqName, length)) - for line in linesFromAnnotationTablesFile: - if line[0] == "#": - continue - tok = line.split() - if len(tok) == 0: - break - source = tok[0] - format = tok[1] - table = tok[2] - tableseq = "" - if len(tok) == 4: - tableseq = tok[3] - if format == 'path' : - annotations = self._getPathFeatures(table, tableseq, seqName, source, feature, frame) - elif format == 'set' : - annotations = self._getSetFeatures(table, seqName, source, feature, frame) - else: - raise Exception("Wrong format : %s" % format) - outFile.write(annotations) - outFile.close() - #TODO: check getNbLinesInSingleFile() to handle big files - if not self._isGFF3WithoutAnnotation and FileUtils.getNbLinesInSingleFile(fileName) == 2: - os.remove(fileName) - elif self._isWithSequence: - outFile = open(fileName, "a") - outFile.write("##FASTA\n") - iBioseq = iTSA.getBioseqFromHeader(seqName) - iBioseq.write(outFile) - outFile.close() - else: - count = 1 - for line in linesFromAnnotationTablesFile: - if line[0] == "#": - continue - tok = line.split() - if len(tok) == 0: - break - source = tok[0] - format = tok[1] - table = tok[2] - tableseq = "" - if len(tok) == 4: - tableseq = tok[3] - fileName = "%s_Annot%i.gff3" % (seqName, count) - outFile = open(fileName, "w") - outFile.write("##gff-version 3\n") - outFile.write("##sequence-region %s 1 %s\n" % (seqName, length)) - if format == 'path' : - annotations = self._getPathFeatures(table, tableseq, seqName, source, feature, frame) - elif format == 'set' : - annotations = self._getSetFeatures(table, seqName, source, feature, frame) - else: - raise Exception("Wrong format : %s" % format) - outFile.write(annotations) - outFile.close() - #TODO: check getNbLinesInSingleFile() to handle big files - if not self._isGFF3WithoutAnnotation and FileUtils.getNbLinesInSingleFile(fileName) == 2: - os.remove(fileName) - elif self._isWithSequence: - outFile = open(fileName, "a") - outFile.write("##FASTA\n") - iBioseq = iTSA.getBioseqFromHeader(seqName) - iBioseq.write(outFile) - outFile.close() - count += 1 - - self._iDB.close() - - if self._verbose > 0: - print "END GFF3Maker" - sys.stdout.flush() - -if __name__ == "__main__": - iGFF3Maker = GFF3Maker() - iGFF3Maker.setAttributesFromCmdLine() - iGFF3Maker.run() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/GameXmlMaker.py --- a/commons/tools/GameXmlMaker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,384 +0,0 @@ -#!/usr/bin/env python - -##@file GameXmlMaker.py - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import glob -import sys -import xml.dom.minidom -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.seq.BioseqDB import BioseqDB -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.sql.TableSetAdaptator import TableSetAdaptator -from commons.core.sql.TableMapAdaptator import TableMapAdaptator - -## GameXmlMaker exports . -# -class GameXmlMaker(object): - - def __init__(self, inFastaName = "", tablesFileName = "", configFileName = "", verbose = 0): - self._inFastaName = inFastaName - self._tablesFileName = tablesFileName - self._configFileName = configFileName - self._verbose = verbose - self._gameXMLFileName = "" - - def setAttributesFromCmdLine(self): - description = "GameXmlMaker with -f option <=> step 1 : create gff files (write only the sequence and not the annotation. Only one sequence in each file)\n" - description += "GameXmlMaker with -t option <=> step 2 : add annotations in each file\n" - parser = RepetOptionParser(description = description) - parser.add_option("-f", "--inseq", dest = "inFastaName", action = "store", type = "string", help = "'fasta' file or 'seq' table recording the input sequences (required to generate new '.gamexml' files)", default = "") - parser.add_option("-t", "--tablesfile", dest = "tablesFileName", action = "store", type = "string", help = "tabulated file of table name to use to update the GameXML files (fields: tier name, format, table name)", default = "") - parser.add_option("-g", "--gameXML", dest = "gameXML", action = "store", type = "string", help = "gameXML file to update (if not specified, update all gameXML files in directory", default = "") - parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "configuration file for database connection", default = "") - parser.add_option("-v", "--verbose", dest = "verbose", action = "store", type = "int", help = "verbosity level (default=0, else 1 or 2)", default = 0) - (options, args) = parser.parse_args() - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setInFastaName(options.inFastaName) - self.setTablesFileName(options.tablesFileName) - self.setGameXMLFileName(options.gameXML) - self.setConfigFileName(options.configFileName) - self.setVerbose(options.verbose) - - def setInFastaName(self, inFastaName): - self._inFastaName = inFastaName - - def setTablesFileName(self, tablesFileName): - self._tablesFileName = tablesFileName - - def setGameXMLFileName(self, gamexmlFileName): - self._gameXMLFileName = gamexmlFileName - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def setVerbose(self, verbose): - self._verbose = verbose - - def checkOptions(self): - if self._inFastaName == "" and self._tablesFileName == "": - raise Exception("ERROR: options -f or -t required") - - if self._configFileName != "": - if not FileUtils.isRessourceExists(self._configFileName): - raise Exception("ERROR: configuration file does not exist!") - - def run(self): - self.checkOptions() - if self._verbose > 0: - print "START GameXmlMaker" - sys.stdout.flush() - - if self._inFastaName != "": - self._createGameXMLFiles() - - if self._tablesFileName != "": - lXMLNewFile = [] - if self._gameXMLFileName == "": - lXMLNewFile = glob.glob("*.gamexml") - else: - lXMLNewFile.append(self._gameXMLFileName) - - for newGamexmlFile in lXMLNewFile: - self._updateGameXMLFileFromlTablesFile(newGamexmlFile) - - if self._verbose > 0: - print "END GFF3Maker" - sys.stdout.flush() - - ## Create as many XML files as sequences given in fasta file. - # - def _createGameXMLFiles(self): - if self._verbose > 0: - print "reading file %s" % self._inFastaName - sys.stdout.flush() - - iBioseqDB = BioseqDB(self._inFastaName) - - if self._verbose > 0: - print "nb of sequences = %i" % iBioseqDB.getSize() - sys.stdout.flush() - - for iBioseq in iBioseqDB.db: - self._writeGameXMLFileFromBioseq(iBioseq) - - def _writeGameXMLFileFromBioseq(self, iBioseq): - """ - write new '.gamexml' file with and tags - """ - docXML = xml.dom.minidom.getDOMImplementation().createDocument(None, 'game', None) - root = docXML.documentElement - - seq = docXML.createElement('seq') - seq.setAttribute('id', iBioseq.getHeader()) - seq.setAttribute('focus', 'true') - root.appendChild(seq) - - seqNameTag = docXML.createElement('name') - seqNameTag.appendChild(docXML.createTextNode(iBioseq.getHeader())) - seq.appendChild(seqNameTag) - - residuesTag = docXML.createElement('residues') - residuesTag.appendChild(docXML.createTextNode(iBioseq.getSequence())) - seq.appendChild(residuesTag) - - mapPos = docXML.createElement('map_position') - root.appendChild(mapPos) - - arm = docXML.createElement('arm') - arm.appendChild(docXML.createTextNode(iBioseq.getHeader())) - mapPos.appendChild(arm) - - span = docXML.createElement('span') - mapPos.appendChild(span) - - start = docXML.createElement('start') - start.appendChild(docXML.createTextNode('1')) - span.appendChild(start) - - end = docXML.createElement('end') - end.appendChild(docXML.createTextNode(str(iBioseq.getLength()))) - span.appendChild(end) - - fileName = "%s.gamexml" % iBioseq.getHeader() - docXML.writexml(open(fileName, "w")) - - if self._verbose > 0: - print "file '%s' written" % fileName - sys.stdout.flush() - - - def _parseResultSpanInfo(self, element, type): - Qstart = -1 - Qend = -1 - Sstart = -1 - Send = -1 - query = "" - subject = "" - identity = 0 - id = "" - - if type == "path": - Qstart = element.getQueryStart() - Qend = element.getQueryEnd() - Sstart = element.getSubjectStart() - Send = element.getSubjectEnd() - query = element.getQueryName() - subject = element.getSubjectName() - identity = element.getIdentity() - id = element.getIdentifier() - - elif type == "set": - Qstart = element.getStart() - Qend = element.getEnd() - query = element.getName() - subject = element.getName() - id = element.getId() - - elif type == "map": - Qstart = element.getStart() - Qend = element.getEnd() - query = element.getSeqname() - subject = element.getName() - id = "-1" - - return (Qstart,Qend,Sstart,Send,query,subject,identity,id) - - def _addPathSpan(self, docXML, spanInfo, parent): - Qstart,Qend,Sstart,Send,query,subject,identity,id = spanInfo - Qstart = str(Qstart) - Qend = str(Qend) - Sstart = str(Sstart) - Send = str(Send) - identity = str(identity) - id = str(id) - - resultSpan = docXML.createElement('result_span') - parent.appendChild(resultSpan) - - relship1 = docXML.createElement('seq_relationship') - relship1.setAttribute('type', 'query') - relship1.setAttribute('seq', query) - relship2 = docXML.createElement('seq_relationship') - relship2.setAttribute('type', 'subject') - relship2.setAttribute('seq', '%s::%s' % (subject, id)) - score = docXML.createElement('score') - resultSpan.appendChild(relship1) - resultSpan.appendChild(relship2) - score.appendChild(docXML.createTextNode(identity)) - resultSpan.appendChild(score) - sp1 = docXML.createElement('span') - sp2 = docXML.createElement('span') - start1 = docXML.createElement('start') - start1.appendChild(docXML.createTextNode(Qstart)) - start2 = docXML.createElement('start') - start2.appendChild(docXML.createTextNode(Sstart)) - end1 = docXML.createElement('end') - end1.appendChild(docXML.createTextNode(Qend)) - end2 = docXML.createElement('end') - end2.appendChild(docXML.createTextNode(Send)) - relship1.appendChild(sp1) - sp1.appendChild(start1) - sp1.appendChild(end1) - relship2.appendChild(sp2) - sp2.appendChild(start2) - sp2.appendChild(end2) - - def _addComputationalAnalysisTags(self, docXML, programName): - computationalAnalysis = None - - lComputationalAnalysis = docXML.getElementsByTagName('computational_analysis') - for computationalAnalysisTag in lComputationalAnalysis: - if computationalAnalysisTag.getElementsByTagName("program")[0].nodeValue == programName: - computationalAnalysis = computationalAnalysisTag - break - - if computationalAnalysis == None : - computationalAnalysis = docXML.createElement('computational_analysis') - root = docXML.documentElement - root.appendChild(computationalAnalysis) - - program = docXML.createElement('program') - program.appendChild(docXML.createTextNode(programName)) - computationalAnalysis.appendChild(program) - - db = docXML.createElement('database') - db.appendChild(docXML.createTextNode('db')) - computationalAnalysis.appendChild(db) - - return computationalAnalysis - - def _addResultSetFromPath(self, docXML, iPath, parent): - computationalAnalysis = parent - resultSet = docXML.createElement('result_set') - resultSet.setAttribute('id', str(iPath.getIdentifier())) - computationalAnalysis.appendChild(resultSet) - resultSetName = docXML.createElement('name') - resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iPath.getSubjectName(),str(iPath.getIdentifier())))) - resultSet.appendChild(resultSetName) - return resultSet - - def _addResultSetFromSet(self, docXML, iSet, parent): - computationalAnalysis = parent - resultSet = docXML.createElement('result_set') - resultSet.setAttribute('id', str(iSet.getId())) - computationalAnalysis.appendChild(resultSet) - resultSetName = docXML.createElement('name') - resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iSet.getName(),str(iSet.getId())))) - resultSet.appendChild(resultSetName) - return resultSet - - def _addResultSetFromMap(self, docXML, iMap, parent): - computationalAnalysis = parent - resultSet = docXML.createElement('result_set') - resultSet.setAttribute('id', "-1") - computationalAnalysis.appendChild(resultSet) - resultSetName = docXML.createElement('name') - resultSetName.appendChild(docXML.createTextNode("%s::%s" %(iMap.getName(), "-1"))) - resultSet.appendChild(resultSetName) - return resultSet - - def _updateGameXMLFileFromlTablesFile(self, gameXMLFile): - docXML = xml.dom.minidom.parse(gameXMLFile) - - f = open(self._tablesFileName, "r") - line = f.readline() - - while line: - if not line.startswith("#"): - list = line.split() - programName = list[0] - format = list[1] - table = list[2] - - gameXMLFileName = os.path.splitext(gameXMLFile)[0] - computationalAnalysis = self._addComputationalAnalysisTags(docXML,programName) - if format == "path": - iDB = DbFactory.createInstance(self._configFileName) - iTpa = TablePathAdaptator(iDB, table) - - lPaths = iTpa.getPathListFromQuery(gameXMLFileName) - dResultSets = {} - - for iPath in lPaths: - if dResultSets.get(iPath.getIdentifier()) is None: - resultSet = self._addResultSetFromPath(docXML, iPath,computationalAnalysis) - dResultSets[iPath.getIdentifier()] = resultSet - else: - resultSet = dResultSets[iPath.getIdentifier()] - spanInfo = self._parseResultSpanInfo(iPath, "path") - self._addPathSpan(docXML, spanInfo, resultSet) - - if format == "set": - iDB = DbFactory.createInstance(self._configFileName) - iTsa = TableSetAdaptator(iDB, table) - lSet = iTsa.getSetListFromSeqName(gameXMLFileName) - - dResultSets = {} - - for iSet in lSet: - if dResultSets.get(iSet.getId()) is None: - resultSet = self._addResultSetFromSet(docXML, iSet,computationalAnalysis) - dResultSets[iSet.getId()] = resultSet - else: - resultSet = dResultSets[iSet.getId()] - - spanInfo = self._parseResultSpanInfo(iSet, "set") - self._addPathSpan(docXML, spanInfo, resultSet) - - if format == "map": - iDB = DbFactory.createInstance(self._configFileName) - iTma = TableMapAdaptator(iDB, table) - lMap = iTma.getMapListFromChr(gameXMLFileName) - dResultSets = {} - for iMap in lMap: - resultSet = self._addResultSetFromMap(docXML, iMap,computationalAnalysis) - spanInfo = self._parseResultSpanInfo(iMap, "map") - self._addPathSpan(docXML, spanInfo, resultSet) - - line = f.readline() - - outputGameXMLFile = open(gameXMLFile, "w") - xmlstr = docXML.toxml() - outputGameXMLFile.write(xmlstr) - outputGameXMLFile.close() - -if __name__ == "__main__": - iGameXmlMaker = GameXmlMaker() - iGameXmlMaker.setAttributesFromCmdLine() - iGameXmlMaker.run() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/GetMultAlignAndPhylogenyPerTErefSeq.py --- a/commons/tools/GetMultAlignAndPhylogenyPerTErefSeq.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,547 +0,0 @@ -#!/usr/bin/env python - -##@file -# For each TE reference sequence, it computes a multiple alignment and a phylogeny of all its copies. -# usage: GetMultAlignAndPhylogenyPerTErefSeq.py [ options ] -# options: -# -h: this help -# -S: step (0: all steps [default], 1:file generation, 2:multiple alignements, 3:phylogenies) -# -p: table with the annotations (format=path) -# -s: table with the TE reference sequences (format=seq) -# -g: table with the genome sequence (format=seq) -# -r: name or file with TE reference sequence(s) (all by default) -# -m: MSA method (default=Refalign/Map) -# -l: minimum length of copies (default=100) -# -n: number of longest copies to use (default=20) -# -y: minimum copy proportion compare to references (default=0.5) -# -R: keep the reference sequence (only with Refalign) -# -C: configuration file -# -q: queue name -# -c: clean -# -d: temporary directory -# -v: verbosity level (default=0/1) - -import os -import sys -import glob -import ConfigParser - -import pyRepet.launcher.programLauncher - -from commons.core.coord.PathUtils import PathUtils -from commons.core.seq.FastaUtils import FastaUtils -from commons.core.coord.SetUtils import SetUtils -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.tools.OrientSequences import OrientSequences -from ConfigParser import MissingSectionHeaderError -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.LoggerFactory import LoggerFactory -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.launcher import LaunchMap -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory -from commons.core.launcher.Launcher import Launcher -from commons.core.utils.FileUtils import FileUtils - - -LOG_DEPTH = "repet.tools" - -## For each TE reference sequence, it computes a multiple alignment and a phylogeny of all its copies. -# -class GetMultAlignAndPhylogenyPerTErefSeq(object): - - def __init__(self, pathTableName="",refSeqTableName="", genomeSeqTableName="", step=0, mSAmethod="RefAlign",keepRefseq=False, configFileName= "", clean = True, verbosity=3): - """ - Constructor. - """ - self.step = step - self._pathTable = pathTableName - self._refSeqTable = refSeqTableName - self._genomeSeqTable = genomeSeqTableName - self._TErefseq = "" - self._MSAmethod = mSAmethod - self._minCopyLength = 100 - self._nbLongestCopies = 20 - self._minPropCopy = 0.5 - self._keepRefseq = keepRefseq - self.setConfigFileName(configFileName) - self._queue = "" - self._tmpDir = "" - self._clean = clean - self._verbosity = verbosity - self._db = None - self._tpaAnnot = None - self._tsaRef = None - self._pL = pyRepet.launcher.programLauncher.programLauncher() - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def setAttributesFromCmdLine(self): - desc = "For each TE reference sequence, it computes a multiple alignment and a phylogeny of all its copies.\n" - #Commented: it's not true, Config File is mandatory! -# desc += "Connection to the database parameters are retrieved from the environment" - - #TODO: format options as other scripts (have a look at LaunchTemplate) - parser = RepetOptionParser(description = desc, epilog = "") - parser.add_option("-S", "--step", dest = "step" , action = "store", type = "int", help = "step (0: all steps [default], 1:file generation, 2:multiple alignments, 3:phylogenies)", default = 0 ) - parser.add_option("-p", "--pathTable", dest = "path", action= "store", type = "string", help = "(mandatory) table with the annotations (format=path)", default = "") - parser.add_option("-s", "--refSeqTable",dest = "refSeqTable", action= "store", type = "string", help = "(mandatory) table with the TE reference sequences (format=seq)", default = "") - parser.add_option("-g", "--genomeSeqTable",dest = "genomeSeqTable",action= "store", type = "string", help = "(mandatory) table with the genome sequence (format=seq)", default = "") - parser.add_option("-r", "--TErefseq",dest = "TErefseq", action= "store", type = "string", help = "name or file with TE reference sequence(s) (all by default)", default = "") - parser.add_option("-m", "--MSAmethod",dest = "MSAmethod", action= "store", type = "string", help = "MSA method (default=RefAlign/Map)", default = "RefAlign") - parser.add_option("-l", "--minCopyLength",dest = "minCopyLength", action= "store", type = "int", help = "minimum length of copies (default=100)", default = 100) - parser.add_option("-n", "--nbLongestCopies",dest = "nbLongestCopies", action= "store", type = "int", help = "number of longest copies to use (default=20)", default = 20) - parser.add_option("-y", "--minPropCopy",dest = "minPropCopy", action= "store", type = "float", help = "minimum copy proportion compare to references (default=0.5)", default = 0.5) - parser.add_option("-R", "--keepRefseq",dest = "keepRefseq", action="store_true", help = "keep the reference sequence (only with Refalign)", default = False) - parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "(mandatory) config file name to set database connection", default = "") - parser.add_option("-q", "--queue",dest = "queue", action= "store", type = "string", help = "queue name", default = "") - parser.add_option("-c", "--clean", action="store_false", dest = "clean", help = "don't clean", default = True) - parser.add_option("-d", "--tmpDir",dest = "tmpDir", action= "store", type = "string", help = "temporary directory", default = "") - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity level (default=0)", default = 0) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setConfigFileName(options.configFileName) - self.setStep(options.step) - self.setPathTable(options.path) - self.setRefSeqTable(options.refSeqTable) - self.setGenomeSeqTable(options.genomeSeqTable) - self.setTErefseq(options.TErefseq) - self.setMSAmethod(options.MSAmethod) - self.setMinCopyLength(options.minCopyLength) - self.setNbLongestCopies(options.nbLongestCopies) - self.setMinPropCopy(options.minPropCopy) - self.setKeepRefseq(options.keepRefseq) - self.setQueue(options.queue) - self.setClean(options.clean) - self.setTmpDir(options.tmpDir) - self.setVerbosity(options.verbosity) - - def setStep(self, step): - self.step = step - - def setPathTable(self, path): - self._pathTable = path - - def setRefSeqTable(self, refSeqTable): - self._refSeqTable = refSeqTable - - def setGenomeSeqTable(self, genomeSeqTable): - self._genomeSeqTable = genomeSeqTable - - def setTErefseq(self, TErefseq): - self._TErefseq = TErefseq - - def setMSAmethod(self, MSAmethod): - self._MSAmethod = MSAmethod - - def setMinCopyLength(self, minCopyLength): - self._minCopyLength = minCopyLength - - def setNbLongestCopies(self, nbLongestCopies): - self._nbLongestCopies = nbLongestCopies - - def setMinPropCopy(self, minPropCopy): - self._minPropCopy = minPropCopy - - def setKeepRefseq(self, keepRefseq): - self._keepRefseq = keepRefseq - - def setQueue(self, queue): - self._queue = queue - - def setClean(self, clean): - self._clean = clean - - def setTmpDir(self, tmpDir): - self._tmpDir = tmpDir - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def setup_env(self): - configFileHandle = open(self._configFileName) - # Use RepetConfigParser? - config = ConfigParser.ConfigParser() - try : - config.readfp(configFileHandle) - except MissingSectionHeaderError: - self._logAndRaise("Configuration file %s must begin with a section header" % self._configFileName) - - os.environ["REPET_HOST"] = config.get("repet_env", "repet_host") - os.environ["REPET_USER"] = config.get("repet_env", "repet_user") - os.environ["REPET_PW"] = config.get("repet_env", "repet_pw") - os.environ["REPET_DB"] = config.get("repet_env", "repet_db") - os.environ["REPET_PORT"] = config.get("repet_env", "repet_port") - os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager") - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def checkAttributes( self ): - """ - Check the attributes are valid before running the algorithm. - """ - if self._pathTable == "": - self._logAndRaise("PathTable is mandatory") - if self._refSeqTable == "": - self._logAndRaise("RefSeqTable is mandatory") - if self._genomeSeqTable == "": - self._logAndRaise("GenomeSeqTable is mandatory") - if self._configFileName == "": - self._logAndRaise("Configuration file is mandatory") - else: - if FileUtils.isRessourceExists(self._configFileName): - self.setup_env() - else: - self._logAndRaise("Configuration file '%s' does not exist!" % self._configFileName) - - if ( self.step == 2 or self.step == 3 ) and self._MSAmethod not in ["RefAlign","Map"]: - if self._MSAmethod == None or self._MSAmethod == "": - self._logAndRaise("Missing method option") - self._logAndRaise("Method '%s' not yet available" % ( self._MSAmethod )) - - if self._tmpDir == "": - self._tmpDir = os.getcwd() - - def connectSql(self): - self._db = DbFactory().createInstance(configFileName = self._configFileName, verbosity = 1) - self._tpaAnnot = TablePathAdaptator(self._db, self._pathTable) - self._tsaRef = TableSeqAdaptator(self._db,self._refSeqTable) - - def getNamesOfTErefSeq( self ): - """ - Return a list with the names of reference TEs. - """ - lNamesTErefSeq = [] - if self._TErefseq == "": - lNamesTErefSeq = self._tsaRef.getAccessionsList() - else: - if os.path.isfile( self._TErefseq ): - refseqFileHandler = open( self._TErefseq, "r" ) - while True: - line = refseqFileHandler.readline() - if line == "": - break - lNamesTErefSeq.append( line[:-1].split("\t")[0] ) - refseqFileHandler.close() - else: - lNamesTErefSeq = [ self._TErefseq ] - for name in lNamesTErefSeq: - if not self._tsaRef.isAccessionInTable( name ): - self._log.warning("'%s' not in table '%s'" % (name, self._refSeqTable)) - lNamesTErefSeq.remove( name ) - lNamesTErefSeq.sort() - self._log.info("nb of TE reference sequences: %d" % (len(lNamesTErefSeq))) - return lNamesTErefSeq - - - def getTErefSeqInFastaFiles( self, lNamesTErefSeq ): - """ - Save sequences of reference TEs in fasta files. - """ - for name in lNamesTErefSeq: - self._log.debug("save sequence of '%s'..." % ( name )) - self._tsaRef.saveAccessionsListInFastaFile( [name], name+".fa" ) - - def getCopiesInFastaFilesPerTErefSeq( self, lNamesTErefSeq ): - """ - Save sequences of TE copies in fasta files. - """ - self._log.info("retrieve the copies...") - tsaChr = TableSeqAdaptator( self._db, self._genomeSeqTable ) - totalNbCopies = 0 - totalNbSavedCopies = 0 - for name in lNamesTErefSeq: - nbCopies = 0 - if os.path.exists(name+"_copies.fa"): - continue - outFile = open( name+"_copies.fa", "w" ) - self._log.debug("Fetching path nums for subject: %s " % name) - lPathNums = self._tpaAnnot.getIdListSortedByDecreasingChainLengthFromSubject(name) - nbCopies = len(lPathNums) - totalNbCopies += nbCopies - self._log.debug("refseq '%s': %d copies" % ( name, nbCopies )) - i = 0 - nbSavedCopies = 0 - nbSavedFragments = 0 - lengthRefseq = self._tsaRef.getSeqLengthFromAccession( name ) - while i < len(lPathNums) and nbSavedCopies < self._nbLongestCopies: - lPaths = self._tpaAnnot.getPathListFromId( lPathNums[i] ) - lSets = PathUtils.getSetListFromQueries( lPaths ) - copyLength = SetUtils.getCumulLength( lSets ) - if copyLength >= self._minCopyLength \ - and copyLength >= self._minPropCopy * lengthRefseq: - bs = tsaChr.getBioseqFromSetList( lSets ) - bs.write(outFile) - nbSavedCopies += 1 - nbSavedFragments += len(lPaths) - i += 1 - - self._log.debug(" (saved: %d copies, %d fragments)\n" % ( nbSavedCopies, nbSavedFragments ) ) - outFile.close() - totalNbSavedCopies += nbSavedCopies - if nbSavedCopies == 0 and nbCopies != 0: - self._log.warning("No copy >= %d" % ( self._minCopyLength )) - self._log.info("nb of copies: %d (%d saved)" % ( totalNbCopies, totalNbSavedCopies )) - - def filter4Alignments( self, lNamesTErefSeq ): - """ - Filter TE copy sequences according to their length. - """ - self._log.info("filtering copies...") - if len(lNamesTErefSeq) == 1: - if not os.path.exists( "%s_copies.fa" % ( lNamesTErefSeq[0] ) ): - self._logAndRaise("first run step 1") - lInFiles = [ "%s_copies.fa" % ( lNamesTErefSeq[0] ) ] - else: - lInFiles = glob.glob( "*_copies.fa" ) - if len(lInFiles) == 0: - self._logAndRaise("no file '*_copies.fa'") - count = 0 - for inFileName in lInFiles: - if os.path.exists( "%s.filtered" % ( inFileName ) ): - continue - count += 1 - self._log.debug("TE %d --> %s" %(count,inFileName)) - FastaUtils.dbLengthFilter( self._minCopyLength, inFileName, verbose=self._verbosity ) - FastaUtils.dbLongestSequences( self._nbLongestCopies, inFileName+".Sup"+str(self._minCopyLength), verbose=self._verbosity ) - os.rename( inFileName+".Sup"+str(self._minCopyLength)+".best"+str(self._nbLongestCopies), inFileName+".filtered" ) - os.remove( inFileName+".Sup"+str(self._minCopyLength) ) - os.remove( inFileName+".Inf"+str(self._minCopyLength) ) - self._log.info("files filtered: %d" % (count)) - - def buildInFiles4Launcher( self, lNamesTErefSeq ): - """ - Save sequences of TE copies with reference in fasta files for launcher usage. - """ - self._log.info("building input files for launcher...") - for name in lNamesTErefSeq: - if os.path.exists( "%s_all.fa.oriented" % ( name ) ): - continue - if FastaUtils.dbSize( "%s_copies.fa.filtered" % ( name ) ) > 0: - os.system( "cat "+name+".fa "+ name+"_copies.fa.filtered > " + name+"_all.fa" ) - ors = OrientSequences(inFileName= "%s_all.fa" %(name), prgToOrient="mummer", clean=True, verbosity =self._verbosity - 1) - ors.run() - ors.clean() - if len( glob.glob("*_all.fa.oriented") ) == 0: - self._logAndRaise("no copies") - self._log.info("done building input files for launcher...") - - def renameFile( self, fromName, toName): - lFiles = glob.glob( "*%s" %fromName ) - for f in lFiles: - os.rename( f, f.replace(fromName,toName)) - - def _preparejobs(self, iLauncher, cDir): - self._log.info("Preparing Align jobs") - lCmdsTuples = [] - print(self.queriesDir,self.alignFileSuffix) - queryFiles = glob.glob("%s/%s" % (self.queriesDir,self.alignFileSuffix)) - print("queryFiles",queryFiles) - for queryFile in queryFiles:#os.listdir(self.queriesDir): - lCmds = [] - lCmdStart = [] - lCmdFinish = [] #['shutil.move("%s/*" %newDir, "../" )'] - queryFilePath = os.path.join(self.queriesDir,queryFile) - lCmds.append(self._createLaunchAlignCommands(iLauncher, queryFilePath)) - #lCmdFinish.append("shutil.move(\"%s.%s\", \"%s/%s.%s\")" % (benchName,self.outputformat,self.resultsDir,benchName,self.outputformat)) - lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - self._log.info("Finished preparing Align jobs") - return lCmdsTuples - - def _preparePhyMljobs(self, iLauncher, cDir): - self._log.info("Preparing PhyMl jobs") - lCmdsTuples = [] - queryFiles = glob.glob("%s/%s" % (self.queriesDir,self.phyloFileSuffix)) - print("queryFiles",queryFiles) - for queryFile in queryFiles:#os.listdir(self.queriesDir): - lCmds = [] - lCmdStart = [] - lCmdFinish = [] #['shutil.move("%s/*" %newDir, "../" )'] - queryFilePath = os.path.join(self.queriesDir,queryFile) - lCmds.append(self._createLaunchPhyMLCommands(iLauncher, queryFilePath)) - lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - self._log.info("Finished preparing PhyMl jobs") - return lCmdsTuples - - def _createLaunchAlignCommands(self, iLauncher, query): - if self._MSAmethod == "Map": - prg = "LaunchMap.py" - elif self._MSAmethod == "RefAlign": - prg = "LaunchRefAlign.py" - - lArgs = [] - lArgs.append("-i %s" % query) - lArgs.append(" -o %s.fa_aln" % query) - lArgs.append("-v 1" ) - - if self._MSAmethod == "RefAlign" and self._keepRefseq: - lArgs.append("-r " ) - - self._log.debug("Prepared Align commands : %s %s" % (prg, " ".join(lArgs))) - - - return iLauncher.getSystemCommand("%s" % prg, lArgs) - - def launchMultAlignments(self, lNamesTErefSeq): - """ - Make multiple alignments via Map for each TE family - """ - self.queriesDir = os.getcwd() - - if len(lNamesTErefSeq) == 1: - self.alignFileSuffix = "%s_all.fa.oriented" % (lNamesTErefSeq[0]) - else: - self.alignFileSuffix = "*_all.fa.oriented" - - queue = self._queue - cDir = os.getcwd() - tmpDir = self._tmpDir - groupid = "%s_%s" % ( self._refSeqTable, self._MSAmethod ) - acronym = "Align" - iDb = DbFactory.createInstance(configFileName=self._configFileName) - iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs") - iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid) - lCmdsTuples = self._preparejobs(iLauncher, cDir) - iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._clean) - - self.renameFile("_all.fa.oriented.fa_aln", "_all.fa.oriented_%s.fa_aln" % (self._MSAmethod.lower()) ) - -# def __makeMultAlignments( self, lNamesTErefSeq ): -# """ -# Make multiple alignments via Map or Refalign for each TE family -# """ -# self._pL.reset("") -# if self._MSAmethod == "Map": -# -# prg = os.environ["REPET_PATH"] + "/bin/srptMAP.py" -# elif self._MSAmethod == "RefAlign": -# prg = os.environ["REPET_PATH"] + "/bin/srptRefalign.py" -# cmd = prg -# cmd += " -g %s_%s" % ( self._refSeqTable, self._MSAmethod ) -# cmd += " -q %s" % ( os.getcwd() ) -# if len(lNamesTErefSeq) == 1: -# cmd += " -S %s_all.fa.oriented" % ( lNamesTErefSeq[0] ) -# else: -# cmd += " -S '*_all.fa.oriented'" -# cmd += " -Q %s" % ( self._queue ) -# cmd += " -C %s" % ( self._configFileName ) -# if self._MSAmethod == "Refalign" and self._keepRefseq: -# cmd += " -r" -# if not self._clean : -# cmd += " -c" -# if self._tmpDir != "": -# cmd += " -d %s" % ( self._tmpDir ) -# cmd += " -v %d" % ( self._verbosity ) -# self._pL.launch( prg, cmd ) -# lFiles = glob.glob( "*_all.fa.oriented.fa_aln" ) -# for f in lFiles: -# os.rename( f, f.replace("_all.fa.oriented.fa_aln","_all.fa.oriented_%s.fa_aln" % (self._MSAmethod.lower()) ) ) - - - def filter4phylogenies( self, verbosity=0 ): - """ - Filter TE copy alignment for better phylogenies. - """ - self._log.info("Filtering MSA") - lInFiles = glob.glob( "*_all.fa.oriented_%s.fa_aln" % ( self._MSAmethod.lower() ) ) - count = 0 - for inFileName in lInFiles: - count += 1 - self._log.debug("clean MSA %d --> %s" % (count,inFileName)) - alignDB = AlignedBioseqDB() - alignDB.load(inFileName) - alignDB.cleanMSA() - if alignDB.getSize() > 2: - alignDB.save( inFileName + ".clean" ) - self._log.debug("clean!") - else: - self._log.debug("skip!") - self._log.info("MSA cleaned: %d" % count) - - - def _createLaunchPhyMLCommands(self, iLauncher, query): -# prg = os.environ["REPET_PATH"] + "/bin/srptPhyML.py" -# cmd = prg -# cmd += " -g %s_PHY_%s" % ( self._refSeqTable, os.getpid() ) -# cmd += " -q %s" % ( os.getcwd() ) -# cmd += " -S '*_all.fa.oriented_%s.fa_aln.clean'" % ( self._MSAmethod.lower() ) -# cmd += " -Q %s" % ( self._queue ) -# cmd += " -C %s" % ( self._configFileName ) - - prg = "LaunchPhyML.py" - lArgs = [] - lArgs.append("-i %s" % query) - lArgs.append("-o %s.fa_phylo" % query) - lArgs.append("-v %d" % (self._verbosity-1)) - - self._log.debug("Prepared Phyml commands : %s %s" % (prg, " ".join(lArgs))) - return iLauncher.getSystemCommand("%s" % prg, lArgs) - - def makePhylogenies( self ): - """ - Launch PhyML on each TE family. - """ - self.phyloFileSuffix = "*_all.fa.oriented_%s.fa_aln.clean" % ( self._MSAmethod.lower() ) - - queue = self._queue - cDir = os.getcwd() - tmpDir = self._tmpDir - groupid = "%s_PHY_%s" % ( self._refSeqTable, os.getpid() ) - acronym = "Phylo" - iDb = DbFactory.createInstance(configFileName=self._configFileName) - iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs") - iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid) - lCmdsTuples = self._preparePhyMljobs(iLauncher, cDir) - iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._clean) - - - def start( self ): - """ - Useful commands before running the program. - """ - self.checkAttributes() - self._log.info("START GetMultAlignAndPhylogenyPerTErefSeq.py STEP %d" % self.step) - self.connectSql() - - def end( self ): - """ - Useful commands before ending the program. - """ - self._db.close() - self._log.info("END GetMultAlignAndPhylogenyPerTErefSeq.py STEP %d" % self.step) - - def run( self ): - """ - Run the program. - """ - LoggerFactory.setLevel(self._log, self._verbosity) - self.start() - lNamesTErefSeq = self.getNamesOfTErefSeq() - self._log.debug("lNamesTErefSeq: %s" % " ".join(lNamesTErefSeq)) - - if self.step in [0, 1]: - self.getTErefSeqInFastaFiles( lNamesTErefSeq ) - self.getCopiesInFastaFilesPerTErefSeq( lNamesTErefSeq ) - - if self.step in [0, 2]: - self.filter4Alignments(lNamesTErefSeq) - self.buildInFiles4Launcher(lNamesTErefSeq) - self.launchMultAlignments(lNamesTErefSeq) - - if self.step in [0, 3]: - self.filter4phylogenies(verbosity=self._verbosity) - self.makePhylogenies() - self.end() - -if __name__ == "__main__": - iGetMultAlignAndPhylogenyPerTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq() - iGetMultAlignAndPhylogenyPerTErefSeq.setAttributesFromCmdLine() - iGetMultAlignAndPhylogenyPerTErefSeq.run() - diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/GetSpecificTELibAccordingToAnnotation.py --- a/commons/tools/GetSpecificTELibAccordingToAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,178 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -import os -import sys -from commons.core.sql.DbMySql import DbMySql -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.core.LoggerFactory import LoggerFactory - -LOG_DEPTH = "repet.tools" -LOG_FORMAT = "%(message)s" -#TODO: use configuration file - -## Get 3 annotation files, using output from TEannot: -#- consensus with one or more full length copy, -#- consensus with one or more full length fragment, -#- consensus without copy - -class GetSpecificTELibAccordingToAnnotation(object): - - def __init__(self, inInfoFileName = "", tableName = "", verbose = 0): - self._inInfoFileName = inInfoFileName - self._tableName = tableName - self._verbose = verbose - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbose, LOG_FORMAT) - - def setAttributesFromCmdLine(self): - desc = "Splits a GiveInfoTEannot \"statsPerTE.txt\" file in 3 subfiles containing consensus which have at least one copy, one full length fragment or one full length copy. " - desc += "A TEs library is built according to each category. Connection to the database parameters are retrieved from the environment" - - examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n" - examples += "\t$ python GetSpecificTELibAccordingToAnnotation.py -i MyTEannotAnalysis_chr_allTEs_nr_noSSR_join_path_statsPerTE.txt -t MyTEannotAnalysis_refTEs_seq" - examples += "\n\t" - examples += "\n\n" - - parser = RepetOptionParser(description = desc, epilog = examples) - parser.add_option("-i", "--file", dest = "inInfoFileName", action = "store", type = "string", help = "input file (mandatory) = output file from GiveInfoTEannot.py (e.g. _chr_allTEs_nr_noSSR_join_path_statsPerTE.txt)", default = "") - parser.add_option("-t", "--table", dest = "tableName", action = "store", type = "string", help = "table name of TEs sequences (mandatory, seq format, e.g. _refTEs_seq)", default = "") - parser.add_option("-v", "--verbose", dest = "verbose", action = "store", type = "int", help = "verbosity level (default=0, else 1)", default = 0) - (options, args) = parser.parse_args() - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setInInfoFileName(options.inInfoFileName) - self.setTableName(options.tableName) - self.setVerbose(options.verbose) - - def setTableName(self, tableName): - self._tableName = tableName - - def setInInfoFileName(self, inInfoFileName): - self._inInfoFileName = inInfoFileName - - def setVerbose(self, verbose): - self._verbose = verbose - - def checkOptions(self): - if self._inInfoFileName != "": - if not FileUtils.isRessourceExists(self._inClassifFileName): - self._logAndRaise("ERROR: Input GiveInfoTEannot.txt output file does not exist!") - else: - self._logAndRaise("ERROR: No specified -i option!") - - if self._tableName != "": - iDb = DbMySql() - if not iDb.doesTableExist(self._tableName): - self._logAndRaise("ERROR: table does not exist!") - iDb.close() - else: - self._logAndRaise("ERROR: No specified -t option!") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def writeFastaFileFromGiveInfoTEAnnot(self, fileName): - fFileHandler = open(fileName,"r") - lineHeader = fFileHandler.readline() - line = fFileHandler.readline() - lConsensusName = [] - while line: - lConsensusName.append(line.split()[0]) - line = fFileHandler.readline() - - fFileHandler.close() - iDb = DbMySql() - iTSA = TableSeqAdaptator(iDb, self._tableName) - outPutFileName = "%s.fa" % os.path.splitext(fileName)[0] - iTSA.saveAccessionsListInFastaFile(lConsensusName, outPutFileName) - iDb.close() - - def run(self): - LoggerFactory.setLevel(self._log, self._verbose) - - outInfoFileNameFullCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0] - outInfoFileNameCopy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0] - outInfoFileNameFullFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inInfoFileName))[0] - - outInfoFileFullCopy = open(outInfoFileNameFullCopy, "w") - outInfoFileCopy = open(outInfoFileNameCopy, "w") - outInfoFileFullFrag = open(outInfoFileNameFullFrag, "w") - - self._log.info("START GetSpecificTELibAccordingToAnnotation\n input info file: %s" % self._inInfoFileName) - - inFileFh = open(self._inInfoFileName, "r") - line = inFileFh.readline() - lHeaders = line.split() - if "fullLgthCopies" not in lHeaders: - self._logAndRaise("ERROR: No headers in %s!" % self._inInfoFileName ) - - outInfoFileFullCopy.write(line) - outInfoFileCopy.write(line) - outInfoFileFullFrag.write(line) - - line = inFileFh.readline() - while line: - dTokens = {} - for index, token in enumerate(line.split()): - dTokens[lHeaders[index]] = token - - if int(dTokens["fullLgthCopies"]) > 0: - outInfoFileFullCopy.write(line) - if int(dTokens["copies"]) > 0: - outInfoFileCopy.write(line) - if int(dTokens["fullLgthFrags"]) > 0: - outInfoFileFullFrag.write(line) - line = inFileFh.readline() - - inFileFh.close() - outInfoFileFullCopy.close() - outInfoFileCopy.close() - outInfoFileFullFrag.close() - - self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameFullCopy) - self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameCopy) - self.writeFastaFileFromGiveInfoTEAnnot(outInfoFileNameFullFrag) - - self._log.info("END GetSpecificTELibAccordingToAnnotation\n" ) - - return 0 - -if __name__ == '__main__': - iGetTELib = GetSpecificTELibAccordingToAnnotation() - iGetTELib.setAttributesFromCmdLine() - iGetTELib.run() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py --- a/commons/tools/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,123 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -from commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align import HmmpfamOutput2align -from commons.pyRepetUnit.align.hmmOutputParsing.HmmscanOutput2align import HmmscanOutput2align -from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat -from commons.core.utils.FileUtils import FileUtils - -#------------------------------------------------------------------------------ - -def help(): - - """ - Give the command-line parameters. - """ - - print "" - print "usage: ",sys.argv[0],"[ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='hmmpfam Output' or 'hmmscan Output)" - print " -o: name of the output file (default=inFileName+'.align')" - print " -T: name of the consensus File (To launch the transformation of aa positions in nt positions and Filter positive score, default=no transformation)" - print " -v: verbose (default=0/1/2)" - print " -p: name of program (default=hmmpfam, but you can specify hmmscan too)" - print " -c: clean" - print "" - -#------------------------------------------------------------------------------ - -def main(): - - inFileName = "" - outFileName = "" - verbose = 0 - clean = False - consensusFileName = "" - program = "hmmpfam" - - try: - opts,args=getopt.getopt(sys.argv[1:],"hi:o:T:v:p:c") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - elif o == "-T": - consensusFileName = a - elif o == "-v": - verbose = int(a) - elif o == "-p": - program = a - elif o == "-c": - clean = True - - if inFileName == "": - print "*** Error: missing compulsory options" - help() - sys.exit(1) - - if verbose > 0: - print "beginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s.align" % ( inFileName ) - - if program == "hmmpfam": - hmmpfamOutput2align = HmmpfamOutput2align( ) - hmmpfamOutput2align.setInputFile( inFileName ) - if consensusFileName == "": - hmmpfamOutput2align.setOutputFile( outFileName ) - else: - hmmpfamOutput2align.setOutputFile( outFileName + ".tmp" ) - hmmpfamOutput2align.run( ) - else: - if program == "hmmscan": - hmmscanOutput2align = HmmscanOutput2align( ) - hmmscanOutput2align.setInputFile( inFileName ) - if consensusFileName == "": - hmmscanOutput2align.setOutputFile( outFileName ) - else: - hmmscanOutput2align.setOutputFile( outFileName + ".tmp" ) - hmmscanOutput2align.run( ) - else: - print "\nWarning: You must specify a valid program (-p option). Only hmmpfam or hmmscan are supported !\n" - - if consensusFileName != "": - alignTransformation = TransformAACoordIntoNtCoordInAlignFormat() - alignTransformation.setInFileName( outFileName + ".tmp" ) - alignTransformation.setOutFileName( outFileName ) - alignTransformation.setConsensusFileName( consensusFileName ) - alignTransformation.setIsFiltered(True) - alignTransformation.run() - os.remove( outFileName + ".tmp" ) - - - if clean == True: - os.remove( inFileName ) - - if verbose > 0: - if FileUtils.isRessourceExists( outFileName ) and not(FileUtils.isEmpty( outFileName )): - print "%s finished successfully" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - else: - print "warning %s execution failed" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#------------------------------------------------------------------------------ - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/LaunchBlaster.py --- a/commons/tools/LaunchBlaster.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,204 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -import subprocess - -LOG_DEPTH = "repet.tools" - -##Launch BLASTER -# -class LaunchBlaster(object): - - def __init__(self, queryFileName = "", subjectFileName = "", evalue = 1e-300, identity = 90, length = 100, doAllByall = False, type = "ncbi", nbCPU = 1, program="blastn",extraParams="", doClean = False, verbosity = 0): - self._queryFileName = queryFileName - self.setSubjectFileName(subjectFileName) - self._eValue = evalue - self._identity = identity - self._length = length - self._doAllByall = doAllByall - self._blastType = type - self._program = program - self._extraParams = extraParams - self._nbCPU = nbCPU - self._doClean = doClean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "Launch Blaster." - epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python LaunchBlaster.py -q query.fa -v 0" - epilog += "\n\t" - epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n" - epilog += "\t$ python LaunchBlaster.py -q query.fa -s nr.fa -c -v 2" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [default: query] [format: fasta]", default = "") - parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "Blast e-value [default: 1e-300]", default = "1e-300") - parser.add_option("-d", "--id", dest = "identity", action = "store", type = "int", help = "Blast identity [default: 90]", default = 90) - parser.add_option("-l", "--length", dest = "length", action = "store", type = "int", help = "Minimal hit length [default: 100]", default = 100) - parser.add_option("-a", "--aba", dest = "doAllByall", action = "store_true", help = "all-by-all Blast [default: False]", default = False) - parser.add_option("-t", "--type", dest = "type", action = "store", type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]", default = "ncbi") - parser.add_option("-u", "--program", dest = "program", action = "store", type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]", default = "blastn") - parser.add_option("-x", "--extraParams",dest = "extraParams", action = "store", type = "string", help = "Additional blast program parameters[default: '']", default = "") - parser.add_option("-n", "--ncpu", dest = "cpu", action = "store", type = "int", help = "Number of CPUs to use [default: 1]", default = 1) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setQueryFileName(options.query) - self.setSubjectFileName(options.subject) - self.setEvalue(options.evalue) - self.setIdentity(options.identity) - self.setLength(options.length) - self.setDoAllByall(options.doAllByall) - self.setType(options.type) - self.setProgram(options.program) - self.setExtraParams(options.extraParams) - self.setCPU(options.cpu) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - - def setQueryFileName(self, queryFileName): - self._queryFileName = queryFileName - - def setSubjectFileName(self, subjectFileName): - if subjectFileName == "": - self._subjectFileName = self._queryFileName - else: - self._subjectFileName = subjectFileName - - def setEvalue(self, evalue): - self._eValue = evalue - - def setIdentity(self, identity): - self._identity = identity - - def setLength(self, length): - self._length = length - - def setDoAllByall(self, doAllByall): - self._doAllByall = doAllByall - - def setType(self, blastType): - self._blastType = blastType - - def setProgram(self, program): - self._program = program - - def setExtraParams(self, extraParams): - self._extraParams = extraParams - - def setCPU(self, cpu): - self._nbCPU = cpu - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self._queryFileName == "": - self._logAndRaise("ERROR: Missing input fasta file name") - - lBlastType = ["ncbi", "wu", "blastplus"] - if self._blastType.lower() not in lBlastType: - self._logAndRaise("ERROR: unknown Blast type '%s' - correct values are %s" % (self._blastType, lBlastType)) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def _getBlasterCmd(self): - lArgs = [] - lArgs.append("-n %s" % self._program) - lArgs.append("-q %s" % self._queryFileName) - lArgs.append("-s %s" % self._subjectFileName) - lArgs.append("-B %s" % self._queryFileName) - if self._doAllByall: - lArgs.append("-a") - lArgs.append("-E %s" % self._eValue) - lArgs.append("-L %s" % self._length) - lArgs.append("-I %s" % self._identity) - if self._blastType == "ncbi": - lArgs.append("-N") - lArgs.append("-p '-a %s %s'" % (self._nbCPU, self._extraParams)) - elif self._blastType == "wu": - lArgs.append("-W") - lArgs.append("-p '-cpus=%s %s'" % (self._nbCPU, self._extraParams)) - elif self._blastType == "blastplus": - lArgs.append("-X") - lArgs.append("-p '-num_threads %s %s'" % (self._nbCPU, self._extraParams)) -# TODO: check the check option at the beginning of step 2 to allow to launch megablast for blast and blast+ -# elif config.get(sectionName, "blast") == "mega": -# lArgs.append("-N") -# lArgs.append("-n megablast") -# elif config.get(sectionName, "blast") == "megablastplus": -# lArgs.append("-X") -# lArgs.append("-n megablast") - if self._doClean: - lArgs.append("-c") - lArgs.append("-v %i" % (self._verbosity - 1)) - return self._getSystemCommand("blaster", lArgs) - - def _getSystemCommand(self, prg, lArgs): - systemCmd = prg - for arg in lArgs: - systemCmd += " " + arg - return systemCmd - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START LaunchBlaster") - self._log.debug("Query file name: %s" % self._queryFileName) - self._log.debug("Subject file name: %s" % self._subjectFileName) - if self._doClean: - self._log.warning("Files will be cleaned") - cmd = self._getBlasterCmd() - process = subprocess.Popen(cmd, shell = True) - self._log.debug("Running : %s" % cmd) - process.communicate() - if process.returncode != 0: - self._logAndRaise("ERROR when launching '%s'" % cmd) - self._log.info("END LaunchBlaster") - -if __name__ == "__main__": - iLaunch = LaunchBlaster() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/LaunchBlasterInParallel.py --- a/commons/tools/LaunchBlasterInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,301 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import shutil -from commons.core.LoggerFactory import LoggerFactory -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory -from commons.core.launcher.Launcher import Launcher -from commons.core.utils.FileUtils import FileUtils -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker -from commons.tools.MergeMatchsFiles import MergeMatchsFiles - -LOG_DEPTH = "repet.tools" - -##Launch BLASTER in parallel -# -class LaunchBlasterInParallel(object): - - def __init__(self, queryDirectory = "", subjectFilePath = "", outFileName = "", configFileName = "", groupId = "", queryPattern = ".*\.fa", \ - doAllByall = False, nbCPU = 1, eValue="1e-300", type = "ncbi", program="blastn", extraParams="", verbosity = 0): - self._queryDirectory = queryDirectory - self._queryPattern = queryPattern - self.setSubjectFilePath(subjectFilePath) - self._outFileName = outFileName - self._configFileName = configFileName - self.setGroupId(groupId) - self._doAllByall = doAllByall - self._blastType = type - self._program = program - self._extraParams = extraParams - self._nbCPU = nbCPU - self._jobSectionName = "jobs" - self._blasterSectionName = "alignment" - self._prepareDataSectionName = "prepare_data" - self._eValue = eValue - - self._doClean = None - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "Launch Blaster in parallel." - epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python LaunchBlasterInParallel.py -q query -o query.align -v 0" - epilog += "\n\t" - epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n" - epilog += "\t$ python LaunchBlasterInParallel.py -q query -o query.align -s nr.fa -c -v 2" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta directory absolute path [compulsory]", default = "") - parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta absolute path [compulsory] [format: fasta]", default = "") - parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output align file name [compulsory] [format: align]", default = "") - parser.add_option("-C", "--config", dest = "configFileName",action = "store", type = "string", help = "configuration file name [compulsory] [format: cfg]", default = "") - parser.add_option("-g", "--groupId", dest = "groupId", action = "store", type = "string", help = "jobs groupId [default: Blaster_]", default = "") - parser.add_option("-p", "--queryPattern",dest = "queryPattern", action = "store", type = "string", help = "query file pattern [default: .*\.fa]", default = ".*\.fa") - parser.add_option("-a", "--aba", dest = "doAllByall", action = "store_true", help = "all-by-all Blast [default: False]", default = False) - parser.add_option("-e", "--eValue", dest = "eValue", action = "store", type = "string", help = "Blast e-value [default: 1e300]", default = "1e-300") - parser.add_option("-t", "--type", dest = "type", action = "store", type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]", default = "ncbi") - parser.add_option("-u", "--program", dest = "program", action = "store", type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]", default = "blastn") - parser.add_option("-x", "--extraParams",dest = "extraParams", action = "store", type = "string", help = "Additional blast program parameters[default: '']", default = "") - parser.add_option("-n", "--ncpu", dest = "cpu", action = "store", type = "int", help = "Number of CPUs to use [default: 1]", default = 1) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setQueryDirectory(options.query) - self.setQueryPattern(options.queryPattern) - self.setSubjectFilePath(options.subject) - self.setOutFileName(options.outFileName) - self.setConfigFileName(options.configFileName) - self.setGroupId(options.groupId) - self.setDoAllByall(options.doAllByall) - self.setEValue(options.eValue) - self.setType(options.type) - self.setProgram(options.program) - self.setExtraParams(options.extraParams) - self.setCPU(options.cpu) - self.setVerbosity(options.verbosity) - - def setQueryDirectory(self, queryDirectory): - self._queryDirectory = queryDirectory - - def setQueryPattern(self, queryPattern): - self._queryPattern = queryPattern - - def setSubjectFilePath(self, subjectFilePath): - self._subjectFilePath = subjectFilePath - self._subjectFileName = os.path.basename(subjectFilePath) - - def setOutFileName(self, outFileName): - self._outFileName = outFileName - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def setGroupId(self, groupId): - if groupId == "": - self._groupId = "Blaster_%s" % os.getpid() - else: - self._groupId = groupId - - def setDoAllByall(self, doAllByall): - self._doAllByall = doAllByall - - def setType(self, blastType): - self._blastType = blastType - - def setProgram(self, program): - self._program = program - - def setExtraParams(self, extraParams): - self._extraParams = extraParams - - def setEValue(self, eValue): - self._eValue = eValue - - def setCPU(self, cpu): - self._nbCPU = cpu - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self._queryPattern == "": - self._logAndRaise("ERROR: Missing input fasta file name") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def _checkConfig(self): - iConfigRules = ConfigRules() - iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True) - iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string") - iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string") - iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool") - iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool") - iConfigRules.addRuleOption(section=self._blasterSectionName, option ="blast", mandatory=True, type="string", set = ("ncbi", "blastplus", "wu")) - iConfigRules.addRuleOption(section=self._blasterSectionName, option ="Evalue", mandatory=True, type="string") - iConfigRules.addRuleOption(section=self._blasterSectionName, option ="length", mandatory=True, type="string") - iConfigRules.addRuleOption(section=self._blasterSectionName, option ="identity", mandatory=True, type="string") - - iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) - self._iConfig = iConfigChecker.getConfig() - self._setAttributesFromConfig() - - def _setAttributesFromConfig(self): - self._chunkLength = self._iConfig.get(self._prepareDataSectionName, "chunk_length") - self._chunkOverlap = self._iConfig.get(self._prepareDataSectionName, "chunk_overlap") - self._resources = self._iConfig.get(self._jobSectionName, "resources") - self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir") - self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy") - self._doClean = self._iConfig.get(self._jobSectionName, "clean") - self._blastType = self._iConfig.get(self._blasterSectionName, "blast") - self._eValue = self._iConfig.get(self._blasterSectionName, "Evalue") - self._length = self._iConfig.get(self._blasterSectionName, "length") - self._identity = self._iConfig.get(self._blasterSectionName, "identity") - - if self._isCopyOnNode and not self._tmpDir: - self._isCopyOnNode = False - self._log.debug("The copy option is: %s." % self._isCopyOnNode) - - def _getLaunchBlasterCmd(self, iLauncher, file): - lArgs = [] - lArgs.append("-u %s" % self._program) - lArgs.append("-q %s" % file) - lArgs.append("-s %s" % self._subjectFileName) - if self._doAllByall: - lArgs.append("-a") - lArgs.append("-e %s" % self._eValue) - lArgs.append("-l %s" % self._length) - lArgs.append("-d %s" % self._identity) - lArgs.append("-t %s" % self._blastType) - lArgs.append("-x '%s'" % self._extraParams) - if self._doClean: - lArgs.append("-c") - lArgs.append("-v %i" % (self._verbosity - 1)) - return iLauncher.getSystemCommand("LaunchBlaster.py", lArgs) - - def _getRmvPairAlignInChunkOverlapsCmd(self, iLauncher, inFileName, outFileName): - lArgs = [] - lArgs.append("-i %s" % inFileName) - lArgs.append("-l %s" % self._chunkLength) - lArgs.append("-o %s" % self._chunkOverlap) - lArgs.append("-m 10") - lArgs.append("-O %s" % outFileName) - lArgs.append("-v %d" % (self._verbosity - 1)) - return iLauncher.getSystemCommand("RmvPairAlignInChunkOverlaps.py", lArgs) - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkConfig() - self._checkOptions() - self._log.info("START LaunchBlasterInParallel") - self._log.debug("Query file name: %s" % self._queryPattern) - self._log.debug("Subject file name: %s" % self._subjectFileName) - - cDir = os.getcwd() - if not self._tmpDir: - self._tmpDir = cDir - - acronym = "Blaster" - iDb = DbFactory.createInstance() - jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs") - iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode) - - lCmdsTuples = [] - fileSize = float(os.path.getsize(self._subjectFilePath) + 5000000) / 1000000000 - - lCmdSize = [] - lCmdCopy = [] - if self._isCopyOnNode: - lCmdSize.append("fileSize = %f" % fileSize) - lCmdCopy.append("shutil.copy(\"%s\", \".\")" % self._subjectFilePath) - - lFiles = FileUtils.getFileNamesList(self._queryDirectory, self._queryPattern) - for file in lFiles: - lCmds = [] - lCmds.append(self._getLaunchBlasterCmd(iLauncher, file)) - lCmdStart = [] - if self._isCopyOnNode: - lCmdStart.append("os.symlink(\"../%s\", \"%s\")" % (self._subjectFileName, self._subjectFileName)) - lCmdStart.append("shutil.copy(\"%s/%s\", \".\")" % (self._queryDirectory, file)) - else: - lCmdStart.append("os.symlink(\"%s\", \"%s\")" % (self._subjectFilePath, self._subjectFileName)) - lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (self._queryDirectory, file, file)) - lCmdFinish = [] - lCmdFinish.append("if os.path.exists(\"%s.align\"):" % file) - lCmdFinish.append("\tshutil.move(\"%s.align\", \"%s/.\" )" % (file, cDir)) - lCmdFinish.append("shutil.move(\"%s.param\", \"%s/.\" )" % (file, cDir)) - lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy)) - - iLauncher.runLauncherForMultipleJobs("Blaster", lCmdsTuples, self._doClean, self._isCopyOnNode) - - tmpFileName = "tmp_%s.align" % os.getpid() - iMMF = MergeMatchsFiles("align", "tmp_%s" % os.getpid(), allByAll = self._doAllByall, clean = self._doClean) - iMMF.run() - - if self._doAllByall: - iDb = DbFactory.createInstance() - jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs") - iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, "%s_RmvPairAlignInChunkOverlaps" % self._groupId) - - lCmdsTuples = [] - lCmds = [] - lCmds.append(self._getRmvPairAlignInChunkOverlapsCmd(iLauncher, tmpFileName, self._outFileName)) - lCmdStart = [] - lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, tmpFileName, tmpFileName)) - lCmdFinish = [] - lCmdFinish.append("shutil.move(\"%s\", \"%s/.\")" % (self._outFileName, cDir)) - lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - - iLauncher.runLauncherForMultipleJobs("RmvPairAlignInChunkOverlaps", lCmdsTuples, self._doClean) - if self._doClean: - os.remove(tmpFileName) - else: - shutil.move(tmpFileName, self._outFileName) - - if self._doClean: - FileUtils.removeFilesByPattern("*.param") - - self._log.info("END LaunchBlasterInParallel") - -if __name__ == "__main__": - iLaunch = LaunchBlasterInParallel() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/LaunchMatcherInParallel.py --- a/commons/tools/LaunchMatcherInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,285 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory -from commons.core.launcher.Launcher import Launcher -from commons.core.launcher.LauncherUtils import LauncherUtils -from commons.core.utils.FileUtils import FileUtils -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker -from commons.core.coord.AlignUtils import AlignUtils -import shutil -import os - -LOG_DEPTH = "repet.tools" - - -class LaunchMatcherInParallel(object): - def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", alignPattern = ".*\.align", \ - config = "", groupId = "", maxFileSize = 1000000, mergeResults=True, workingDir="tmpMatcher", doClean = False, verbosity = 0): - self._alignFileName = align - self._queryFileName = queryFileName - self.setSubjectFileName(subjectFileName) - self.setOutPrefix(prefix) - self._alignPattern = alignPattern - self._doJoin = doJoin - self._eValue = evalue - self._keepConflict = keepConflict - self._configFileName = config - self.setGroupId(groupId) - self._maxFileSize = maxFileSize - self._mergeResults = mergeResults - self._doClean = doClean - self._workingDir = workingDir - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - self._jobSectionName = "jobs" - - def setAttributesFromCmdLine(self): - description = "Launch Matcher in parallel." - epilog = "\nExample 1: launch without verbosity and keep temporary files.\n" - epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -v 0" - epilog += "\n\t" - epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n" - epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -q query.fa -s subject.fa -o query -c -v 2" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-a", "--align", dest = "align", action = "store", type = "string", help = "input align file name [compulsory] [format: align]", default = "") - parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [optional] [format: fasta]", default = "") - parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [optional] [format: fasta]", default = "") - parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "E-value filter [default: 1e10]", default = "1e-10") - parser.add_option("-j", "--join", dest = "doJoin", action = "store_true", help = "join matches [default: False]", default = False) - parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true", help = "keep conflicting subjects [default: False]", default = False) - parser.add_option("-o", "--outPrefix", dest = "outPrefix", action = "store", type = "string", help = "output file prefix [default: align file name]", default = "") - parser.add_option("-p", "--alignPattern",dest = "alignPattern", action = "store", type = "string", help = "align file pattern [default: .*\.align]", default = ".*\.align") - parser.add_option("-n", "--maxFileSize",dest = "maxFileSize", action = "store", type = "int", help = "max file size (1 file for 1 job) [default: 100000]", default = 10000) - parser.add_option("-m", "--notMergeResults",dest = "notMergeResults", action = "store_false", help = "don't merge results files [default: True]", default = True) - parser.add_option("-w", "--workingDir",dest = "workingDir", action = "store", type = "string", help = "working directory [default: tmpMatcher]", default = "tmpMatcher") - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setAlignFileName(options.align) - self.setQueryFileName(options.query) - self.setSubjectFileName(options.subject) - self.setEvalue(options.evalue) - self.setDoJoin(options.doJoin) - self.setKeepConflicts(options.keepConflict) - self.setOutPrefix(options.outPrefix) - self.setAlignPattern(options.alignPattern) - self.setMaxFileSize(options.maxFileSize) - self.setMergeResults(options.notMergeResults) - self.setWorkingDir(options.workingDir) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def setAlignFileName(self, alignFileName): - self._alignFileName = alignFileName - - def setQueryFileName(self, queryFileName): - self._queryFileName = queryFileName - - def setSubjectFileName(self, subjectFileName): - self._subjectFileName = subjectFileName - - def setEvalue(self, evalue): - self._eValue = evalue - - def setDoJoin(self, doJoin): - self._doJoin = doJoin - - def setKeepConflicts(self, keepConflict): - self._keepConflict = keepConflict - - def setOutPrefix(self, outPrefix): - if outPrefix == "": - self._outPrefix = self._alignFileName - else: - self._outPrefix = outPrefix - - def setAlignPattern(self, alignPattern): - self._alignPattern = alignPattern - - def setGroupId(self, groupId): - if groupId == "": - self._groupId = "Matcher_%s" % os.getpid() - else: - self._groupId = groupId - - def setMaxFileSize(self, maxFileSize): - self._maxFileSize = maxFileSize - - def setMergeResults(self, mergeResults): - self._mergeResults = mergeResults - - def setWorkingDir(self, workingDir): - self._workingDir = workingDir - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if self._alignFileName == "": - self._logAndRaise("ERROR: Missing input align file name") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def _checkConfig(self): - iConfigRules = ConfigRules() - iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True) - iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string") - iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string") - iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool") - iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool") - - iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) - self._iConfig = iConfigChecker.getConfig() - self._setAttributesFromConfig() - - def _setAttributesFromConfig(self): - self._resources = self._iConfig.get(self._jobSectionName, "resources") - self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir") - self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy") - self._doClean = self._iConfig.get(self._jobSectionName, "clean") - - if self._isCopyOnNode and not self._tmpDir: - self._isCopyOnNode = False - self._log.debug("The copy option is: %s." % self._isCopyOnNode) - - def _getLaunchMatcherCmd(self, iLauncher, file): - lArgs = [] - lArgs.append("-a %s" % file) - if self._queryFileName: - lArgs.append("-q %s" % self._queryFileName) - if self._subjectFileName: - lArgs.append("-s %s" % self._subjectFileName) - lArgs.append("-e %s" % self._eValue) - lArgs.append("-o %s" % file) - if self._doJoin: - lArgs.append("-j") - if self._keepConflict: - lArgs.append("-k") - lArgs.append("-v %i" % (self._verbosity - 1)) - return iLauncher.getSystemCommand("LaunchMatcher.py", lArgs) - - def _splitAlignFilePerSeq(self): - lAlign = AlignUtils.getAlignListFromFile(self._alignFileName) - lAlignList = AlignUtils.splitAlignListByQueryName(lAlign) - inputFileNameWithoutExtension = os.path.splitext(os.path.basename(self._alignFileName))[0] - AlignUtils.createAlignFiles(lAlignList, inputFileNameWithoutExtension, self._workingDir) - - def _writeTabHeader(self, outTabFileName): - with open(outTabFileName, 'w') as f: - f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkConfig() - self._checkOptions() - - self._log.info("START LaunchMatcherInParallel") - self._log.debug("Align file name: %s" % self._alignFileName) - self._log.debug("Query file name: %s" % self._queryFileName) - self._log.debug("Subject file name: %s" % self._subjectFileName) - if not os.path.exists(self._workingDir): - os.makedirs(self._workingDir) - else: - self._doClean = False - self._splitAlignFilePerSeq() - os.chdir(self._workingDir) - os.symlink("../%s" % self._queryFileName, self._queryFileName) - if self._queryFileName != self._subjectFileName: - os.symlink("../%s" % self._subjectFileName, self._subjectFileName) - - cDir = os.getcwd() - if not self._tmpDir: - self._tmpDir = cDir - - acronym = "Matcher" - iDb = DbFactory.createInstance() - jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs") - iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode) - - lCmdsTuples = [] - lCmdSize = [] - lCmdCopy = [] - - lFiles = FileUtils.getFileNamesList(".", self._alignPattern) - lFileSizeTuples = [] - for fileName in lFiles: - fileSize = os.path.getsize(fileName) - lFileSizeTuples.append((fileName, fileSize)) - lFileSizeList = LauncherUtils.createHomogeneousSizeList(lFileSizeTuples, self._maxFileSize) - - for lFiles in lFileSizeList: - lCmds = [] - lCmdStart = [] - lCmdFinish = [] - if self._queryFileName: - lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._queryFileName, self._queryFileName)) - if self._subjectFileName and self._subjectFileName != self._queryFileName: - lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._subjectFileName, self._subjectFileName)) - for file in lFiles: - lCmds.append(self._getLaunchMatcherCmd(iLauncher, file)) - lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, file, file)) - lCmdFinish.append("if os.path.exists(\"%s.match.path\"):" % file) - lCmdFinish.append("\tshutil.move(\"%s.match.path\", \"%s/.\" )" % (file, cDir)) - lCmdFinish.append("if os.path.exists(\"%s.match.tab\"):" % file) - lCmdFinish.append("\tshutil.move(\"%s.match.tab\", \"%s/.\" )" % (file, cDir)) - lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy)) - - iLauncher.runLauncherForMultipleJobs("Matcher", lCmdsTuples, self._doClean, self._isCopyOnNode) - - if self._mergeResults: - FileUtils.catFilesByPattern("*.match.path", "../%s.match.path" % self._outPrefix) - if self._queryFileName or self._subjectFileName: - outTabFileName = "../%s.match.tab" % self._outPrefix - self._writeTabHeader(outTabFileName) - FileUtils.catFilesByPattern("*.match.tab", outTabFileName, skipHeaders = True) - os.chdir("..") - if self._doClean and self._mergeResults: - self._log.warning("Working directory will be cleaned") - shutil.rmtree(self._workingDir) - self._log.info("END LaunchMatchInParallel") - -if __name__ == "__main__": - iLaunch = LaunchMatcherInParallel() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/ListAndDropTables.py --- a/commons/tools/ListAndDropTables.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,157 +0,0 @@ -#!/usr/bin/env python - -##@file -# List and drop MySQL tables. -# -# usage: ListAndDropTables.py [ options ] -# options: -# -h: this help -# -l: tables to list (can be a pattern, '*' for all) -# -d: tables to drop (can be a pattern, '*' for all) -# -C: configuration file -# -v: verbose (default=0/1) -# it doesn't drop 'info_tables' - - -import sys -import getopt -from commons.core.sql.DbMySql import DbMySql - - -class ListAndDropTables( object ): - - def __init__( self ): - self._action = "list" - self._tableNames = "" - self._configFileName = "" - self._verbose = 0 - self._db = None - - - def help( self ): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " -l: tables to list (can be a pattern, '*' for all)" - print " -d: tables to drop (can be a pattern, '*' for all)" - print " -C: configuration file (otherwise, use env variables)" - print " -v: verbose (default=0/1)" - print "Note: it doesn't drop 'info_tables'." - print - - - def setAttributesFromCmdLine( self ): - try: - opts, args = getopt.getopt(sys.argv[1:],"hl:d:C:v:") - except getopt.GetoptError, err: - print str(err); self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-l": - self._action = "list" - self._tableNames = a - elif o == "-d": - self._action = "drop" - self._tableNames = a - elif o == "-C": - self._configFileName = a - elif o == "-v": - self._verbose = int(a) - - - def checkAttributes( self ): - """ - Before running, check the required attributes are properly filled. - """ - if self._tableNames == "": - print "ERROR: missing input table" - self.help() - sys.exit(1) -# if self._configFileName == "": -# print "ERROR: missing configuration file" -# self.help() -# sys.exit(1) - - - def getlistTables( self ): - """ - Return a list with the table names corresponding to the given pattern. - """ - lTables = [] - if self._tableNames != "*": - sql_cmd = "SHOW TABLES like '%%%s%%'" % ( self._tableNames ) - else: - sql_cmd = "SHOW TABLES" - self._db.execute( sql_cmd ) - res = self._db.fetchall() - for i in res: - lTables.append( i[0] ) - return lTables - - - def list( self ): - """ - List the tables corresponding to the pattern. - """ - lTables = i.getlistTables() - if len(lTables) == 0: - print "no table corresponding to '%s'" % ( self._tableNames ) - else: - print "list of tables:" - for t in lTables: - print t - print "%i tables corresponding to '%s'" % ( len(lTables), self._tableNames ) - sys.stdout.flush() - - - def drop( self ): - """ - Drop the tables corresponding to the pattern. - """ - lTables = i.getlistTables() - if len(lTables) == 0: - print "no table corresponding to '%s'" % ( self._tableNames ) - else: - print "deleting %i tables corresponding to '%s'" % ( len(lTables), self._tableNames ) - for t in lTables: - if t != "info_tables": - self._db.dropTable( t ) - sys.stdout.flush() - - - def start( self ): - self.checkAttributes() - if self._verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - if self._configFileName != "": - self._db = DbMySql( cfgFileName = self._configFileName ) - else: - if self._verbose > 0: - print "WARNING: use environment variables to connect to MySQL" - sys.stdout.flush() - self._db = DbMySql() - - - def end( self ): - self._db.close() - if self._verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - - def run( self ): - self.start() - if i._action == "list": - i.list() - if i._action == "drop": - i.drop() - self.end() - - -if __name__ == "__main__": - i = ListAndDropTables() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/MergeMatchsFiles.py --- a/commons/tools/MergeMatchsFiles.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -from commons.core.coord.Align import Align -import shutil -import os -import sys - -class MergeMatchsFiles(object): - - def __init__(self, fileType, outFileBaseName, allByAll = False, clean = True, verbose = 0): - self._fileType = fileType - self._outFileBaseName = outFileBaseName - self._allByAll = allByAll - self._verbose = verbose - self._clean = clean - - def _filterRedundantMatches( self, inFile, outFile ): - """ - When a pairwise alignment is launched ~ all-by-all (ie one batch against all chunks), - one filters the redundant matches. For instance we keep 'chunk3-1-100-chunk7-11-110-...' - and we discards 'chunk7-11-110-chunk3-1-100-...'. - Also we keep 'chunk5-1-100-chunk5-11-110-...' and we discards - 'chunk5-11-110-chunk5-1-100-...'. - For this of course the results need to be sorted by query, on plus strand, - and in ascending coordinates (always the case with Blaster). - """ - inFileHandler = open( inFile, "r" ) - outFileHandler = open( outFile, "w" ) - iAlign = Align() - countMatches = 0 - tick = 100000 - while True: - line = inFileHandler.readline() - if line == "": - break - countMatches += 1 - iAlign.setFromString( line ) - if "chunk" not in iAlign.range_query.seqname \ - or "chunk" not in iAlign.range_subject.seqname: - print "ERROR: 'chunk' not in seqname" - sys.exit(1) - if int(iAlign.range_query.seqname.split("chunk")[1]) < int(iAlign.range_subject.seqname.split("chunk")[1]): - iAlign.write( outFileHandler ) - elif int(iAlign.range_query.seqname.split("chunk")[1]) == int(iAlign.range_subject.seqname.split("chunk")[1]): - if iAlign.range_query.getMin() < iAlign.range_subject.getMin(): - iAlign.write( outFileHandler ) - if countMatches % tick == 0: # need to free buffer frequently as file can be big - outFileHandler.flush() - os.fsync( outFileHandler.fileno() ) - inFileHandler.close() - outFileHandler.close() - - def run(self): - if self._verbose > 1: - print "concatenate the results of each job" - sys.stdout.flush() - - tmpFileName = "%s.%s_tmp" % (self._outFileBaseName, self._fileType) - outFileName = "%s.%s" % (self._outFileBaseName, self._fileType) - pattern = "*.%s" % self._fileType - - if os.path.exists(tmpFileName): - os.remove(tmpFileName) - - FileUtils.catFilesByPattern(pattern, tmpFileName) - if self._clean: - FileUtils.removeFilesByPattern(pattern) - - if self._fileType == "align": - if self._allByAll: - self._filterRedundantMatches(tmpFileName, outFileName) - else: - shutil.move(tmpFileName, outFileName) - else: - prg = "%s/bin/%snum2id" % (os.environ["REPET_PATH"], self._fileType) - cmd = prg - cmd += " -i %s" % tmpFileName - cmd += " -o %s" % outFileName - cmd += " -v %i" % (self._verbose - 1) - log = os.system(cmd) - if log != 0: - print "*** Error: %s returned %i" % (prg, log) - sys.exit(1) - if self._clean and FileUtils.isRessourceExists(tmpFileName): - os.remove(tmpFileName) \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/MysqlConnect.py --- a/commons/tools/MysqlConnect.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.sql.DbMySql import DbMySql -from commons.core.utils.RepetOptionParser import RepetOptionParser - -def main(): - description = "Check MySQL connection on a node" - usage = "MysqlConnect.py -n hostname" - - parser = RepetOptionParser(description = description, usage = usage, version = "v1.0") - parser.add_option( "-n", "--node", dest = "node", type = "string", help = "node name", default = "") - parser.add_option( "-C", "--config", dest = "config", type = "string", help = "path to config file", default = "") - - options, args = parser.parse_args() - - node = options.node - - try: - if options.config != "": - idbMySQL = DbMySql(cfgFileName = options.config) - else: - idbMySQL = DbMySql() - print "SUCCESS to connect to MySQL database from '%s'" % node - except SystemExit: - print "FAILED to connect to MySQL database from '%s'" % node - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/OrientSequences.py --- a/commons/tools/OrientSequences.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,375 +0,0 @@ -#!/usr/bin/env python - -""" -Interface to orient sequences before making a multiple alignment. -Use hashing or suffix tree to get an idea of the appropriate strand. -Use 'orienter' by default, otherwise use 'mummer'. -""" - -import sys -import os -import glob -import getopt - -from commons.core.seq.BioseqDB import BioseqDB -import pyRepet.seq.fastaDB -from commons.core.checker.CheckerUtils import CheckerUtils - -class OrientSequences( object ): - """ - Interface to orient sequences before making a multiple alignment. - Use hashing or suffix tree to get an idea of the appropriate strand. - Use 'orienter' by default, otherwise use 'mummer'. - """ - - def __init__(self, inFileName="", minMatchLength=10, prgToOrient = "orienter", outFileName="", clean=False, verbosity=1): - """ - Constructor. - """ - self._inFileName = inFileName - self._minMatchLength = minMatchLength - self._prgToOrient = prgToOrient - self._outFileName = outFileName - self._clean = clean - self._verbose = verbosity - - def help( self ): - """ - Display the help on stdout. - """ - print - print "usage:",sys.argv[0].split("/")[-1],"[options]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='fasta')" - print " -m: minimum match length (default=10)" - print " -p: program to use first (default=orienter/mummer)" - print " -o: name of the output file (default=inFileName+'.oriented')" - print " -c: clean" - print " -v: verbosity level (0/default=1/2)" - print - - def setAttributesFromCmdLine( self ): - """ - Set the attributes from the command-line. - """ - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:m:p:o:cv:") - except getopt.GetoptError, err: - print str(err); self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-i": - self.setInputFileName( a ) - elif o == "-m": - self.setMinMatchLength( a ) - elif o == "-p": - self.setPrgToOrient( a ) - elif o == "-o": - self.setOutputFileName( a ) - elif o == "-c": - self.setClean() - elif o == "-v": - self.setVerbosityLevel( a ) - - def setInputFileName( self, inFileName ): - self._inFileName = inFileName - - def setMinMatchLength( self, minMatchLength ): - self._minMatchLength = int(minMatchLength) - - def setPrgToOrient( self, prgToOrient ): - self._prgToOrient = prgToOrient - - def setOutputFileName( self, outFileName ): - self._outFileName = outFileName - - def setClean( self ): - self._clean = True - - def setVerbosityLevel( self, verbose ): - self._verbose = int(verbose) - - def checkAttributes( self ): - """ - Check the attributes are valid before running the algorithm. - """ - if self._inFileName == "": - print "ERROR: missing input file name" - self.help(); sys.exit(1) - if not os.path.exists( self._inFileName ): - print "ERROR: input file '%s' doesn't exist" % ( self._inFileName ) - self.help(); sys.exit(1) - if self._prgToOrient not in [ "orienter", "mummer" ]: - print "ERROR: unknown program '%s'" % ( self._prgToOrient ) - self.help(); sys.exit(1) - if self._outFileName == "": - self._outFileName = "%s.oriented" % ( self._inFileName ) - - def useOrienter( self ): - """ - Use 'orienter'. - @return: exit value of 'orienter' - """ - prg = "orienter" - cmd = prg - cmd += " -k" -# cmd += " -l %i" % ( self._minMatchLength ) - cmd += " -v %i" % ( self._verbose ) - cmd += " %s" % ( self._inFileName ) - log = os.system( cmd ) - if log == 0 and self._outFileName.split(".")[-1] != "oriented": - os.rename( self._inFileName + ".oriented", self._outFileName ) - return log - - def compareInputSequencesWithMummer( self, nbInSeq ): - """ - Launch MUmmer on two single-sequence fasta files to find all maximal matches regardless of their uniqueness and record stdout. - Only N(N-1)/2 comparisons are made. - @param nbInSeq: number of input sequences - @type nbInSeq: integer - """ - if self._verbose > 0: - print "aligning input sequences..." - sys.stdout.flush() - if not CheckerUtils.isExecutableInUserPath( "mummer" ): - msg = "ERROR: 'mummer' is not in your PATH" - sys.stderr.write( "%s\n" % ( msg ) ) - sys.exit(1) - lInFiles = glob.glob( "batch_*.fa" ) - for i in range( 1, nbInSeq+1 ): - for j in range( i+1, nbInSeq+1 ): - if self._verbose > 1: - print "launch MUmmer on %i versus %i" % ( i, j ) - sys.stdout.flush() - prg = "mummer" - cmd = prg - cmd += " -maxmatch" - cmd += " -l %i" % ( self._minMatchLength ) - cmd += " -b" - cmd += " -F" - cmd += " batch_%s.fa" % ( str(j).zfill( len( str( len(lInFiles) ) ) ) ) - cmd += " batch_%s.fa" % ( str(i).zfill( len( str( len(lInFiles) ) ) ) ) - cmd += " > mummer_%i_vs_%i.txt" % ( i, j ) - if self._verbose < 3: - cmd += " 2> /dev/null" - returnStatus = os.system( cmd ) - if returnStatus != 0: - msg = "ERROR: '%s' returned '%i'" % ( prg, returnStatus ) - sys.stderr.write( "%s\n" % ( msg ) ) - sys.exit(1) - - def parseMummerOutput( self, mummerFileName, nameSeq1, nameSeq2 ): - """ - Parse the output from MUmmer. - @param mummerFileName: file with the output from MUmmer - @type mummerFileName: string - @param nameSeq1: name of the first sequence in the pairwise comparison - @type nameSeq1: string - @param nameSeq2: name of the first sequence in the pairwise comparison - @type nameSeq2: string - @return: dictionary whose keys are strands and values the number of maximal matches - """ - if self._verbose > 1: - print "parse '%s'" % ( mummerFileName ) - sys.stdout.flush() - dStrand2NbMatches = {} - mummerF = open( mummerFileName, "r" ) - strand = "direct" - nbMatches = 0 - line = mummerF.readline() - while True: - if line == "": - break - if line[0] == ">": - if nameSeq1 not in line: - print "ERROR" - print nameSeq1 - print nameSeq2 - sys.exit(1) - if "Reverse" in line: - dStrand2NbMatches[ strand ] = nbMatches - strand = "reverse" - nbMatches = 0 - else: - nbMatches += 1 - line = mummerF.readline() - dStrand2NbMatches[ strand ] = nbMatches - mummerF.close() - if self._verbose > 1: - print " direct: %i maximal matches" % ( dStrand2NbMatches["direct"] ) - print " reverse: %i maximal matches" % ( dStrand2NbMatches["reverse"] ) - sys.stdout.flush() - return dStrand2NbMatches - - def getCumulativeMatchLengthsOnBothStrandForEachPairwiseComparison( self, lInHeaders, nbInSeq ): - """ - For each pairwise comparison, retrieve the number of matches on both strand. - @param lInHeaders: list of the sequence headers - @type lInHeaders: list of strings - @param nbInSeq: number of input sequences - @type nbInSeq: integer - @return: dictionary whose keys are pairwise comparisons and values are number of matches on both strands - """ - dMatrix = {} - for i in range( 1, nbInSeq+1 ): - for j in range( i+1, nbInSeq+1 ): - pairComp = "%i_vs_%i" % ( i, j ) - dStrand2NbMatches = self.parseMummerOutput( "mummer_%s.txt" % ( pairComp ), lInHeaders[i-1], lInHeaders[j-1] ) - dMatrix[ pairComp ] = dStrand2NbMatches - return dMatrix - - def showResultsAsOrienter( self, nbInSeq, dMatrix ): - """ - Not used for the moment but can be useful... - """ - for i in range( 1, nbInSeq+1 ): - for j in range( i+1, nbInSeq+1 ): - pairComp = "%i_vs_%i" % ( i, j ) - string = "aligning %i with %i" % ( i, j ) - string += " %i %i" % ( dMatrix[pairComp]["direct"], dMatrix[pairComp]["reverse"] ) - string += " max=%i" % ( max( dMatrix[pairComp]["direct"], dMatrix[pairComp]["reverse"] ) ) - if dMatrix[pairComp]["reverse"] > dMatrix[pairComp]["direct"]: - string += " strand=-" - string += " nb=%i" % ( dMatrix[pairComp]["reverse"] ) - else: - string += " strand=+" - string += " nb=%i" % ( dMatrix[pairComp]["direct"] ) - print string; sys.stdout.flush() - - def getSequencesToReverseFromMatrix( self, dMatrix, lNewHeaders ): - """ - Retrieve the sequences than need to be re-oriented. - @param dMatrix: - @type dMatrix: - @param lInHeaders: list of the new sequence headers - @type lInHeaders: list of strings - @return: list of headers corresponding to sequences than need to be re-oriented - """ - lSeqToOrient = [] - - for i in range( 1, len(lNewHeaders)+1 ): - for j in range( i+1, len(lNewHeaders)+1 ): - comp = "%i_vs_%i" % ( i, j ) - nbDirectMatches = dMatrix[ comp ][ "direct" ] - nbReverseMatches = dMatrix[ comp ][ "reverse" ] - if self._verbose > 1: - print "%s: direct=%i reverse=%i" % ( comp, nbDirectMatches, nbReverseMatches ) - if nbReverseMatches > nbDirectMatches and lNewHeaders[i-1] not in lSeqToOrient: - if lNewHeaders[ j-1 ] not in lSeqToOrient: - if self._verbose > 2: - "need to reverse '%s'" % ( lNewHeaders[j-1] ) - lSeqToOrient.append( lNewHeaders[ j-1 ] ) - return lSeqToOrient - - - def getSequencesToReverse( self ): - """ - Return a list with the headers of the sequences to reverse. - """ - lSequenceHeadersToReverse = [] - - if self._prgToOrient == "orienter": - exitStatus = self.useOrienter() - if exitStatus == 0: - self.end() - sys.exit(0) - if exitStatus != 0: - print "\nWARNING: 'orienter' had a problem, switching to 'mummer'" - sys.stdout.flush() - - lInHeaders = pyRepet.seq.fastaDB.dbHeaders( self._inFileName ) - nbInSeq = len( lInHeaders ) - if self._verbose > 0: - print "nb of input sequences: %i" % ( nbInSeq ) - sys.stdout.flush() - - pyRepet.seq.fastaDB.shortenSeqHeaders( self._inFileName, 1 ) - tmpFileName = "%s.shortH" % ( self._inFileName ) - lNewHeaders = pyRepet.seq.fastaDB.dbHeaders( tmpFileName ) - dNew2Init = pyRepet.seq.fastaDB.retrieveLinksNewInitialHeaders( "%slink" % ( tmpFileName ) ) - - pyRepet.seq.fastaDB.dbSplit( tmpFileName, nbSeqPerBatch=1, newDir=True ) - os.chdir( "batches" ) - self.compareInputSequencesWithMummer( nbInSeq ) - dMatrix = self.getCumulativeMatchLengthsOnBothStrandForEachPairwiseComparison( lNewHeaders, nbInSeq ) - os.chdir( ".." ) - - lNewHeadersToReverse = self.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) - for newH in lNewHeadersToReverse: - lSequenceHeadersToReverse.append( dNew2Init[ newH ] ) - if self._verbose > 0: - print "nb of sequences to reverse: %i" % ( len(lNewHeadersToReverse) ) - for initH in lSequenceHeadersToReverse: print " %s" % ( initH ) - sys.stdout.flush() - - if self._clean: - os.remove( tmpFileName ) - os.remove( "%slink" % ( tmpFileName ) ) - - return lSequenceHeadersToReverse - - def orientInputSequences( self, lSequenceHeadersToReverse, tmpFileName="" ): - """ - Save input sequences while re-orienting those needing it. - @param lSequenceHeadersToReverse: list of headers corresponding to sequences than need to be re-oriented - @type lSequenceHeadersToReverse: list of strings - @param tmpFileName: name of a fasta file (inFileName by default) - @type tmpFileName: string - """ - if self._verbose > 0: - print "saving oriented sequences..." - sys.stdout.flush() - if tmpFileName == "": - tmpFileName = self._inFileName - inDB = BioseqDB( tmpFileName ) - outDB = BioseqDB() - for bs in inDB.db: - if bs.header in lSequenceHeadersToReverse: - bs.reverseComplement() - bs.header += " re-oriented" - outDB.add( bs ) - outDB.save( self._outFileName ) - - def clean( self ): - if os.path.exists( "batches" ): - os.system( "rm -rf batches" ) - if os.path.exists( "orienter_error.log" ): - os.remove( "orienter_error.log" ) - for f in glob.glob( "core.*" ): - os.remove( f ) - - def start( self ): - """ - Useful commands before running the program. - """ - self.checkAttributes() - if self._verbose > 0: - print "START %s" % ( type(self).__name__ ) - print "input file: %s" % ( self._inFileName ) - sys.stdout.flush() - - def end( self ): - """ - Useful commands before ending the program. - """ - if self._clean: - self.clean() - if self._verbose > 0: - print "END %s" % ( type(self).__name__ ) - sys.stdout.flush() - - def run( self ): - """ - Run the program. - """ - self.start() - lSequenceHeadersToReverse = self.getSequencesToReverse() - self.orientInputSequences( lSequenceHeadersToReverse ) - self.end() - -if __name__ == "__main__": - i = OrientSequences() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/PostAnalyzeTELib.py --- a/commons/tools/PostAnalyzeTELib.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,301 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.stat.Stat import Stat -from commons.core.seq.BioseqDB import BioseqDB -from commons.launcher.LaunchBlastclust import LaunchBlastclust -from commons.tools.AnnotationStats import AnnotationStats -import os - -CONSENSUS = "TE" -CLUSTER = "Cluster" -LOG_DEPTH = "repet.tools" -LOG_FORMAT = "%(message)s" - -class PostAnalyzeTELib(object): - - def __init__(self, analysis = 1, fastaFileName = "", clusterFileName = "", pathTableName="", seqTableName="", genomeSize=0, configFileName = "", doClean = False, verbosity = 3): - self._analysis = analysis - self._fastaFileName = fastaFileName - self._pathTableName = pathTableName - self._seqTableName = seqTableName - self._genomeSize = genomeSize - if self._analysis == 1: - self.setBioseqDB() - self._identity = 0 - self._coverage = 80 - self._applyCovThresholdOnBothSeq = False - self.setClusterFileName(clusterFileName) - self.setStatPerClusterFileName() - self.setClassifStatPerClusterFileName() - self.setAnnotationStatsPerTEFileName() - self.setAnnotationStatsPerClusterFileName() - self._doClean = doClean - self._verbosity = verbosity - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity, LOG_FORMAT) - - def setAttributesFromCmdLine(self): - description = "Tool to post-analyze a TE library : clusterize, give stats on cluster, on annotation,...\n" - epilog = "\nExample 1: clustering (e.g. to detect redundancy)\n" - epilog += "\t$ python PostAnalyzeTELib.py -a 1 -i TElib.fa -L 98 -S 95 -b\n" - epilog += "Example 2: classification stats per cluster\n" - epilog += "\t$ python PostAnalyzeTELib.py -a 2 -t TElib.tab\n" - epilog += "Example 3: annotation stats per consensus\n" - epilog += "\t$ python PostAnalyzeTELib.py -a 3 -p project_chr_allTEs_nr_noSSR_join_path -s project_refTEs_seq -g 129919500\n" - epilog += "Example 4: annotation stats per cluster\n" - epilog += "\t$ python PostAnalyzeTELib.py -a 4 -t TElib.tab -p project_chr_allTEs_nr_noSSR_join_path -s project_refTEs_seq -g 129919500\n" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-a", "--analysis", dest = "analysis", action = "store", type = "int", help = "analysis number [default: 1, 2, 3, 4]", default = 1) - parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "fasta file name [for analysis 1] [format: fasta]", default = "") - parser.add_option("-L", "--coverage", dest = "coverage", action = "store", type = "int", help = "length coverage threshold [for analysis 1] [format: %] [default: 80]", default = 80) - parser.add_option("-S", "--identity", dest = "identity", action = "store", type = "int", help = "identity threshold [for analysis 1 with BlastClust] [format: %] [default: 0 => no threshold]", default = 0) - parser.add_option("-b", "--both", dest = "bothSeq", action = "store_true", help = "require coverage on both neighbours [for analysis 1] [default: False]", default = False) - parser.add_option("-t", "--cluster", dest = "clusterFileName", action = "store", type = "string", help = "cluster file name [for analysis 2 and 4] [default: .tab]", default = "") - parser.add_option("-p", "--path", dest = "pathTableName", action = "store", type = "string", help = "name of the table (_path) with the annotated TE copies [for analysis 3 and 4]", default = "") - parser.add_option("-s", "--seq", dest = "seqTableName", action = "store", type = "string", help = "name of the table (_seq) with the TE reference sequences [for analysis 3 and 4]", default = "") - parser.add_option("-g", "--genome", dest = "genomeSize", action = "store", type = "int", help = "genome size [for analysis 3 and 4]", default = None) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setAnalysis(options.analysis) - if self._analysis == 1: - self.setFastaFileName(options.fastaFileName) - self.setBioseqDB() - self.setIdentity(options.identity) - self.setCoverage(options.coverage) - self.setApplyCovThresholdOnBothSeq(options.bothSeq) - self.setClusterFileName(options.clusterFileName) - self.setPathTableName(options.pathTableName) - self.setSeqTableName(options.seqTableName) - self.setStatPerClusterFileName() - self.setClassifStatPerClusterFileName() - self.setAnnotationStatsPerTEFileName() - self.setAnnotationStatsPerClusterFileName() - self.setGenomeSize(options.genomeSize) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def setAnalysis(self, analysis): - self._analysis = analysis - - def setFastaFileName(self, fastaFileName): - self._fastaFileName = fastaFileName - - def setBioseqDB(self): - self._iBioseqDB = BioseqDB(name = self._fastaFileName) - - def setIdentity(self, identity): - self._identity = identity - - def setCoverage(self, coverage): - self._coverage = coverage - - def setApplyCovThresholdOnBothSeq(self, bothSeq): - self._applyCovThresholdOnBothSeq = bothSeq - - def setClusterFileName(self, clusterFileName): - if clusterFileName == "": - self._clusterFileName = "%s.tab" % os.path.splitext(os.path.basename(self._fastaFileName))[0] - else: - self._clusterFileName = clusterFileName - - def setStatPerClusterFileName(self): - self._statPerClusterFileName = "%s.statsPerCluster.tab" % os.path.splitext(self._clusterFileName)[0] - self._globalStatPerClusterFileName = "%s.globalStatsPerCluster.txt" % os.path.splitext(self._clusterFileName)[0] - - def setClassifStatPerClusterFileName(self): - self._classifStatPerClusterFileName = "%s.classifStatsPerCluster.tab" % os.path.splitext(self._clusterFileName)[0] - - def setAnnotationStatsPerTEFileName(self): - self._annotStatsPerTEFileName = "%s.annotStatsPerTE.tab" % self._pathTableName - self._globalAnnotStatsPerTEFileName = "%s.globalAnnotStatsPerTE.txt" % self._pathTableName - - def setAnnotationStatsPerClusterFileName(self): - self._annotStatsPerClusterFileName = "%s.annotStatsPerCluster.tab" % self._pathTableName - - def setPathTableName(self, pathTableName): - self._pathTableName = pathTableName - - def setSeqTableName(self, seqTableName): - self._seqTableName = seqTableName - - def setGenomeSize(self, genomeSize): - self._genomeSize = genomeSize - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def _checkOptions(self): - if (self._fastaFileName == "" or not FileUtils.isRessourceExists(self._fastaFileName)) and self._analysis == 1: - self._logAndRaise("ERROR: Missing fasta file" ) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self._checkOptions() - self._log.info("START PostAnalyzeTELib analysis %d" % self._analysis) - if self._analysis == 1: - #TODO: option to choose clustering program (blastclust, MCL, uclust,...) - self._log.debug("TE lib: %s" % self._fastaFileName) - self._log.info("Launch blastclust...") - iLaunchBlastclust = LaunchBlastclust(clean = self._doClean) - iLaunchBlastclust.setTmpFileName(self._clusterFileName) - iLaunchBlastclust.setIdentityThreshold(self._identity) - iLaunchBlastclust.setCoverageThreshold(self._coverage/100.0) - if self._applyCovThresholdOnBothSeq: - iLaunchBlastclust.setBothSequences("T") - else: - iLaunchBlastclust.setBothSequences("F") - iLaunchBlastclust.setVerbosityLevel(self._verbosity - 3) - iLaunchBlastclust.launchBlastclust(self._fastaFileName) - self._log.info("Compute stats...") - self._giveStatsOnTEClusters() - if self._analysis == 2: - #TODO add global stats (e.g.: nb of cluster without PotentialChimeric, nb of clusters with LTR...) ? - self._log.debug("Consensus cluster file name: %s" % self._clusterFileName) - self._log.info("Compute classification stats...") - self._giveStatsOnConsensusClusters() - if self._analysis == 3: - #TODO: in option, save stats in DB - self._log.info("Compute annotation stats per TE...") - iAnnotationStats = AnnotationStats(analysisName="TE", seqTableName=self._seqTableName, pathTableName=self._pathTableName,\ - genomeLength=self._genomeSize, statsFileName=self._annotStatsPerTEFileName, globalStatsFileName=self._globalAnnotStatsPerTEFileName, verbosity=self._verbosity-1) - iAnnotationStats.run() - if self._analysis == 4: - self._log.info("Compute annotation stats per cluster...") - iAnnotationStats = AnnotationStats(analysisName="Cluster", clusterFileName=self._clusterFileName, seqTableName=self._seqTableName, pathTableName=self._pathTableName,\ - genomeLength=self._genomeSize, statsFileName=self._annotStatsPerClusterFileName, verbosity=self._verbosity-1) - iAnnotationStats.run() - self._log.info("END PostAnalyzeTELib analysis %d" % self._analysis) - - def _giveStatsOnConsensusClusters(self): - with open(self._classifStatPerClusterFileName, "w") as f: - f.write("cluster\tnoCat\tPotentialChimeric\tcomp\tincomp\tclassifs (nbTEs)\n") - with open(self._clusterFileName) as fCluster: - for clusterId, line in enumerate(fCluster): - dClassifNb = {} - nbIncomp =0 - nbComp=0 - nbChim=0 - nbNoCat=0 - lConsensus = line.split() - for consensus in lConsensus: - classifInfos = consensus.split("_")[0] - - if "-incomp" in classifInfos: - nbIncomp += 1 - classifInfos = classifInfos.replace("-incomp","") - if "-comp" in classifInfos: - nbComp += 1 - classifInfos = classifInfos.replace("-comp","") - if "-chim" in classifInfos: - nbChim += 1 - classifInfos = classifInfos.replace("-chim","") - if "noCat" in classifInfos: - nbNoCat += 1 - classifInfos = classifInfos.replace("noCat","") - - classif = classifInfos.split("-")[-1] - if classif != "": - if dClassifNb.get(classif, None) is None: - dClassifNb[classif] = 0 - dClassifNb[classif] +=1 - - occurences= [] - for classif, occs in dClassifNb.items(): - occurences.append("%s (%d)" % (classif, occs)) - - f.write("%d\t%d\t%d\t%d\t%d\t%s\n" % (clusterId+1, nbNoCat, nbChim\ - , nbComp, nbIncomp,"\t".join(occurences))) - - def _giveStatsOnTEClusters(self): - with open(self._clusterFileName) as fCluster: - with open(self._statPerClusterFileName, 'w') as fStatPerCluster: - fStatPerCluster.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n") - line = fCluster.readline() - clusterNb = 0 - clusterSeqList= line.split() - minClusterSize = len(clusterSeqList) - maxClusterSize = 0 - totalSeqNb = 0 - seqNbInBigClusters = 0 - dClusterSize2ClusterNb = {1:0, 2:0, 3:0} - while line: - clusterSeqList= line.split() - seqNb = len(clusterSeqList) - totalSeqNb += seqNb - if seqNb > 2: - seqNbInBigClusters += seqNb - dClusterSize2ClusterNb[3] += 1 - else: - dClusterSize2ClusterNb[seqNb] += 1 - if seqNb > maxClusterSize: - maxClusterSize = seqNb - if seqNb < minClusterSize: - minClusterSize = seqNb - line = fCluster.readline() - clusterNb += 1 - clusterSeqLengths = self._iBioseqDB.getSeqLengthByListOfName(clusterSeqList) - iStatSeqLengths = Stat(clusterSeqLengths) - fStatPerCluster.write("%d\t%d\t%d\t%d\t%d\t%d\n" %(clusterNb, seqNb, min(clusterSeqLengths), max(clusterSeqLengths), iStatSeqLengths.mean(), iStatSeqLengths.median())) - - with open(self._globalStatPerClusterFileName, 'w') as fG: - fG.write("nb of clusters: %d\n" % clusterNb) - fG.write("nb of clusters with 1 sequence: %d\n" % dClusterSize2ClusterNb[1]) - fG.write("nb of clusters with 2 sequences: %d\n" % dClusterSize2ClusterNb[2]) - fG.write("nb of clusters with >2 sequences: %d (%d sequences)\n" % (dClusterSize2ClusterNb[3], seqNbInBigClusters)) - fG.write("nb of sequences: %d\n" % totalSeqNb) - fG.write("nb of sequences in the largest cluster: %d\n" % maxClusterSize) - fG.write("nb of sequences in the smallest cluster: %d\n" % minClusterSize) - lSeqSizes = self._iBioseqDB.getListOfSequencesLength() - iStat = Stat(lSeqSizes) - fG.write("size of the smallest sequence: %d\n" % min(lSeqSizes)) - fG.write("size of the largest sequence: %d\n" % max(lSeqSizes)) - fG.write("average sequences size: %d\n" % iStat.mean()) - fG.write("median sequences size: %d\n" % iStat.median()) - -if __name__ == "__main__": - iLaunch = PostAnalyzeTELib() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/PrepareBatches.py --- a/commons/tools/PrepareBatches.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import sys -from ConfigParser import NoSectionError, NoOptionError -from commons.core.checker.CheckerUtils import CheckerUtils -from commons.core.checker.CheckerException import CheckerException -from commons.core.utils.FileUtils import FileUtils -from commons.core.seq.FastaUtils import FastaUtils - -class PrepareBatches(object): - - def __init__(self, pipelineName, projectDir, projectName, iConfig, verbose): - self._pipelineName = pipelineName - self._projectDir = projectDir - self._projectName = projectName - self._iConfig = iConfig - self._verbose = verbose - - def run(self): - if self._verbose > 0: - print "beginning of step 1" - sys.stdout.flush() - if FileUtils.isRessourceExists("%s_db" % self._projectName): - print "ERROR: directory '%s_db' already exists" % self._projectName - sys.exit(1) - - os.mkdir("%s_db" % self._projectName) - os.chdir("%s_db" % self._projectName) - genomeFastaFileName = "%s.fa" % self._projectName - os.symlink("../%s" % genomeFastaFileName, genomeFastaFileName) - sectionName = "prepare_batches" - self._checkConfig(sectionName) - - separator = "\n" - inGenomeFileHandler = open(genomeFastaFileName, "r") - try: - CheckerUtils.checkHeaders(inGenomeFileHandler) - except CheckerException, e: - print "Error in file %s. Wrong headers are :" % genomeFastaFileName - print separator.join(e.messages) - print "Authorized characters are : a-z A-Z 0-9 - . : _\n" - inGenomeFileHandler.close() - sys.exit(1) - inGenomeFileHandler.close() - - doClean = False - if self._iConfig.get(sectionName, "clean") == "yes": - doClean = True - chunkFilePrefix = "%s_chunks" % self._projectName - chunkLength = int(self._iConfig.get(sectionName, "chunk_length")) - chunkOverlap = int(self._iConfig.get(sectionName, "chunk_overlap")) - FastaUtils.dbChunks(genomeFastaFileName, chunkLength, chunkOverlap, 0, chunkFilePrefix, doClean, self._verbose) - - nbSeq = int(self._iConfig.get(sectionName, "nb_seq_per_batch")) - FastaUtils.splitFastaFileInBatches("%s.fa" % chunkFilePrefix, nbSeq * chunkLength) - - if self._iConfig.get(sectionName, "clean") == "yes": - FileUtils.removeFilesByPattern("%s.fa*" % self._projectName) - - os.chdir( ".." ) - if self._verbose > 0: - print "step 1 finished successfully" - sys.stdout.flush() - - def _checkConfig(self, sectionName): - try: - CheckerUtils.checkSectionInConfigFile(self._iConfig, sectionName) - except NoSectionError: - print "ERROR: the section %s must be in your configuration file" % sectionName - sys.exit(1) - try: - CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_length") - except NoOptionError: - print "ERROR: the option 'chunk_length' must be defined in %s in your configuration file" % sectionName - sys.exit(1) - try: - CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_overlap") - except NoOptionError: - print "ERROR: the option 'chunk_overlap' must be defined in %s in your configuration file" % sectionName - sys.exit(1) - try: - CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "nb_seq_per_batch") - except NoOptionError: - print "ERROR: the option 'nb_seq_per_batch' must be defined in %s in your configuration file" % sectionName - sys.exit(1) - try: - CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "resources") - except NoOptionError: - print "ERROR: the option 'resources' must be defined in %s in your configuration file" % sectionName - sys.exit(1) - try: - CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "tmpDir") - except NoOptionError: - print "ERROR: the option 'tmpDir' must be defined in %s in your configuration file" % sectionName - sys.exit(1) diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/RetrieveInitHeaders.py --- a/commons/tools/RetrieveInitHeaders.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,150 +0,0 @@ -#! /usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -from optparse import OptionParser -from commons.core.sql.DbMySql import DbMySql - -class RetrieveInitHeaders(object): - - def __init__(self, inTableName = "", linkFileName = "", outTableName = "", isQueryHeaders = True, clean = False, verbose = 0): - self._inTableName = inTableName - self._linkFileName = linkFileName - if outTableName == "": - self._outTableName = self._inTableName - else: - self._outTableName = outTableName - self._isQueryHeaders = isQueryHeaders - self._clean = clean - self._verbose = verbose - self._iDb = None - self._tmpTableName = "%s_tmp" % self._inTableName - - #TODO: can handle config file - #TODO: description, help... - def setAttributesFromCmdLine(self): - description = "" - parser = OptionParser(description = description) - parser.add_option("-i", "--input", dest = "inTableName", type = "string", help = "", default = "") - parser.add_option("-l", "--link", dest = "linkFileName", type = "string", help = "", default = "") - parser.add_option("-o", "--output", dest = "outTableName", type = "string", help = "(default = input table name)", default = "") - parser.add_option("-s", "--subject", dest = "isQueryHeaders", action = "store_false", help = "change subject name and not query name", default = True) - parser.add_option("-c", "--clean", dest = "clean", action = "store_true", help = "drop input table", default = False) - parser.add_option("-v", "--verbose", dest = "verbose", type = "int", help = "0 or 1", default = 0) - options, args = parser.parse_args() - self.setAttributesFromOptions(options) - - def setAttributesFromOptions(self, options): - self.setInTableName(options.inTableName) - self.setLinkFileName(options.linkFileName) - self.setOutTableName(options.outTableName) - self.setIsQueryHeaders(options.isQueryHeaders) - self.setClean(options.clean) - self.setVerbose(options.verbose) - - def setInTableName(self, inTableName): - self._inTableName = inTableName - self._tmpTableName = "%s_tmp" % self._inTableName - - def setLinkFileName(self, linkFileName): - self._linkFileName = linkFileName - - def setOutTableName(self, outTableName): - if outTableName == "": - self._outTableName = self._inTableName - else: - self._outTableName = outTableName - - def setIsQueryHeaders(self, isQueryHeaders): - self._isQueryHeaders = isQueryHeaders - - def setClean(self, clean): - self._clean = clean - - def setVerbose(self, verbose): - self._verbose = verbose - - #TODO: checkOptions - def checkOptions(self): - pass - - def run(self): - if self._verbose > 0: - print "START RetrieveInitHeaders.py" - self.checkOptions() - - if self._verbose > 0: - print "copy '%s' table to '%s' table" % (self._inTableName, self._tmpTableName) - self._iDb = DbMySql() - self._iDb.copyTable(self._inTableName, self._tmpTableName) - - if self._verbose > 0: - print "read '%s' file" % self._linkFileName - f = open(self._linkFileName) - line = f.readline() - count = 0 - while line: - oldHeader = line.split()[0] - newHeader = line.split()[1] - if self._isQueryHeaders: - self._updateQueryName(oldHeader, newHeader) - else: - self._updateSubjectName(oldHeader, newHeader) - count += 1 - line = f.readline() - f.close() - - if self._verbose > 0: - print "nb of relationships: %i" % count - if self._clean: - self._iDb.dropTable(self._inTableName) - if self._verbose > 0: - print "drop '%s' table" % self._inTableName - if self._verbose > 0: - print "rename '%s' table to '%s' table" % (self._tmpTableName, self._outTableName) - self._iDb.renameTable(self._tmpTableName, self._outTableName) - self._iDb.close() - if self._verbose > 0: - print "END RetrieveInitHeaders.py" - - #TODO: methods must be in TablePathAdaptator ? - def _updateQueryName(self, oldH, newH): - sqlCmd = "UPDATE %s SET query_name = '%s' WHERE query_name = '%s'" % (self._tmpTableName, newH, oldH) - self._iDb.execute(sqlCmd) - - def _updateSubjectName(self, oldH, newH): - sqlCmd = "UPDATE %s SET subject_name = '%s' WHERE subject_name = '%s'" % (self._tmpTableName, newH, oldH) - self._iDb.execute(sqlCmd) - -if __name__ == "__main__": - iRIH = RetrieveInitHeaders() - iRIH.setAttributesFromCmdLine() - iRIH.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/RmvPairAlignInChunkOverlaps.py --- a/commons/tools/RmvPairAlignInChunkOverlaps.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,286 +0,0 @@ -#!/usr/bin/env python - -""" -Remove hits due to chunk overlaps. -""" - -import os -import sys -import getopt -import exceptions -import copy -from commons.core.coord.Align import * - - -class RmvPairAlignInChunkOverlaps( object ): - """ - Remove hits due to chunk overlaps. - """ - - - def __init__( self, inFileName="", chunkLength=200000, chunkOverlap=10000, margin=10, outFileName="", verbose=0 ): - """ - Constructor. - """ - self._inFileName = inFileName - self._chunkLength = chunkLength - self._chunkOverlap = chunkOverlap - self._margin = margin - self._outFileName = outFileName - self._verbose = verbose - - def help( self ): - """ - Display the help. - """ - print - print "usage: %s [ options ]" % ( sys.argv[0] ) - print "options:" - print " -h: this help" - print " -i: name of the input file (format='align')" - print " -l: chunk length (in bp)" - print " -o: chunk overlap (in bp)" - print " -m: margin to remove match included into a chunk overlap (default=10)" - print " -O: name of the output file (default=inFileName+'.not_over')" - print " -v: verbose (default=0/1)" - print - - def setAttributesFromCmdLine( self ): - """ - Set attributes from the command-line arguments. - """ - try: - opts, args = getopt.getopt(sys.argv[1:],"h:i:l:o:m:O:v:") - except getopt.GetoptError, err: - print str(err); self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-i": - self.setInputFileName( a ) - elif o == "-l": - self.setChunkLength( a ) - elif o == "-o": - self.setChunkOverlap( a ) - elif o == "-m": - self.setMargin( a ) - elif o == "-O": - self.setOutputFileName( a ) - elif o == "-v": - self.setVerbosityLevel( a ) - - def setInputFileName( self, inFileName ): - self._inFileName = inFileName - - def setChunkLength( self, chunkLength ): - self._chunkLength = int(chunkLength) - - def setChunkOverlap( self, chunkOverlap ): - self._chunkOverlap = int(chunkOverlap) - - def setMargin( self, margin ): - self._margin = int(margin) - - def setOutputFileName( self, outFileName ): - self._outFileName = outFileName - - def setVerbosityLevel( self, verbose ): - self._verbose = int(verbose) - - def checkAttributes( self ): - """ - Before running, check the required attributes are properly filled. - """ - if self._inFileName == "": - print "ERROR: missing input file"; self.help(); sys.exit(1) - if not os.path.exists(self._inFileName ): - print "ERROR: input file '%s' doesn't exist" %( self._inFileName ) - if self._outFileName == "": - self._outFileName = "%s.not_over" % ( self._inFileName ) - - - def isPairAlignAChunkOverlap( self, a, chunkQuery, chunkSubject ): - """ - Return True if the pairwise alignment exactly corresponds to a 2-chunk overlap, False otherwise. - Take into account cases specific to BLASTER or PALS. - """ - - if a.range_query.isOnDirectStrand() != a.range_subject.isOnDirectStrand(): - if self._verbose > 1: print "on different strand" - return False - - if chunkQuery == chunkSubject + 1: - if self._verbose > 1: print "query > subject" - if a.range_query.start == 1 and a.range_subject.end == self._chunkLength \ - and ( a.range_query.getLength() == self._chunkOverlap \ - or a.range_query.getLength() == self._chunkOverlap + 1 ) \ - and ( a.range_subject.getLength() == self._chunkOverlap \ - or a.range_subject.getLength() == self._chunkOverlap + 1 ): - if self._verbose > 1: print "chunk overlap" - return True - - elif chunkQuery == chunkSubject - 1: - if self._verbose > 1: print "query < subject" - if a.range_query.end == self._chunkLength and a.range_subject.start == 1 \ - and ( a.range_query.getLength() == self._chunkOverlap \ - or a.range_query.getLength() == self._chunkOverlap + 1 ) \ - and ( a.range_subject.getLength() == self._chunkOverlap \ - or a.range_subject.getLength() == self._chunkOverlap + 1 ): - if self._verbose > 1: print "chunk overlap" - return True - - if self._verbose > 1: print "not a chunk overlap" - return False - - - def isInInterval( self, coord, midpoint ): - """ - Check if a given coordinate is inside the interval [midpoint-margin;midpoint+margin]. - """ - if coord >= midpoint - self._margin and coord <= midpoint + self._margin: - return True - return False - - - def isPairAlignWithinAndDueToAChunkOverlap( self, a, chunkQuery, chunkSubject ): - """ - Return True if the pairwise alignment lies within an overlap between two contiguous chunks and is due to it, False otherwise. - """ - uniqLength = self._chunkLength - self._chunkOverlap - - if a.range_query.isOnDirectStrand() != a.range_subject.isOnDirectStrand(): - if self._verbose > 1: print "on different strand" - return False - - if chunkQuery == chunkSubject + 1: - if self._verbose > 1: print "query > subject" - if a.range_query.getMin() >= 1 and a.range_query.getMax() <= self._chunkOverlap \ - and a.range_subject.getMin() >= self._chunkLength - self._chunkOverlap + 1 \ - and a.range_subject.getMax() <= self._chunkLength: - if self._verbose > 1: print "included" - if self.isInInterval( a.range_query.getMin(), a.range_subject.getMin() - uniqLength ) \ - and self.isInInterval( self._chunkOverlap - a.range_query.getMax(), self._chunkLength - a.range_subject.getMax() ): - if self._verbose > 1: print "due to overlap" - return True - else: - if self._verbose > 1: print "not due to overlap" - return False - - elif chunkQuery == chunkSubject - 1: - if self._verbose > 1: print "query < subject" - if a.range_query.getMin() >= self._chunkLength - self._chunkOverlap + 1 \ - and a.range_query.getMax() <= self._chunkLength \ - and a.range_subject.getMin() >= 1 \ - and a.range_subject.getMax() <= self._chunkOverlap: - if self._verbose > 1: print "included" - if self.isInInterval( a.range_subject.getMin(), a.range_query.getMin() - uniqLength ) \ - and self.isInInterval( self._chunkOverlap - a.range_subject.getMax(), self._chunkLength - a.range_query.getMax() ): - if self._verbose > 1: print "due to overlap" - return True - else: - if self._verbose > 1: print "not due to overlap" - return False - - else: - if self._verbose > 1: print "not contiguous chunks" - return False - - if self._verbose > 1: print "not included" - return False - - - def removeChunkOverlaps( self ): - """ - Remove pairwise alignments exactly corresponding to chunk overlaps or those included within such overlaps. - """ - totalNbPairAlign = 0 - nbChunkOverlaps = 0 - d = {} - nbPairAlignWithinChunkOverlaps = 0 - - inF = open( self._inFileName, "r" ) - outF = open( self._outFileName, "w" ) - alignInstance = Align() - - while True: - if not alignInstance.read( inF ): break - totalNbPairAlign += 1 - if self._verbose > 1: alignInstance.show() - - if "chunk" not in alignInstance.range_query.seqname or "chunk" not in alignInstance.range_subject.seqname: - print "WARNING: no 'chunk' in query or subject name"; return False - - chunkQuery = int(alignInstance.range_query.seqname.replace("chunk","")) - chunkSubject = int(alignInstance.range_subject.seqname.replace("chunk","")) - - if abs( chunkSubject - chunkQuery ) > 1: - if self._verbose > 1: print "non contiguous chunks -> keep" - alignInstance.write( outF ) - continue - - if alignInstance.range_query.isOnDirectStrand() != alignInstance.range_subject.isOnDirectStrand(): - if self._verbose > 1: print "on different strand" - alignInstance.write( outF ) - continue - - if abs( chunkSubject - chunkQuery ) == 0: - if alignInstance.range_query.start == 1 \ - and alignInstance.range_query.end == self._chunkLength \ - and alignInstance.range_subject.start == 1 \ - and alignInstance.range_subject.end == self._chunkLength: - if self._verbose > 1: print "self-alignment on whole chunk -> remove" - continue - - if self.isPairAlignAChunkOverlap( alignInstance, chunkQuery, chunkSubject ): - if self._verbose > 1: print "chunk overlap -> remove" - nbChunkOverlaps += 1 - - elif self.isPairAlignWithinAndDueToAChunkOverlap( alignInstance, chunkQuery, chunkSubject ): - if self._verbose > 1: print "within chunk overlap -> remove" - nbPairAlignWithinChunkOverlaps += 1 - - else: - if self._verbose > 1: print "keep" - alignInstance.write( outF ) - - inF.close() - if self._verbose > 0: print "nb of pairwise alignments in input file: %i" % ( totalNbPairAlign ) - if self._verbose > 0: print "nb of chunk overlaps: %i" % ( nbChunkOverlaps ) - if self._verbose > 0: print "nb of pairwise alignments within chunk overlaps: %i" % ( nbPairAlignWithinChunkOverlaps ) - - for names,lAligns in d.items(): - for alignInstance in lAligns: - alignInstance.write( outF ) - outF.close() - - - def start( self ): - """ - Useful commands before running the program. - """ - if self._verbose > 0: - print "START %s" % ( type(self).__name__ ); sys.stdout.flush() - self.checkAttributes() - - - def end( self ): - """ - Useful commands before ending the program. - """ - if self._verbose > 0: - print "END %s" % ( type(self).__name__ ); sys.stdout.flush() - - - def run( self ): - """ - Run the program. - """ - self.start() - self.removeChunkOverlaps() - self.end() - - -if __name__ == '__main__': - i = RmvPairAlignInChunkOverlaps() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/SpliceTEsFromGenome.py --- a/commons/tools/SpliceTEsFromGenome.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,193 +0,0 @@ -#!/usr/bin/env python - -import sys -import os -import getopt - -from commons.core.sql.DbMySql import DbMySql -from commons.core.seq.FastaUtils import FastaUtils -from commons.core.coord.MapUtils import MapUtils -from commons.core.coord.AlignUtils import AlignUtils -from commons.core.coord.PathUtils import PathUtils - - -class SpliceTEsFromGenome( object ): - - def __init__( self ): - self._inputData = "" - self._formatData = "" - self._genomeFile = "" - self._configFile = "" - self._outFile = "" - self._verbose = 0 - self._db = None - - - def help( self ): - print - print "usage: SpliceTEsFromGenome.py [ options ]" - print "options:" - print " -h: this help" - print " -i: input TE coordinates (can be file or table)" - print " TEs as subjects if align or path format" - print " -f: format of the data (map/align/path)" - print " -g: genome file (format=fasta)" - print " -C: configuration file (if table as input)" - print " -o: output fasta file (default=genomeFile+'.splice')" - print " -v: verbosity level (default=0/1)" - print - - - def setAttributesFromCmdLine( self ): - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:f:g:C:o:v:") - except getopt.GetoptError, err: - msg = "%s" % str(err) - sys.stderr.write( "%s\n" % msg ) - self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-i": - self._inputData = a - elif o == "-f": - self._formatData = a - elif o == "-g": - self._genomeFile = a - elif o == "-C": - self._configFile = a - elif o =="-o": - self._outFile = a - elif o == "-v": - self._verbose = int(a) - - - def checkAttributes( self ): - if self._inputData == "": - msg = "ERROR: missing input data (-i)" - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._inputData ): - if not os.path.exists( self._configFile ): - msg = "ERROR: neither input file '%s' nor configuration file '%s'" % ( self._inputData, self._configFile ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._configFile ): - msg = "ERROR: can't find config file '%s'" % ( self._configFile ) - sys.stderr.write( "%s\n" % msg ) - sys.exit(1) - self._db = DbMySql( cfgFileName=self._configFile ) - if not self._db.doesTableExist( self._inputData ): - msg = "ERROR: can't find table '%s'" % ( self._inputData ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if self._formatData == "": - msg = "ERROR: need to precise format (-f)" - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if self._formatData not in [ "map", "align", "path" ]: - msg = "ERROR: format '%s' not yet supported" % ( self._formatData ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if self._genomeFile == "": - msg = "ERROR: missing genome file (-g)" - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if not os.path.exists( self._genomeFile ): - msg = "ERROR: can't find genome file '%s'" % ( self._genomeFile ) - sys.stderr.write( "%s\n" % msg ) - self.help() - sys.exit(1) - if self._outFile == "": - self._outFile = "%s.splice" % ( self._genomeFile ) - if self._verbose > 0: - print "output fasta file: %s" % self._outFile - - - def getCoordsAsMapFile( self ): - if self._verbose > 0: - print "get TE coordinates as 'Map' file" - sys.stdout.flush() - if self._db != None: - cmd = "srptExportTable.py" - cmd += " -i %s" % ( self._inputData ) - cmd += " -C %s" % ( self._configFile ) - cmd += " -o %s.%s" % ( self._inputData, self._formatData ) - returnStatus = os.system( cmd ) - if returnStatus != 0: - msg = "ERROR while exporting data from table" - sys.stderr.write( "%s\n" % msg ) - sys.exit(1) - self._inputData += ".%s" % ( self._formatData ) - - if self._formatData == "map": - return self._inputData - elif self._formatData == "align": - mapFile = "%s.map" % ( self._inputData ) - AlignUtils.convertAlignFileIntoMapFileWithSubjectsOnQueries( self._inputData, mapFile ) - return mapFile - elif self._formatData == "path": - mapFile = "%s.map" % ( self._inputData ) - PathUtils.convertPathFileIntoMapFileWithSubjectsOnQueries( self._inputData, mapFile ) - return mapFile - - - def mergeCoordsInMapFile( self, mapFile ): - if self._verbose > 0: - print "merge TE coordinates" - sys.stdout.flush() - mergeFile = "%s.merge" % ( mapFile ) - MapUtils.mergeCoordsInFile( mapFile, mergeFile ) - if self._formatData != "map" or self._db != None: - os.remove( mapFile ) - return mergeFile - - - def spliceFastaFromCoords( self, mergeFile ): - if self._verbose > 0: - print "splice TE copies from the genome" - sys.stdout.flush() - FastaUtils.spliceFromCoords( self._genomeFile, - mergeFile, - self._outFile ) - - os.remove( mergeFile ) - - - def start( self ): - self.checkAttributes() - if self._verbose > 0: - print "START SpliceTEsFromGenome.py" - sys.stdout.flush() - - - def end( self ): - if self._db != None: - self._db.close() - if self._verbose > 0: - print "END SpliceTEsFromGenome.py" - sys.stdout.flush() - - - def run( self ): - self.start() - - mapFile = self.getCoordsAsMapFile() - - mergeFile = self.mergeCoordsInMapFile( mapFile ) - - self.spliceFastaFromCoords( mergeFile ) - - self.end() - - -if __name__ == "__main__": - i = SpliceTEsFromGenome() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/SplicerFromAnnotation.py --- a/commons/tools/SplicerFromAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,218 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -import os -import sys -import ConfigParser - -from commons.core.sql.DbMySql import DbMySql -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.parsing.FastaParser import FastaParser -from ConfigParser import MissingSectionHeaderError -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.LoggerFactory import LoggerFactory - -#TODO: use configuration file - -LOG_DEPTH = "repet.tools" - -## Get 3 annotation files, using output from TEannot: -#- consensus with one or more full length copy, -#- consensus with one or more full length fragment, -#- consensus without copy - -class SplicerFromAnnotation(object): - - def __init__(self, inInfoFileName = "", tableName = "", verbose = 0): - self._inInfoFileName = inInfoFileName - self._tableName = tableName - self._verbosity = verbose - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def setAttributesFromCmdLine(self): - desc = "Splice annotations from genome. These annotations are Full Length Copy or Full Length Fragment according to consensus." - desc += "A TEs library and annotation are necessary. Connection to the database parameters are retrieved from the environment" - - examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n" - examples += "\t$ python SplicerFromAnnotation.py -i inputFastaFileName -C configFileName -t MyTEannotAnalysis_refTEs_seq " - examples += "\n\t" - examples += "\n\n" - - parser = RepetOptionParser(description = desc, epilog = examples) - parser.add_option("-i", "--file", dest = "inputFastaFileName", action = "store", type = "string", help = "input file (mandatory) = output file with .splice)") - parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "config file name to set database connection", default = "") - parser.add_option("-t", "--copyType", dest = "copyType" , action = "store", type = "int", help = "type number [default: 1, 2] 1 is Full Length Copy", default = 1 ) - parser.add_option("-I", "--identity", dest = "identity", action= "store", type = "float", help = "identity between 0 and 100 [default: 80]", default = 80) - parser.add_option("-o", "--outputFile",dest = "outputFile", action= "store", type = "string", help = "output fasta file (default=input File + '.splice')", default = "") - parser.add_option("-v", "--verbose", dest = "verbose", action = "store", type = "int", help = "verbosity level (default=0)", default = 0) - (options, args) = parser.parse_args() - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setConfigFileName(options.configFileName) - self.setInputFileName(options.inputFastaFileName) - self.setOutputFileName(options.outputFile) - self.setIdentity(options.identity) - self.setCopyType(options.copyType) - self.setVerbose(options.verbose) - - def setCopyType(self, copyType): - self._copyType = copyType - - def setIdentity(self,identity): - self._identity=identity - - def setInputFileName(self, inputFastaFileName): - self._inputFastaFileName = inputFastaFileName - self._projectName= os.path.basename(self._inputFastaFileName) - self._projectName = self._projectName.split('.')[0] - self._fF=FastaParser(self._inputFastaFileName) - self._fF.getInfos() - self.genomeSize=self._fF.size - self.nbSeqGenome=self._fF.nbSequences - - def setOutputFileName(self,outputFile): - self._outputFileName = outputFile - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - configFileHandle = open(self._configFileName) - config = ConfigParser.ConfigParser() - - try : - config.readfp( configFileHandle ) - except MissingSectionHeaderError: - self._logAndRaise("Config file " + self._configFileName + " must begin with a section header ") - - self.setup_env( config ) - - def setVerbose(self, verbose): - self._verbosity = verbose - - def setup_env(self, config): - os.environ["REPET_HOST"] = config.get("repet_env", "repet_host") - os.environ["REPET_USER"] = config.get("repet_env", "repet_user") - os.environ["REPET_PW"] = config.get("repet_env", "repet_pw") - os.environ["REPET_DB"] = config.get("repet_env", "repet_db") - os.environ["REPET_PORT"] = config.get("repet_env", "repet_port") - os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager") - - def checkOptions(self): - if self._inputFastaFileName != "": - if not FileUtils.isRessourceExists(self._inputFastaFileName): - self._logAndRaise("Input fasta file does not exist!") - else: - self._logAndRaise("No specified -i option! It is mandatory") - - if self._outputFileName =="": - self._outputFileName = os.path.basename(self._inputFastaFileName)+'.splice' - - if self._copyType!=1 or self._copyType!=2: - self._logAndRaise("Copy type must be only 1 or 2!") - if self._configFileName != "": - iDb = DbMySql(cfgFileName = self._configFileName) - iDb.close() - else: - self._logAndRaise("No specified config file name!") - - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - self.checkOptions() - - msg = "START SplicerFromAnnotation" - msg += "\n input info file: %s" % self._inputFastaFileName - msg += "\n Copy type is: %s" % self._copyType - msg += "\n identity is: %s" % self._identity - msg += "\n host is: %s" % os.environ["REPET_HOST"] - msg += "\n user is: %s" % os.environ["REPET_USER"] - msg += "\n DB is: %s" % os.environ["REPET_DB"] - msg += "\n port is: %s" % os.environ["REPET_PORT"] - self._log.debug("%s\n" % msg) - - cmd="PostAnalyzeTELib.py -a 3 -p %s_chr_allTEs_nr_noSSR_join_path -s %s_refTEs_seq -g %s" % (self._projectName,self._projectName,self.genomeSize) - os.system(cmd) - - cmd="GetSpecificTELibAccordingToAnnotation.py -i %s_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab -t %s_refTEs_seq -v 2" % (self._projectName,self._projectName) - os.system(cmd) - - if self._copyType == 1 : - f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt", "r") - else : - f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt", "r") - - lines=f.readlines()[1:] - if len(lines)>0: - lConsensusHeader_copyType=[i.split('\t',1)[0] for i in lines] - db = DbFactory.createInstance() - - sql_cmd = "CREATE TABLE %s_annotationIdentitySup%d_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where identity >=%f" % ( self._projectName,int(self._identity),self._projectName,self._identity) - db.execute( sql_cmd ) - - iTPA = TablePathAdaptator(db, "%s_annotationIdentitySup%d_path" % (self._projectName, int(self._identity))) - lAllDistinctPath=[] - for consensusName in lConsensusHeader_copyType: - lDistinctPath = iTPA.getIdListFromSubject(consensusName) - lAllDistinctPath=lAllDistinctPath+lDistinctPath - - iTPA = TablePathAdaptator(db,"%s_chr_allTEs_nr_noSSR_join_path" % self._projectName) - sql_cmd = "CREATE TABLE %s_annotationToSplice_path LIKE %s_chr_allTEs_nr_noSSR_join_path" % ( self._projectName, self._projectName ) - db.execute( sql_cmd ) - - for pathId in lAllDistinctPath: - sql_cmd = "INSERT INTO %s_annotationToSplice_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where path =%d" % ( self._projectName, self._projectName, pathId ) - db.execute( sql_cmd ) - db.close() - - cmd="SpliceTEsFromGenome.py -i %s_annotationToSplice_path -f path -g %s -o %s -C %s -v 2" % (self._projectName, self._inputFastaFileName, self._outputFileName, self._configFileName) - os.system(cmd) - - else : - msg = "There is no consensus in this copy type.\n" - self._log.info(msg) - f.close() - - self._log.info("END SplicerFromAnnotation") - return 0 - -if __name__ == '__main__': - iGetTELib = SplicerFromAnnotation() - iGetTELib.setAttributesFromCmdLine() - iGetTELib.run() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/TEclassifierPE.py --- a/commons/tools/TEclassifierPE.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,193 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import sys - -if not "REPET_PATH" in os.environ.keys(): - print "ERROR: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append(os.environ["REPET_PATH"]) -if not "PYTHONPATH" in os.environ.keys(): - os.environ["PYTHONPATH"] = os.environ["REPET_PATH"] -else: - os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"]) - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.checker.ConfigChecker import ConfigRules -from commons.core.checker.ConfigChecker import ConfigChecker -from commons.core.seq.FastaUtils import FastaUtils -from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif -from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif -from denovo_pipe.DetectTEFeatures import DetectTEFeatures -from denovo_pipe.LaunchPASTEC import LaunchPASTEC -from PASTEC.StatPastec import StatPastec - -LOG_DEPTH = "repet.tools" -#LOG_FORMAT = "%(message)s" - -####TEclassifier PASTEC Edition -# -class TEclassifierPE(object): - - def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0): - self._fastaFileName = fastaFileName - self._addWickerCode = addWickerCode - self._reverseComp = reverseComp - self._configFileName = configFileName - self._doClean = doClean - self._verbosity = verbosity - self._projectName = "" - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "TE classifier PASTEC Edition.\n" - description += "Detect TE features on consensus and classify them. Give some classification statistics.\n" - description += "Can rename headers with classification info and Wicker's code at the beginning.\n" - description += "Can reverse-complement consensus if they are detected in reverse strand.\n" - description += "Warning : it's highly advised to use sequences in upper case.\n" - epilog = "\n" - epilog += "Example 1: launch and clean temporary files\n" - epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n" - epilog += "\n" - epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n" - epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\n" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-C", "--config", dest = "configFileName",action = "store", type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "") - parser.add_option("-w", "--wicker", dest = "addWickerCode", action = "store_true", help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False) - parser.add_option("-r", "--reverse", dest = "reverseComp", action = "store_true", help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", default = False) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 3, from 1 to 4]", default = 3) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setFastaFileName(options.fastaFileName) - self.setAddWickerCode(options.addWickerCode) - self.setReverseComp(options.reverseComp) - self.setConfigFileName(options.configFileName) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def _checkConfig(self): - iConfigRules = ConfigRules() - iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string") - sectionName = "classif_consensus" - iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool") - iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) - iConfig = iConfigChecker.getConfig() - self._setAttributesFromConfig(iConfig) - - def _setAttributesFromConfig(self, iConfig): - self.setProjectName(iConfig.get("project", "project_name")) - sectionName = "classif_consensus" - self.setDoClean(iConfig.get(sectionName, "clean")) - - def setFastaFileName(self, fastaFileName): - self._fastaFileName = fastaFileName - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def setAddWickerCode(self, addWickerCode): - self._addWickerCode = addWickerCode - - def setReverseComp(self, reverseComp): - self._reverseComp = reverseComp - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def setProjectName(self, projectName): - self._projectName = projectName - - def _checkOptions(self): - if self._fastaFileName == "": - self._logAndRaise("ERROR: Missing input fasta file name") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - if self._configFileName: - self._checkConfig() - self._checkOptions() - self._log.info("START TEclassifier PASTEC Edition") - self._log.debug("Fasta file name: %s" % self._fastaFileName) - nbSeq = FastaUtils.dbSize(self._fastaFileName) - self._log.debug("Total number of sequences: %i)" % nbSeq) - - #TODO: add step => avoid to re-launch DetectTEFeatures, if error with PASTEC (e.g. wrong bank format) - #step 1 - iDF = DetectTEFeatures(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity) - iDF.run() - - #step 2 - iLP = LaunchPASTEC(configFileName = self._configFileName, inputFileName = self._fastaFileName, projectName = self._projectName, verbose = self._verbosity) - iLP.run() - - classifFileName = "%s.classif" % self._projectName - - iSP = StatPastec(classifFileName) - iSP.run() - - if self._reverseComp: - self._log.info("Reverse complement...") - iRevComplAccording2Classif = ReverseComplementAccordingToClassif() - iRevComplAccording2Classif.setFastaFile(self._fastaFileName) - iRevComplAccording2Classif.setClassifFile(classifFileName) - iRevComplAccording2Classif.run() - tmpFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0] - else: - tmpFastaFileName = self._fastaFileName - - if self._addWickerCode: - self._log.info("Rename headers according to Wicker's code...") - iRHC = RenameHeaderClassif(classifFileName, tmpFastaFileName, self._projectName) - iRHC.setOutputFileName("") - iRHC.run() - if self._doClean: - os.remove(tmpFastaFileName) - - self._log.info("END TEclassifier PASTEC Edition") - -if __name__ == "__main__": - iLaunch = TEclassifierPE() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/TEclassifierPE_parallelized.py --- a/commons/tools/TEclassifierPE_parallelized.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,261 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import sys -import shutil - -if not "REPET_PATH" in os.environ.keys(): - print "ERROR: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append(os.environ["REPET_PATH"]) -if not "PYTHONPATH" in os.environ.keys(): - os.environ["PYTHONPATH"] = os.environ["REPET_PATH"] -else: - os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"]) - -from commons.core.LoggerFactory import LoggerFactory -from commons.core.utils.RepetOptionParser import RepetOptionParser -from commons.core.utils.FileUtils import FileUtils -from commons.core.checker.ConfigChecker import ConfigRules -from commons.core.checker.ConfigChecker import ConfigChecker -from commons.core.seq.FastaUtils import FastaUtils -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory -from commons.core.launcher.Launcher import Launcher -from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif -from denovo_pipe.DetectTEFeatures_parallelized import DetectTEFeatures_parallelized -from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif -from denovo_pipe.LaunchPASTEC import LaunchPASTEC -from PASTEC.StatPastec import StatPastec - -LOG_DEPTH = "repet.tools" -#LOG_FORMAT = "%(message)s" - -####TEclassifier PASTEC Edition - parallelized -# -class TEclassifierPE_parallelized(object): - - def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0): - self._fastaFileName = fastaFileName - self._addWickerCode = addWickerCode - self._reverseComp = reverseComp - self._configFileName = configFileName - self._doClean = doClean - self._verbosity = verbosity - self._projectName = "" - self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity) - - def setAttributesFromCmdLine(self): - description = "TE classifier PASTEC Edition.\n" - description += "Detect TE features on consensus and classify them. Give some classification statistics.\n" - description += "Can rename headers with classification info and Wicker's code at the beginning.\n" - description += "Can reverse-complement consensus if they are detected in reverse strand.\n" - epilog = "\n" - epilog += "Example 1: launch and clean temporary files\n" - epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n" - epilog += "\n" - epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n" - epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\n" - parser = RepetOptionParser(description = description, epilog = epilog) - parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "") - parser.add_option("-C", "--config", dest = "configFileName",action = "store", type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "") - parser.add_option("-w", "--wicker", dest = "addWickerCode", action = "store_true", help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False) - parser.add_option("-r", "--reverse", dest = "reverseComp", action = "store_true", help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", default = False) - parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False) - parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 3, from 1 to 4]", default = 3) - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - def _setAttributesFromOptions(self, options): - self.setFastaFileName(options.fastaFileName) - self.setAddWickerCode(options.addWickerCode) - self.setReverseComp(options.reverseComp) - self.setConfigFileName(options.configFileName) - self.setDoClean(options.doClean) - self.setVerbosity(options.verbosity) - - def _checkConfig(self): - iConfigRules = ConfigRules() - iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string") - sectionName = "classif_consensus" - iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool") - iConfigRules.addRuleOption(section=sectionName, option ="limit_job_nb", type="int") - iConfigRules.addRuleOption(section=sectionName, option ="resources", type="string") - iConfigRules.addRuleOption(section=sectionName, option ="tmpDir", type="string") - iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) - iConfig = iConfigChecker.getConfig() - self._setAttributesFromConfig(iConfig) - - def _setAttributesFromConfig(self, iConfig): - self.setProjectName(iConfig.get("project", "project_name")) - sectionName = "classif_consensus" - self.setDoClean(iConfig.get(sectionName, "clean")) - self._maxJobNb = iConfig.get(sectionName, "limit_job_nb") - self._resources = iConfig.get(sectionName, "resources") - self._tmpDir = iConfig.get(sectionName, "tmpDir") - - def setFastaFileName(self, fastaFileName): - self._fastaFileName = fastaFileName - - def setConfigFileName(self, configFileName): - self._configFileName = configFileName - - def setAddWickerCode(self, addWickerCode): - self._addWickerCode = addWickerCode - - def setReverseComp(self, reverseComp): - self._reverseComp = reverseComp - - def setDoClean(self, doClean): - self._doClean = doClean - - def setVerbosity(self, verbosity): - self._verbosity = verbosity - - def setProjectName(self, projectName): - self._projectName = projectName - - def _checkOptions(self): - if self._fastaFileName == "": - self._logAndRaise("ERROR: Missing input fasta file name") - - def _logAndRaise(self, errorMsg): - self._log.error(errorMsg) - raise Exception(errorMsg) - -# def setup_env(config): -# os.environ["REPET_HOST"] = config.get("repet_env", "repet_host") -# os.environ["REPET_USER"] = config.get("repet_env", "repet_user") -# os.environ["REPET_PW"] = config.get("repet_env", "repet_pw") -# os.environ["REPET_DB"] = config.get("repet_env", "repet_db") -# os.environ["REPET_PORT"] = config.get("repet_env", "repet_port") -# os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager") -# os.environ["REPET_QUEUE"] = config.get("repet_env", "repet_job_manager") -# os.environ["REPET_JOBS"] = "MySQL" - - def getPASTECcommand(self, iLauncher, fileName): - lArgs = [] - lArgs.append("-C %s" % self._configFileName) - lArgs.append("-P %s" % self._projectName) - lArgs.append("-S 2") - lArgs.append("-i %s" % fileName) - lArgs.append("-v %s" % self._verbosity) - return iLauncher.getSystemCommand("LaunchPASTEC.py", lArgs) - - def run(self): - LoggerFactory.setLevel(self._log, self._verbosity) - if self._configFileName: - self._checkConfig() - self._checkOptions() - self._log.info("START TEclassifier PASTEC Edition") - self._log.debug("Fasta file name: %s" % self._fastaFileName) - nbSeq = FastaUtils.dbSize(self._fastaFileName) - self._log.debug("Total number of sequences: %i)" % nbSeq) - - self._log.debug("Launch DetectTEFeatures on each batch") - iDF = DetectTEFeatures_parallelized(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity) - iDF.run() - - self._log.debug("Insert banks in database") - iLP = LaunchPASTEC(self._configFileName, "1", projectName = self._projectName, verbose = self._verbosity) - iLP.run() - - self._log.info("Split fasta file") - if self._maxJobNb == 0 or nbSeq / self._maxJobNb <= 1.0: - nbSeqPerBatch = nbSeq - else: - nbSeqPerBatch = nbSeq / self._maxJobNb + 1 - FastaUtils.dbSplit(self._fastaFileName, nbSeqPerBatch, True, verbose = self._verbosity - 2) - - self._log.info("Launch PASTEC on each batch") - queue = self._resources - cDir = os.getcwd() - if self._tmpDir != "": - tmpDir = self._tmpDir - else: - tmpDir = cDir - - #TODO: allow not to parallelize - groupid = "%s_PASTEC" % self._projectName - acronym = "PASTEC" - iDb = DbFactory.createInstance() - iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs") - iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid) - lCmdsTuples = [] - lFiles = FileUtils.getFileNamesList("%s/batches" % cDir, "batch_") - if len(lFiles) == 0: - self._logAndRaise("ERROR: directory 'batches' is empty") - classifFileName = "%s.classif" % self._projectName - count = 0 - for file in lFiles: - count += 1 - lCmds = [self.getPASTECcommand(iLauncher, file)] - lCmdStart = [] - lCmdStart.append("shutil.copy(\"%s/batches/%s\", \".\")" % (cDir, file)) - lCmdStart.append("shutil.copy(\"%s/%s\", \".\")" % (cDir, self._configFileName)) - lCmdFinish = [] - lCmdFinish.append("shutil.move(\"%s\", \"%s/%s_%i\")" % (classifFileName, cDir, classifFileName, count)) - lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish)) - iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._doClean) - - FileUtils.catFilesByPattern("%s_*" % classifFileName, classifFileName) - if self._doClean: - FileUtils.removeFilesByPattern("%s_*" % classifFileName) - shutil.rmtree("batches") - - self._log.debug("Compute stats about classification") - iSP = StatPastec(classifFileName) - iSP.run() - - if self._reverseComp: - self._log.debug("Reverse complement") - iRevComplAccording2Classif = ReverseComplementAccordingToClassif() - iRevComplAccording2Classif.setFastaFile(self._fastaFileName) - iRevComplAccording2Classif.setClassifFile(classifFileName) - iRevComplAccording2Classif.run() - newFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0] - else: - newFastaFileName = self._fastaFileName - - if self._addWickerCode: - self._log.debug("Rename headers according to Wicker's code") - iRHC = RenameHeaderClassif(classifFileName, newFastaFileName, self._projectName) - iRHC.setOutputFileName("") - iRHC.run() - - self._log.info("END TEclassifier PASTEC Edition") - -if __name__ == "__main__": - iLaunch = TEclassifierPE_parallelized() - iLaunch.setAttributesFromCmdLine() - iLaunch.run() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/__init__.py diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/blast2align.py --- a/commons/tools/blast2align.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ -#!/usr/bin/env python - -import sys -import getopt - - -def help(): - print - print "usage: blast2align.py [ options ]" - print "options:" - print " -h: this help" - print " -i: input file name (format=tabulated BLAST)" - print " -o: output file name (format=align, default=inFileName+'.align')" - print - - -def blast2align( inFile, outFile ): - inFileHandler = open( inFile, "r" ) - outFileHandler = open( outFile, "w" ) - while True: - line = inFileHandler.readline() - if line == "": - break - if line[0] != "#": - data = line.split("\t") - qryName = data[0] - sbjName = data[1] - percId = data[2] - qryStart = data[6] - qryEnd = data[7] - sbjStart = data[8] - sbjEnd = data[9] - Eval = data[10] - bitScore = data[11][:-1] - string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Eval, bitScore, percId ) - outFileHandler.write( string ) - inFileHandler.close() - outFileHandler.close() - - -def main(): - inFileName = "" - outFileName = "" - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:o:") - except getopt.GetoptError, err: - sys.stderr.write( "%s\n" % str(err) ) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - - if inFileName == "": - msg = "ERROR: missing input file name (-i)" - sys.stderr.write( "%s\n" % msg ) - help() - sys.exit(1) - - if outFileName == "": - outFileName = inFileName + ".align" - - blast2align( inFileName, outFileName ) - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/dbBestLength.py --- a/commons/tools/dbBestLength.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -#!/usr/bin/env python - -## @file -# This program extracts the n longest sequences from the input fasta file. -# usage: dbBestLength.py [ options ] -# options: -# -h: this help -# -i: name of the input fasta file -# -n: maximum number of sequences in the output file (default=20) -# -o: name of the output fasta file (default=inFileName+'.best20') -# -v: verbose (default=0/1/2) - -import os -import sys -import getopt - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -from pyRepet.seq.fastaDB import * - - -def help(): - """ - Give the list of the command-line options. - """ - print - print "usage: dbBestLength.py [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input fasta file" - print " -n: maximum number of sequences in the output file (default=20)" - print " -o: name of the output fasta file (default=inFileName+'.best20')" - print " -v: verbose (default=0/1/2)" - print - - -def main(): - """ - This program extracts the n longest sequences from the input fasta file. - """ - - inFileName = "" - nbSeq = 20 - outFileName = "" - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:n:o:v:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-n": - nbSeq = a - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing input file (-i)" - help() - sys.exit(1) - - if verbose > 0: - print "START dbBestLength.py" - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s.best%s" % ( inFileName, nbSeq ) - - log = dbBestLength( nbSeq, inFileName, outFileName, verbose ) - if log != 0: - print "ERROR: dbBestLength() returned %i" % ( log ) - sys.exit(1) - - if verbose > 0: - print "END dbBestLength.py" - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/dbConsensus.py --- a/commons/tools/dbConsensus.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,133 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - -import os -import sys -import getopt - -##@file -# usage: dbConsensus.py [ options ] -# options: -# -h: this help -# -i: name of the input file (format=aligned fasta) -# -n: minimum number of nucleotides in a column to edit a consensus (default=1) -# -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0) -# -o: name of the output file (default=inFileName+'.cons') -# -v: verbose (default=0/1/2) - -if not os.environ.has_key( "REPET_PATH" ): - print "ERROR: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -import commons.core.seq.AlignedBioseqDB - - -def help(): - """ - Give the list of the command-line options. - """ - print - print "usage:",sys.argv[0]," [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format=aligned fasta)" - print " -n: minimum number of nucleotides in a column to edit a consensus (default=1)" - print " -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0)" - print " -o: name of the output file (default=inFileName+'.cons')" - print " -H: format the header with pyramid and piles informations (SATannot)" - print " -v: verbose (default=0/1/2)" - print - - -def main(): - - inFileName = "" - minNbNt = 1 - minPropNt = 0.0 - outFileName = "" - header_SATannot = False - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:n:p:o:v:H") - except getopt.GetoptError, err: - print str(err); help(); sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-n": - minNbNt = int(a) - elif o == "-p": - minPropNt = float(a) - elif o == "-o": - outFileName = a - elif o == "-H": - header_SATannot = True - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing input file name" - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - alnDB = commons.core.seq.AlignedBioseqDB.AlignedBioseqDB( inFileName ) - - if alnDB.getSize() < minNbNt: - print "WARNING: not enough sequences (<%i)" % ( minNbNt ) - - else: - consensus = alnDB.getConsensus( minNbNt, minPropNt, verbose, header_SATannot) - if consensus != None: - consensus.upCase() - if outFileName == "": - outFileName = "%s.cons" % ( inFileName ) - outFile = open( outFileName, "w" ) - consensus.write( outFile ) - outFile.close() - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -if __name__ == "__main__": - main () diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/dbShuffle.py --- a/commons/tools/dbShuffle.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,108 +0,0 @@ -#!/usr/bin/env python - -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -import os -import sys -import getopt - -from commons.core.seq.FastaUtils import FastaUtils - - -def help(): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " INPUT: use '-i' or '-I'" - print " -i: name of the input file (fasta format)" - print " -I: name of the input directory (containing fasta files)" - print " OUTPUT: use '-o' or '-O'" - print " -o: name of the output file (use only with '-i')" - print " -O: name of the output directory (use only with '-I')" - print " output file are: prefix of input fasta file + '_shuffle.fa')" - print " -v: verbose (default=0/1/2)" - print - - -def main(): - inData = "" - outData = "" - verbose = 0 - try: - opts, args = getopt.getopt( sys.argv[1:], "hi:I:o:O:v:" ) - except getopt.GetoptError, err: - sys.stderr.write( "%s\n" % str(err) ) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inData = a - elif o == "-I": - inData = a - elif o == "-o": - outData = a - elif o == "-O": - outData = a - elif o == "-v": - verbose = int(a) - - if inData == "" or ( not os.path.isfile( inData ) \ - and not os.path.isdir( inData ) ): - msg = "ERROR: missing input file or directory (-i or -I)" - sys.stderr.write( "%s\n" % msg ) - help() - sys.exit(1) - - if outData == "": - print "ERROR: missing name of output file or directory (-o or -O)" - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - FastaUtils.dbShuffle( inData, outData, verbose ) - - if verbose > 0: - print "END %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/dbSplit.py --- a/commons/tools/dbSplit.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -#!/usr/bin/env python - - -##@file -# Split the input fasta file in several output files -# usage: dbSplit.py [ options ] -# options: -# -h: this help -# -i: name of the input file (format='fasta') -# -n: number of sequences per output file (default=1) -# -d: record the output fasta files in a directory called 'batches' -# -s: use the sequence header if '-n 1' (otherwise 'batch_00X')" -# -p: use a prefix for the output files (default='batch')" -# -v: verbose (default=0/1) - - -import sys -import getopt - -from commons.core.seq.FastaUtils import FastaUtils - - -## Give the list of the command-line options -# -def help(): - print - print "usage: dbSplit.py [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (format='fasta')" - print " -n: number of sequences per batch file (default=1)" - print " -d: record the output fasta files in a directory called 'batches'" - print " -s: use the sequence header if '-n 1' (otherwise 'batch_00X')" - print " -p: use a prefix for the output files (default='batch')" - print " -v: verbosity level (default=0/1/2)" - print - - -## Split the input fasta file in several output files -# -def main(): - inFile = "" - nbSeqPerBatch = 1 - newDir = False - useSeqHeader = False - prefix = "batch" - verbose = 0 - - try: - opts, args = getopt.getopt( sys.argv[1:], "hi:n:dsp:v:" ) - except getopt.GetoptError, err: - sys.stderr.write( "%s\n" % ( str(err) ) ) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFile = a - elif o == "-n": - nbSeqPerBatch = int(a) - elif o == "-d": - newDir = True - elif o == "-s": - useSeqHeader = True - elif o == "-p": - prefix = a - elif o == "-v": - verbose = int(a) - - if inFile == "": - msg = "ERROR: missing input file (-i)" - sys.stderr.write( "%s\n" % ( msg ) ) - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - FastaUtils.dbSplit( inFile, nbSeqPerBatch, newDir, useSeqHeader, prefix, verbose ) - - if verbose > 0: - print "END %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/filterOutMatcher.py --- a/commons/tools/filterOutMatcher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,155 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -import logging - -if not os.environ.has_key( "REPET_PATH" ): - print "ERROR: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) -import pyRepet.coord.MatchDB -import pyRepet.seq.BioseqDB - - -def help(): - """ - Give the list of the command-line options. - """ - print - print "usage: %s [ options ]" % ( sys.argv[0] ) - print "options:" - print " -h: this help" - print " -q: fasta filename of the queries" - print " -s: fasta filename of the subjects (same as queries if left blank)" - print " -m: output file from Matcher (format='tab')" - print " -o: name of the output query file (format=fasta, default=qryFileName+'.filtered')" - print " -i: identity threshold (default=0.95)" - print " -l: length threshold (default=0.98)" - print " -L: name of a 'log' file (usually from 'rmvRedundancy.py')" - print " -v: verbose (default=0/1)" - print - - -def writeOutQuery( qryDB, outFileName, lQryToKeep ): - """ - Write in a fasta file the queries than haven't been filtered (i.e. they are not included in any subject). - """ - outFile = open( outFileName, "w" ) - nbRmvSeq = 0 - for bs in qryDB.db: - if bs.header in lQryToKeep: - bs.write( outFile ) - else: - nbRmvSeq += 1 - outFile.close() - if verbose > 0: - print "%i removed queries out of %i" % ( nbRmvSeq, qryDB.getSize() ); sys.stdout.flush() - - -def main(): - """ - This program filters the ouput from Matcher by removing queries 'included' in subjects. - """ - qryFileName = "" - sbjFileName = "" - tabFileName = "" - outFileName = "" - thresIdentity = 0.95 # remove the seq if it is identical to 95% of another seq - thresLength = 0.98 # and if its length is 98% of that seq - logFileName = "" - global verbose - verbose = 0 - try: - opts, args = getopt.getopt(sys.argv[1:],"h:q:s:m:o:i:l:L:v:") - except getopt.GetoptError: - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-q": - qryFileName = a - elif o == "-s": - sbjFileName = a - elif o == "-m": - tabFileName = a - elif o == "-o": - outFileName = a - elif o == "-i": - thresIdentity = float(a) - elif o == "-l": - thresLength = float(a) - elif o == "-L": - logFileName = a - elif o == "-v": - verbose = int(a) - if qryFileName == "" or tabFileName == "": - print "ERROR: missing compulsory options" - help() - sys.exit(1) - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - # prepare the 'log' file - handler = logging.FileHandler( logFileName ) - formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" ) - handler.setFormatter( formatter ) - logging.getLogger('').addHandler( handler ) - logging.getLogger('').setLevel( logging.DEBUG ) - logging.info( "use '%s' on '%s'" % ( sys.argv[0].split("/")[-1], tabFileName ) ) - - if sbjFileName == "": - sbjFileName = qryFileName - if outFileName == "": - outFileName = "%s.filtered" % ( qryFileName ) - - # load the input fasta file corresponding to the queries - qryDB = pyRepet.seq.BioseqDB.BioseqDB( qryFileName ) - if sbjFileName != qryFileName: - string = "nb of input sequences (as query only): %i" % ( qryDB.getSize() ); sys.stdout.flush() - logging.info( string ) - if verbose > 0: print string - else: - string = "nb of input sequences (as query and subject): %i" % ( qryDB.getSize() ); sys.stdout.flush() - logging.info( string ) - if verbose > 0: print string - - # load the input 'tab' file - matchDB = pyRepet.coord.MatchDB.MatchDB() - tabFile = open( tabFileName, "r" ) - matchDB.read( tabFile, thresIdentity, thresLength, verbose ) - tabFile.close() - longString = "" - string = "nb of matches (id>=%.2f,qlgth>=%.2f): %i" % ( thresIdentity, thresLength, matchDB.getNbMatchesWithThres( thresIdentity, thresLength ) ) - longString += "\n%s" % ( string ) - if verbose > 0: print string - string = "nb of distinct queries having matches (id>=%.2f,qlgth>=%.2f): %i" % ( thresIdentity, thresLength, matchDB.getNbDistinctQryWithThres( thresIdentity, thresLength ) ) - longString += "\n%s" % ( string ) - if verbose > 0: print string - logging.info( longString ) - sys.stdout.flush() - - lQryToKeep = matchDB.filterDiffQrySbj( qryDB, thresIdentity, thresLength, verbose - 1 ) - - # here, possibility to save the information about by which match a specific query has been removed - - string = "%i queries to be kept" % ( len(lQryToKeep) ); sys.stdout.flush() - logging.info( string ) - if verbose > 0: print string - - # write the output fasta file without the included queries - writeOutQuery( qryDB, outFileName, lQryToKeep ) - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main () diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/getCumulLengthFromTEannot.py --- a/commons/tools/getCumulLengthFromTEannot.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,201 +0,0 @@ -#!/usr/bin/env python - -##@file -# usage: getCumulLengthFromTEannot.py [ options ] -# options: -# -h: this help -# -i: table with the annotations (format=path) -# -r: name of a TE reference sequence (if empty, all subjects are considered) -# -g: length of the genome (in bp) -# -C: configuration file -# -c: clean -# -v: verbosity level (default=0/1) - - -import sys -import os -import getopt -from commons.core.sql.DbMySql import DbMySql -from commons.core.sql.TablePathAdaptator import TablePathAdaptator - - -class getCumulLengthFromTEannot( object ): - """ - Give the cumulative length of TE annotations (subjects mapped on queries). - """ - - def __init__( self ): - """ - Constructor. - """ - self._tableName = "" - self._TErefseq = "" - self._genomeLength = 0 - self._configFileName = "" - self._clean = False - self._verbose = 0 - self._db = None - self._tpA = None - - - def help( self ): - """ - Display the help on stdout. - """ - print - print "usage: getCumulLengthFromTEannot.py [ options ]" - print "options:" - print " -h: this help" - print " -i: table with the annotations (format=path)" - print " -r: name of a TE reference sequence (if empty, all subjects are considered)" - print " -g: length of the genome (in bp)" - print " -C: configuration file" - print " -c: clean" - print " -v: verbosity level (default=0/1)" - print - - - def setAttributesFromCmdLine( self ): - """ - Set the attributes from the command-line. - """ - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:r:g:C:cv:") - except getopt.GetoptError, err: - print str(err); self.help(); sys.exit(1) - for o,a in opts: - if o == "-h": - self.help(); sys.exit(0) - elif o == "-i": - self.setInputTable( a ) - elif o == "-r": - self.setTErefseq( a ) - elif o == "-g": - self.setGenomeLength( a ) - elif o == "-C": - self.setConfigFileName( a ) - elif o == "-c": - self.setClean() - elif o == "-v": - self.setVerbosityLevel( a ) - - - def setInputTable( self, inTable ): - self._tableName = inTable - - def setTErefseq( self, a ): - self._TErefseq = a - - def setGenomeLength( self, genomeLength ): - self._genomeLength = int(genomeLength) - - def setConfigFileName( self, configFileName ): - self._configFileName = configFileName - - def setClean( self ): - self._clean = True - - def setVerbosityLevel( self, verbose ): - self._verbose = int(verbose) - - def checkAttributes( self ): - """ - Check the attributes are valid before running the algorithm. - """ - if self._tableName == "": - print "ERROR: missing input table"; self.help(); sys.exit(1) - - - def setAdaptatorToTable( self ): - self._db = DbMySql( cfgFileName=self._configFileName ) - self._tpA = TablePathAdaptator( self._db, self._tableName ) - - - def getAllSubjectsAsMapOfQueries( self ): - mapFileName = "%s.map" % self._tableName - mapFile = open( mapFileName, "w" ) - if self._TErefseq != "": - lPathnums = self._tpA.getIdListFromSubject( self._TErefseq ) - else: - lPathnums = self._tpA.getIdList() - if self._verbose > 0: - print "nb of paths: %i" % ( len(lPathnums) ) - for pathnum in lPathnums: - lPaths = self._tpA.getPathListFromId( pathnum ) - for path in lPaths: - map = path.getSubjectAsMapOfQuery() - map.write( mapFile ) - mapFile.close() - return mapFileName - - - def mergeRanges( self, mapFileName ): - mergeFileName = "%s.merge" % mapFileName - prg = os.environ["REPET_PATH"] + "/bin/mapOp" - cmd = prg - cmd += " -q %s" % ( mapFileName ) - cmd += " -m" - cmd += " 2>&1 > /dev/null" - log = os.system( cmd ) - if log != 0: - print "*** Error: %s returned %i" % ( prg, log ) - sys.exit(1) - if self._clean: - os.remove( mapFileName ) - return mergeFileName - - - def getCumulLength( self, mergeFileName ): - mergeFile = open( mergeFileName, "r" ) - total = 0 - while True: - line = mergeFile.readline() - if line == "": - break - tok = line.split("\t") - total += abs( int(tok[3]) - int(tok[2]) ) + 1 - mergeFile.close() - if self._clean: - os.remove( mergeFileName ) - return total - - - def start( self ): - """ - Useful commands before running the program. - """ - self.checkAttributes() - if self._verbose > 0: - print "START %s" % ( type(self).__name__ ); sys.stdout.flush() - self.setAdaptatorToTable() - - - def end( self, mapFileName, mergeFileName ): - """ - Useful commands before ending the program. - """ - self._db.close() - if self._verbose > 0: - print "END %s" % ( type(self).__name__ ); sys.stdout.flush() - - - def run( self ): - """ - Run the program. - """ - self.start() - - mapFileName = self.getAllSubjectsAsMapOfQueries() - mergeFileName = self.mergeRanges( mapFileName ) - total = self.getCumulLength( mergeFileName ) - print "cumulative length: %i bp" % total - if self._genomeLength > 0: - print "TE content: %.2f%%" % ( 100 * total / float(self._genomeLength) ) - - self.end( mapFileName, mergeFileName ) - - -if __name__ == "__main__": - i = getCumulLengthFromTEannot() - i.setAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/pathnum2id.py --- a/commons/tools/pathnum2id.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt - -def setup_env(): - if "REPET_PATH" in os.environ.keys(): - sys.path.append( os.environ["REPET_PATH"] ) - else: - print "*** Error: no environment variable REPET_PATH ***" - sys.exit(1) -setup_env() - -from commons.core.parsing.PathNum2Id import PathNum2Id - -#----------------------------------------------------------------------------- - -def help(): - - print "" - print "usage:",sys.argv[0]," [ options ]" - print "option:" - print " -h: this help" - print " -i: input file name (path format)" - print " -o: output file name (path format, default=inFileName+'.path')" - print "" - -#----------------------------------------------------------------------------- - -def main(): - - inFileName = "" - outFileName = "" - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:o:") - except getopt.GetoptError: - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-o": - outFileName = a - - if inFileName == "": - print "*** Error: missing input file name" - help() - sys.exit(1) - - if outFileName == "": - outFileName = inFileName + ".path" - - pathNum2Id = PathNum2Id() - pathNum2Id.setInFileName( inFileName ) - pathNum2Id.setOutFileName( outFileName ) - pathNum2Id.run() - - return 0 - -#----------------------------------------------------------------------------- - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/refalign2fasta.py --- a/commons/tools/refalign2fasta.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,408 +0,0 @@ -#!/usr/bin/env python - -##@file -# Convert the output from Refalign (MSA program) into the 'fasta' format. -# Usually used before subsequent analysis such as the estimation of deletion rate. -# -# usage: refalign2fasta.py [ options ] -# options: -# -h: this help -# -i: name of the input file (output from refalign) -# -r: name of the reference sequence (discard if not provided) -# -g: for the gaps, keep only deletions ('d'), only insertions ('i') or both (default='id') -# -o: name of the output file (default=inFileName'.fa_aln',format='fasta') - -import os -import sys -import getopt -import exceptions - -if not os.environ.has_key( "REPET_PATH" ): - print "ERROR: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -import pyRepet.seq.Bioseq - - -def help(): - """ - Give the list of the command-line options. - """ - print - print "usage:",sys.argv[0]," [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the input file (output from refalign)" - print " -r: name of the reference sequence (discard if not provided)" - print " -g: for the gaps, keep only deletions ('d'), only insertions ('i') or both (default='id')" - print " -o: name of the output file (default=inFileName'.fa_aln',format='fasta')" - print - - -def getAlignments( inFileName ): - """ - Retrieve the alignments from the input file. - - @param inFileName: name of the input file - @type: string - - @return: list of alignments ( refseq, seq, header of seq ) - @rtype: list of 3d-tuples - """ - - lAlign = [] - - inFile = open( inFileName, "r" ) - line = inFile.readline() - while True: - if line == "": - break - refseq, seq, label = line[:-1].split("\t")[:3] - lAlign.append( ( refseq, seq, label ) ) - line = inFile.readline() - inFile.close() - - return lAlign - - -def getGaps( seq ): - """ - Get the gaps on a sequence, start coordinate and length. The start - coordinate of a gap is the # of the nucleotide after which it starts. - - @param seq: sequence to analyse - @type seq: string - - @return: list of gaps ( start coordinate, length ) - @rtype: list of 2d-tuples - """ - - prev = "N" - lGapsOnSeq = [] - i = 0 - lengthGap = 0 - for c in seq: - if c == "-" and prev != "-": - startGap = i - if c != "-" and prev == "-": - lGapsOnSeq.append( ( startGap, lengthGap ) ) - lengthGap = 0 - if c != "-": - i += 1 - else: - lengthGap += 1 - prev = c - - # case with a gap at the end of the sequence - if seq[ len(seq) - 1 ] == "-": - lGapsOnSeq.append( ( startGap, lengthGap ) ) - - return lGapsOnSeq - - -def getGapsOnRefSeq( lAlign ): - """ - Retrieve the gaps on the ref seq in all the alignments. - - @param lAlign: list of alignments ( refseq, seq, header of seq ) - @type lAlign: list of 3d-tuples - - @return: list of gaps per alignment - @rtype: list of lists of 2d-tuples - """ - - lGapsOnRef = [] - - for align in lAlign: - refseq = align[0] - lGapsOnRef.append( getGaps( refseq ) ) - - return lGapsOnRef - - -def insertGap( seq, startGap, lengthGap ): - """ - Get a new seq by inserting a gap in the give seq. - - @param seq: sequence - @type seq: string - - @param startGap: - @type: startGap: integer - - @param lengthGap: length of the gap - @type lengthGap: integer - - @return: new seq made from the give seq by inserting the gap - @rtype: string - """ - - new_seq = seq[:startGap] + (lengthGap*'-') + seq[startGap:] - return new_seq - - -def insertListGaps( inSeq, lGaps ): - """ - Insert all the gaps from the list into the sequence. - - @param inSeq: sequence - @type inSeq: string - - @param lGaps: list of gaps ( start coordinate, length ) - @type: list of 2d-tuples - - @return: sequence with the gaps - @rtype: string - """ - - # insert gaps from the right to the left - lGaps.sort() - lGaps.reverse() - - prevPos = 0 - outSeq = inSeq - - for startGap, lengthGap in lGaps: - if startGap != prevPos: - outSeq = insertGap( outSeq, startGap, lengthGap ) - prevPos = startGap - - return outSeq - - -def insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName ): - """ - Get the ref seq with all its gaps inserted. - - @param lAlign: list of alignments ( refseq, seq, header of seq ) - @type lAlign: list of 3d-tuples - - @param lGapsOnRefSeqPerAlign: list of list of gaps on the seq ref per alignment - @type lGapsOnRefSeqPerAlign: list of list of 2d-tuples - - @param refseqName: name of the reference sequence - @type refseqName: string - - @return: ref seq with all its gaps inserted - @rtype: string - """ - - # retrieve the initial ref seq, ie without any gap - initRefSeq = lAlign[0][0].replace("-","") - - # convert the list of lists of gaps into a list of gaps - flat_lGaps = [] - for gaps in lGapsOnRefSeqPerAlign: - flat_lGaps.extend( gaps ) - - # insert the gaps in the sequence of ref seq - finalRefSeq = insertListGaps( initRefSeq, flat_lGaps ) - - Align_refseq = ( refseqName, finalRefSeq ) - - return Align_refseq - - -def insertgap_seq( lAlign, lGapsOnRefSeqPerAlign ): - """ - Insert in the sequences all the gaps found on the ref seq. - - @param lAlign: list of alignments ( refseq, seq, header of seq ) - @type lAlign: list of 3d-tuples - - @param lGapsOnRefSeqPerAlign: list of list of gaps on the seq ref per alignment - @type lGapsOnRefSeqPerAlign: list of list of 2d-tuples - - @return: list of lists (sequence with gaps, header) - @rtype: list of 2d-tuples - - insert dans les seq les gaps donnes par la liste de liste de gap - retourne une liste des nouvelles seq apres insertion des gaps - """ - - # for each gap, add the nb of the alignment in which it has been found - newlistgap_seq =[] - alignID = 0 - for lGaps in lGapsOnRefSeqPerAlign: - for startGap,lengthGap in lGaps: - newlistgap_seq.append( ( startGap, lengthGap, alignID ) ) - alignID += 1 - newlistgap_seq.sort() - - Align_seq = [] - - # for each alignment - for j in xrange(0,len(lAlign)): - - #create a new list = list of gaps to be inserted in a given seq - newlist = [] - offset = 0 - longmax = 0 - longself = 0 - posprec = 0 - for startGap, lengthGap, alignID in newlistgap_seq: - # when 2 gaps have the same start, we keep the longer one - if startGap != posprec: - if longmax > longself: - newlist.append( (posprec + offset, longmax - longself) ) - offset += longself - longmax=0 - longself=0 - #lorsque le numero de la seq du tuple a la meme valeur que j - #on stocke la valeur de lengthGap - if j == alignID: - longself = lengthGap - #sinon on prend comme valeur de longmax la valeur maximale de longmax et lengthGap - else: - longmax = max(longmax, lengthGap) - posprec = startGap - if longmax > longself: - newlist.append((posprec + offset, longmax - longself)) - - newSeq = insertListGaps( (lAlign[j][1]), newlist ) - header = lAlign[j][2] - Align_seq.append( ( header, newSeq ) ) - - return Align_seq - - -def getSeqWithDeletions( lAlign ): - """ - Get the sequences by putting gaps only when they correspond to a deletion compare to ref seq. - Used for instance when we want to estimate the deletion rate. - - @param lAlign: list of alignments ( refseq, seq, header of seq ) - @type lAlign: list of 3d-tuples - - @return: list of lists ( header, sequence with gaps ) - @rtype: list of 2d-tuples - """ - - Align_seq = [] - - for align in lAlign: - refseq = align[0] - seq = align[1] - header = align[2] - newSeq = "" - for i in xrange(0,len(refseq)): - if refseq[i] != "-": - newSeq += seq[i] - Align_seq.append( ( header, newSeq ) ) - - return Align_seq - - -def saveMSA( outFileName, Align_seq, Align_seqref=None ): - """ - Save the results as a multiple sequence alignment (MSA) in the 'fasta' format. - - @param outFileName: name of the output file - @type outFileName: string - - @param Align_seqref: sequence of ref seq - @type Align_seqref: string - """ - - outFile = open( outFileName, "w" ) - bs = pyRepet.seq.Bioseq.Bioseq() - - # if provided, save the ref seq - if Align_seqref != None: - bs.header = Align_seqref[0] - bs.sequence = Align_seqref[1] - bs.write( outFile ) - - # save the other sequences - for i in Align_seq: - bs.header = i[0] - bs.sequence = i[1] - bs.write( outFile ) - - outFile.close() - - -def saveOnlyWithDeletions( lAlign, refseqName, outFileName ): - Align_seq = getSeqWithDeletions( lAlign ) - if refseqName != "": - Align_seqref = ( refseqName, lAlign[0][0].replace("-","") ) - saveMSA( outFileName, Align_seq, Align_seqref ) - else: - saveMSA( outFileName, Align_seq ) - - -def main(): - - inFileName = "" - refseqName = "" - keepGap = "id" - outFileName = "" - global verbose - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:r:g:o:v:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inFileName = a - elif o == "-r": - refseqName = a - elif o == "-g": - keepGap = a - elif o == "-o": - outFileName = a - elif o == "-v": - verbose = int(a) - - if inFileName == "": - print "ERROR: missing input file name" - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - lAlign = getAlignments( inFileName ) - if verbose > 0: - print "nb of alignments: %i" % ( len(lAlign) ) - sys.stdout.flush() - - if outFileName == "": - outFileName = "%s.fa_aln" % ( inFileName ) - if verbose > 0: - print "output file: '%s'" % ( outFileName ) - - if keepGap == "id": - lGapsOnRefSeqPerAlign = getGapsOnRefSeq( lAlign ) - Align_seq = insertgap_seq( lAlign, lGapsOnRefSeqPerAlign ) - if refseqName != "": - Align_seqref = insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName ) - saveMSA( outFileName, Align_seq, Align_seqref ) - else: - saveMSA( outFileName, Align_seq ) - - elif keepGap == "d": - saveOnlyWithDeletions( lAlign, refseqName, outFileName ) - - elif keepGap == "i": - print "ERROR: '-g i' not yet available" - sys.exit(1) - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__" : - main () diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/removeDescriptionInFastaHeaderProgramLauncher.py --- a/commons/tools/removeDescriptionInFastaHeaderProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -#!/usr/bin/env python - -import re -from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher - -class removeDescriptionInFastaHeaderProgramLauncher(AbstractProgramLauncher): - - def __init__( self ): - AbstractProgramLauncher.__init__( self ) - self._formatInFile = "fasta" - - def run( self ): - self.checkInput() - fastaHandler = open(self.getInputFile(), "r") - lines = fastaHandler.readlines() - fastaHandler.close() - newFastaName = ".".join([self.getInputFile().split(".")[0], "preprocessed", "fasta"]) - - self._writePreprocessedFastaFile(lines, newFastaName) - - def _writePreprocessedFastaFile(self, lines, newFastaName): - newFastaHandler = open(newFastaName, "w") - for line in lines: - if re.match(">", line): - newLine = line.split(" ",1)[0] + "\n" - newFastaHandler.write(newLine) - else: - newFastaHandler.write(line) - newFastaHandler.close() - - - - -if __name__ == "__main__": - i = removeDescriptionInFastaHeaderProgramLauncher() - i.checkAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py --- a/commons/tools/replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -#!/usr/bin/env python - -import re -from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher - -class replaceGreaterThanSymbolInFastaHeaderProgramLauncher(AbstractProgramLauncher): - - def __init__( self ): - AbstractProgramLauncher.__init__( self ) - self._formatInFile = "fasta" - - def run( self ): - self.checkInput() - fastaHandler = open(self.getInputFile(), "r") - lines = fastaHandler.readlines() - fastaHandler.close() - newFastaName = ".".join([self.getInputFile().split(".")[0], "preprocessed", "fasta"]) - - self._writePreprocessedFastaFile(lines, newFastaName) - - def _writePreprocessedFastaFile(self, lines, newFastaName): - newFastaHandler = open(newFastaName, "w") - for line in lines: - if re.match(">", line): - newLine = re.sub("-->|->", " to ", line) - newFastaHandler.write(newLine) - else: - newFastaHandler.write(line) - newFastaHandler.close() - - - - -if __name__ == "__main__": - i = replaceGreaterThanSymbolInFastaHeaderProgramLauncher() - i.checkAttributesFromCmdLine() - i.run() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/setnum2id.py --- a/commons/tools/setnum2id.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -import exceptions - -#----------------------------------------------------------------------------- - -def help(): - - print "\nusage:",sys.argv[0]," [ options ]" - print "option:" - print " -h: this help" - print " -i: input set file" - print "output on stdout\n" - -#----------------------------------------------------------------------------- - -def main(): - - inFileName = "" - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:") - except getopt.GetoptError: - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - if o == "-i": - inFileName = a - - if inFileName == "": - print "*** Error: missing input file name" - help() - sys.exit(1) - - inFile = open( inFileName, "r" ) - line = inFile.readline() - - dID2count = {} - count = 1 - - while 1: - - if line == "": - break - - line = line.split() - - path = line[0] - sbjName = line[1] - qryName = line[2] - qryStart = line[3] - qryEnd = line[4] - - key_id = path + "-" + qryName + "-" + sbjName - if key_id not in dID2count.keys(): - newPath = count - count += 1 - dID2count[ key_id ] = newPath - else: - newPath = dID2count[ key_id ] - - data = str(newPath) + "\t" + sbjName + "\t" + qryName + "\t" - data += qryStart + "\t" + qryEnd - - print data - sys.stdout.flush() - - line = inFile.readline() - - inFile.close() - - return 0 - -#----------------------------------------------------------------------------- - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/srptBlasterMatcher.py --- a/commons/tools/srptBlasterMatcher.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,448 +0,0 @@ -#!/usr/bin/env python - -""" -This program takes a query directory as input, -then launches Blaster and/or Matcher on each file in it, -finally results are optionally gathered in a single file. -""" - -import os -import sys -import getopt -import logging -import glob -import ConfigParser - -from pyRepet.launcher.programLauncher import programLauncher -from pyRepet.launcher import Launcher -from pyRepet.sql.RepetJobMySQL import RepetJob -from commons.core.coord.Align import Align - - -def help(): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " -g: name of the group identifier (same for all the jobs)" - print " -q: name of the query directory" - print " -S: suffix in the query directory (default='*.fa' for Blaster, '*.align' for Matcher)" - print " -s: absolute path to the subject databank" - print " -Q: resources needed on the cluster)" - print " -d: absolute path to the temporary directory" - print " -m: mix of Blaster and/or Matcher" - print " 1: launch Blaster only" - print " 2: launch Matcher only (on '*.align' query files)" - print " 3: launch Blaster+Matcher in the same job" - print " -B: parameters for Blaster (e.g. \"-a -n tblastx\")" - print " -M: parameters for Matcher (e.g. \"-j\")" - print " -Z: collect all the results into a single file" - print " align (after Blaster)" - print " path/tab (after Matcher)" - print " -C: configuration file from TEdenovo or TEannot pipeline" - print " -t: name of the table recording the jobs (default=jobs)" - print " -p: absolute path to project directory (if jobs management via files)" - print " -c: clean (remove job launch files and job stdout)" - print " -v: verbose (default=0/1/2)" - print - - -def filterRedundantMatches( inFile, outFile ): - """ - When a pairwise alignment is launched ~ all-by-all (ie one batch against all chunks), - one filters the redundant matches. For instance we keep 'chunk3-1-100-chunk7-11-110-...' - and we discards 'chunk7-11-110-chunk3-1-100-...'. - Also we keep 'chunk5-1-100-chunk5-11-110-...' and we discards - 'chunk5-11-110-chunk5-1-100-...'. - For this of course the results need to be sorted by query, on plus strand, - and in ascending coordinates (always the case with Blaster). - """ - inFileHandler = open( inFile, "r" ) - outFileHandler = open( outFile, "w" ) - iAlign = Align() - countMatches = 0 - tick = 100000 - while True: - line = inFileHandler.readline() - if line == "": - break - countMatches += 1 - iAlign.setFromString( line ) - if "chunk" not in iAlign.range_query.seqname \ - or "chunk" not in iAlign.range_subject.seqname: - print "ERROR: 'chunk' not in seqname" - sys.exit(1) - if int(iAlign.range_query.seqname.split("chunk")[1]) < int(iAlign.range_subject.seqname.split("chunk")[1]): - iAlign.write( outFileHandler ) - elif int(iAlign.range_query.seqname.split("chunk")[1]) == int(iAlign.range_subject.seqname.split("chunk")[1]): - if iAlign.range_query.getMin() < iAlign.range_subject.getMin(): - iAlign.write( outFileHandler ) - if countMatches % tick == 0: # need to free buffer frequently as file can be big - outFileHandler.flush() - os.fsync( outFileHandler.fileno() ) - inFileHandler.close() - outFileHandler.close() - - -def runCollect( groupid, collect, allByAll ): - """ - Gather the results of each job in a single job and adapt path ID if necessary. - """ - if verbose > 0: - print "concatenate the results of each job"; sys.stdout.flush() - - # retrieve the list of the files - lFiles = glob.glob( "*.%s" % ( collect ) ) - lFiles.sort() - - # concatenate all the individual files - if os.path.exists( "%s.%s_tmp" % ( groupid, collect ) ): - os.remove( "%s.%s_tmp" % ( groupid, collect ) ) - for resFile in lFiles: - prg = "cat" - cmd = prg - cmd += " %s >> %s.%s_tmp" % ( resFile, groupid, collect ) - pL.launch( prg, cmd ) - if clean == True: - prg = "rm" - cmd = prg - cmd += " -f %s" % ( resFile ) - pL.launch( prg, cmd ) - - if os.path.exists( "%s.%s" % ( groupid, collect ) ): - os.remove( "%s.%s" % ( groupid, collect ) ) - - if collect == "align": - if not allByAll: - os.system( "mv %s.%s_tmp %s.%s" % ( groupid, collect, groupid, collect ) ) - else: - filterRedundantMatches( "%s.%s_tmp" % ( groupid, collect ), - "%s.%s" % ( groupid, collect ) ) - - # adapt the path IDs if necessary - elif collect == "path": - prg = os.environ["REPET_PATH"] + "/bin/" - if os.path.exists( prg + "pathnum2id" ): - prg += "pathnum2id" - cmd = prg - cmd += " -i %s.path_tmp" % ( groupid ) - cmd += " -o %s.path" % ( groupid ) - cmd += " -v %i" % ( verbose - 1 ) - pL.launch( prg, cmd ) - else: - prg += "pathnum2id.py" - cmd = prg - cmd += " -i %s.path_tmp" % ( groupid ) - cmd += " -o %s.path" % ( groupid ) - pL.launch( prg, cmd ) - - elif collect == "tab": - prg = os.environ["REPET_PATH"] + "/bin/" - if os.path.exists( prg + "tabnum2id" ): - prg += "tabnum2id" - cmd = prg - cmd += " -i %s.tab_tmp" % ( groupid ) - cmd += " -o %s.tab" % ( groupid ) - cmd += " -v %i" % ( verbose - 1 ) - pL.launch( prg, cmd ) - else: - prg += "tabnum2id.py" - cmd = prg - cmd += " -i %s.tab_tmp" % ( groupid ) - cmd += " -o %s.tab" % ( groupid ) - pL.launch( prg, cmd ) - - if clean == True: - os.remove( "%s.%s_tmp" % ( groupid, collect ) ) - - -def main(): - """ - This program takes a query directory as input, - then launches Blaster and/or Matcher on each file in it, - finally results are optionally gathered in a single file. - """ - - groupid = "" - queryDir = "" - patternSuffix = "" - subjectBank = "" - queue = "" - tmpDir = "" - mix = "" - paramBlaster = "" - paramMatcher = "" - collect = "" - configFileName = "" - jobTable = "jobs" - projectDir = "" - global clean - clean = False - global verbose - verbose = 0 - allByAll = False - - try: - opts, args = getopt.getopt(sys.argv[1:],"hg:q:S:s:Q:d:m:B:M:Z:C:t:p:cv:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-g": - groupid = a - elif o == "-q": - queryDir = a - if queryDir[-1] == "/": - queryDir = queryDir[:-1] - elif o == "-S": - patternSuffix = a - elif o == "-s": - subjectBank = a - elif o == "-Q": - queue = a - elif o == "-d": - tmpDir = a - if tmpDir[-1] == "/": - tmpDir = tmpDir[:-1] - elif o == "-m": - mix = a - elif o == "-B": - paramBlaster = a - elif o == "-M": - paramMatcher = a - elif o == "-C": - configFileName = a - elif o == "-Z": - collect = a - elif o == "-t": - jobTable = a - elif o == "-p": - projectDir = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - - if groupid == "": - print "ERROR: missing group identifier (-g)" - help() - sys.exit(1) - - if queryDir == "": - print "ERROR: missing query directory (-q)" - help() - sys.exit(1) - - if mix in [ "1", "3" ] and subjectBank == "": - print "ERROR: missing subject bank for Blaster" - sys.exit(1) - - if os.environ["REPET_JOBS"] == "files" and projectDir == "": - print "ERROR: missing compulsory options for jobs management via files" - help() - sys.exit(1) - - if not os.path.exists( queryDir ): - print "ERROR: can't find query directory '%s'" % ( queryDir ) - sys.exit(1) - - if verbose > 0: - print "START %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - - logFileName = "%s_pid%s.log" % ( groupid, os.getpid() ) - handler = logging.FileHandler( logFileName ) - formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" ) - handler.setFormatter( formatter ) - logging.getLogger('').addHandler( handler ) - logging.getLogger('').setLevel( logging.DEBUG ) - logging.info( "started" ) - - - if configFileName != "": - if not os.path.exists( configFileName ): - print "ERROR: configuration file '%s' doesn't exist" % ( configFileName ) - sys.exit(1) - config = ConfigParser.ConfigParser() - config.readfp( open(configFileName) ) - host = config.get("repet_env","repet_host") - user = config.get("repet_env","repet_user") - passwd = config.get("repet_env","repet_pw") - dbname = config.get("repet_env","repet_db") - else: - host = os.environ["REPET_HOST"] - user = os.environ["REPET_USER"] - passwd = os.environ["REPET_PW"] - dbname = os.environ["REPET_DB"] - - if os.environ["REPET_JOBS"] == "files": - jobdb = RepetJob( dbname = projectDir + "/" + os.environ["REPET_DB"] ) - elif os.environ["REPET_JOBS"] == "MySQL": - jobdb = RepetJob( user, host, passwd, dbname ) - else: - print "ERROR: REPET_JOBS is '%s'" % ( os.environ["REPET_JOBS"] ) - sys.exit(1) - - - currentDir = os.getcwd() - if tmpDir == "": - tmpDir = currentDir - - global pL - pL = programLauncher() - - if "-a" in paramBlaster: - allByAll = True - - - # if Blaster will be launched, prepare the subject data if necessary - if mix != "2" and not os.path.exists( "%s_cut" % ( subjectBank ) ): - if verbose > 0: - print "prepare subject bank '%s'..." % ( subjectBank.split("/")[-1] ) - sys.stdout.flush() - prg = "blaster" - cmd = prg - cmd += " -q %s" % ( subjectBank ) - cmd += " %s" % ( paramBlaster ) - cmd += " -P" - pL.launch( prg, cmd ) - - - # launch Blaster only (on '*.fa' in queryDir) - if mix == "1": - launcher = Launcher.BlasterLauncher( jobdb, queryDir, subjectBank, paramBlaster, currentDir, tmpDir, jobTable, queue, groupid, "Blaster" ) - if patternSuffix == "": - patternSuffix = "*.fa" - launcher.run( patternSuffix, verbose ) - if clean == True: - launcher.clean() - - # launch Matcher only (on '*.align' in queryDir; don't use '-q' or '-s', only '-m') - elif mix == "2": - launcher = Launcher.MatcherLauncher( jobdb, queryDir, subjectBank, paramMatcher, currentDir, tmpDir, jobTable, queue, groupid, "Matcher" ) - if patternSuffix == "": - patternSuffix = "*.align" - launcher.run( patternSuffix, verbose ) - if clean == True: - launcher.clean() - - # launch Blaster+Matcher (on '*.fa' in queryDir) - elif mix == "3": - launcher = Launcher.Launcher( jobdb, queryDir, subjectBank, paramBlaster, currentDir, tmpDir, jobTable, queue, groupid, "BlasterMatcher" ) - launcher.beginRun() - if patternSuffix == "": - patternSuffix = "*.fa" - lFaFiles = glob.glob( queryDir + "/" + patternSuffix ) - if len(lFaFiles) == 0: - print "ERROR: query directory '%s' is empty of suffix '%s'" % ( queryDir, patternSuffix ) - sys.exit(1) - count = 0 - for inFaName in lFaFiles: - count += 1 - launcher.acronyme = "BlasterMatcher_%i" % ( count ) - launcher.job.jobname = launcher.acronyme - prefix = os.path.basename( inFaName ) - cmd_start = "" - cmd_start += "if not os.path.exists( \"" + prefix + "\" ):\n" - cmd_start += "\tos.system( \"cp " + inFaName + " .\" )\n" - launchB = "" - launchB += "blaster" - launchB += " -q %s" % ( prefix ) - launchB += " -s %s" % ( subjectBank ) - launchB += " -B %s" % ( prefix ) - if paramBlaster != "": - launchB += " %s" % ( paramBlaster ) - cleanB = "" - cleanB += "if not os.path.exists( \"%s/%s.param\" ):\n" % ( currentDir, prefix ) - cleanB += "\tos.system( \"mv %s.param %s\" )\n" % ( prefix, currentDir ) - cleanB += "if os.path.exists( \"" + prefix + ".Nstretch.map\" ):\n" - cleanB += "\tos.remove( \"" + prefix + ".Nstretch.map\" )\n" - cleanB += "if os.path.exists( \"" + prefix + "_cut\" ):\n" - cleanB += "\tos.system( \"rm -f " + prefix + "_cut*\" )\n" - cleanB += "if os.path.exists( \"" + prefix + ".raw\" ):\n" - cleanB += "\tos.remove( \"" + prefix + ".raw\" )\n" - cleanB += "if os.path.exists( \"" + prefix + ".seq_treated\" ):\n" - cleanB += "\tos.remove( \"" + prefix + ".seq_treated\" )\n" - launchM = "" - launchM += os.environ["REPET_PATH"] + "/bin/matcher" - launchM += " -m %s.align" % ( prefix ) - launchM += " -q %s" % ( prefix ) - launchM += " -s %s" % ( subjectBank ) - if paramMatcher != "": - launchM += " %s" % ( paramMatcher ) - cleanM = "" - s = "" - if "-a" in paramMatcher: - s = "match" - else: - s = "clean_match" - if collect == "path": - cleanM += "if not os.path.exists( \"%s/%s.align.%s.path\" ):\n" % ( currentDir, prefix, s ) - cleanM += "\tos.system( \"mv %s.align.%s.path %s\" )\n" % ( prefix, s, currentDir ) - cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".tab\" ):\n" - cleanM += "\tos.remove( \"" + prefix + ".align."+s+".tab\" )\n" - elif collect == "tab": - cleanM += "if not os.path.exists( \"%s/%s.align.%s.tab\" ):\n" % ( currentDir, prefix, s ) - cleanM += "\tos.system( \"mv %s.align.%s.tab %s\" )\n" % ( prefix, s, currentDir ) - cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".path\" ):\n" - cleanM += "\tos.remove( \"" + prefix + ".align."+s+".path\" )\n" - cleanM += "if not os.path.exists( \"%s/%s.align.%s.param\" ):\n" % ( currentDir, prefix, s ) - cleanM += "\tos.system( \"mv %s.align.%s.param %s\" )\n" % ( prefix, s, currentDir ) - if tmpDir != currentDir: - cleanM += "if os.path.exists( \"%s\" ):\n" % ( prefix ) - cleanM += "\tos.remove( \"%s\" )\n" % ( prefix ) - if clean == True: - cleanM += "if os.path.exists( \"" + prefix + ".align\" ):\n" - cleanM += "\tos.remove( \"" + prefix + ".align\" )\n" - else: - cleanM += "if not os.path.exists( \"%s/%s.align\" ):\n" % ( currentDir, prefix ) - cleanM += "\tos.system( \"mv %s.align %s\" )\n" % ( prefix, currentDir ) - cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".fa\" ):\n" - cleanM += "\tos.remove( \"" + prefix + ".align."+s+".fa\" )\n" - cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".map\" ):\n" - cleanM += "\tos.remove( \"" + prefix + ".align."+s+".map\" )\n" - cmd_start += "print \"" + launchB + "\"; sys.stdout.flush()\n" - cmd_start += "log = os.system( \"" + launchB + "\" )\n" - cmd_start += "if log != 0:\n" - cmd_start += launcher.cmd_test( launcher.job, "error", loop=1 ) - cmd_start += "\tsys.exit(1)\n" - cmd_start += cleanB - cmd_start += "print \"" + launchM + "\"; sys.stdout.flush()\n" - cmd_start += "log = os.system( \"" + launchM + "\" )\n" - cmd_start += cleanM - launcher.runSingleJob( cmd_start ) - launcher.acronyme = "BlasterMatcher" - launcher._nbJobs = count - launcher.endRun() - if clean == True: - launcher.clean( "BlasterMatcher_*" ) - - else: - print "ERROR: option '-m %s' not recognized" % ( mix ) - sys.exit(1) - - - if collect != "": - if collect in [ "align", "path", "tab" ]: - runCollect( groupid, collect, allByAll ) - else: - print "ERROR: collect '%s' not implemented" % ( collect ) - sys.exit(1) - - - logging.info( "finished" ) - - if verbose > 0: - print "END %s" % ( sys.argv[0].split("/")[-1] ) - sys.stdout.flush() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/srptCreateTable.py --- a/commons/tools/srptCreateTable.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,134 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -import ConfigParser - -from commons.core.sql.DbMySql import DbMySql - - -def help(): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " -f: name of the input file" - print " -n: name of the MySQL table" - print " -t: table type (fasta|align|path|set|match|map|TEclassif|cluster)" - print " -o: overwrite (default=False)" - print " -c: configuration file from TEdenovo or TEannot pipeline" - print " -H: MySQL host (if no configuration file)" - print " -U: MySQL user (if no configuration file)" - print " -P: MySQL password (if no configuration file)" - print " -D: MySQL database (if no configuration file)" - print " -T: MySQL port (if no configuration file, default=3306)" - print " -v: verbose (default=0/1)" - print - - -def main(): - """ - This program loads data from a file into a MySQL table. - """ - filename = "" - tablename = "" - filetype = "" - overwrite = False - configFileName = "" - host = "" - user = "" - passwd = "" - dbname = "" - port = 0 - verbose = 0 - - try: - opts, args = getopt.getopt( sys.argv[1:], "hf:t:n:oc:H:U:P:D:T:v:" ) - except getopt.GetoptError, err: - sys.stderr.write( "%s\n" % str(err) ) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-f": - filename = a - elif o == "-n": - tablename = a - elif o == "-t": - filetype = a - elif o == "-o": - overwrite = True - elif o == "-c": - configFileName = a - elif o == "-H": - host = a - elif o == "-U": - user = a - elif o == "-P": - passwd = a - elif o == "-D": - dbname = a - elif o == "-T": - port = int(a) - elif o == "-v": - verbose = int(a) - - if filename == "" or tablename == "" or filetype == "": - print "ERROR: missing compulsory options" - help() - sys.exit(1) - - if configFileName != "": - config = ConfigParser.ConfigParser() - config.readfp( open(configFileName) ) - host = config.get("repet_env","repet_host") - user = config.get("repet_env","repet_user") - passwd = config.get("repet_env","repet_pw") - dbname = config.get("repet_env","repet_db") - port = config.get("repet_env","repet_port") - - if host == "" and os.environ.get( "REPET_HOST" ) != "": - host = os.environ.get( "REPET_HOST" ) - if user == "" and os.environ.get( "REPET_USER" ) != "": - user = os.environ.get( "REPET_USER" ) - if passwd == "" and os.environ.get( "REPET_PW" ) != "": - passwd = os.environ.get( "REPET_PW" ) - if dbname == "" and os.environ.get( "REPET_DB" ) != "": - dbname = os.environ.get( "REPET_DB" ) - if port == 0 and os.environ.get( "REPET_PORT" ) != "": - port = int( os.environ.get( "REPET_PORT" ) ) - - if host == "": - print "ERROR: missing host" - sys.exit(1) - if user == "": - print "ERROR: missing user" - sys.exit(1) - if passwd == "": - print "ERROR: missing password" - sys.exit(1) - if dbname == "": - print "ERROR: missing db name" - sys.exit(1) - if port == 0: - print "ERROR: missing port" - sys.exit(1) - - db = DbMySql(user, host, passwd, dbname, port ) - - if not os.path.exists( filename ): - print "ERROR: input file '%s' doesn't exist" % ( filename ) - sys.exit(1) - - db.createTable( tablename, filetype, filename, overwrite) - - db.close() - - return 0 - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/srptExportTable.py --- a/commons/tools/srptExportTable.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,146 +0,0 @@ -#!/usr/bin/env python - -import user, os, sys, getopt, exceptions, ConfigParser - -#----------------------------------------------------------------------------- - -def help(): - - """ - Give the list of the command-line options. - """ - - print - print "usage:",sys.argv[0]," [ options ]" - print "options:" - print " -h: this help" - print " -i: name of the table to export" - print " -o: name of the output file (default=inTable)" - print " -p: extra parameters to add to the SQL query (e.g. 'ORDER BY path')" - print " -k: keep the first line" - print " -C: configuration file from TEdenovo or TEannot pipeline" - print " -H: MySQL host (if no configuration file)" - print " -U: MySQL user (if no configuration file)" - print " -P: MySQL password (if no configuration file)" - print " -D: MySQL database (if no configuration file)" - print " -v: verbose (default=0/1)" - print - -#----------------------------------------------------------------------------- - -def main(): - - """ - This program exports all the data contained in a MySQL table into a flat file in the current directory. - """ - - inTable = "" - outFileName = "" - param = "" - keepFirstLine = False - configFileName = "" - host = "" - user = "" - passwd = "" - dbname = "" - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hi:o:p:kC:H:U:P:D:v:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-i": - inTable = a - elif o == "-o": - outFileName = a - elif o == "-p": - param = a - elif o == "-k": - keepFirstLine = True - elif o == "-C": - configFileName = a - elif o == "-H": - host = a - elif o == "-U": - user = a - elif o == "-P": - passwd = a - elif o == "-D": - dbname = a - elif o == "-v": - verbose = int(a) - - if inTable == "": - print "*** Error: missing input table name" - help() - sys.exit(1) - - if configFileName != "": - config = ConfigParser.ConfigParser() - config.readfp( open(configFileName) ) - host = config.get("repet_env","repet_host") - user = config.get("repet_env","repet_user") - passwd = config.get("repet_env","repet_pw") - dbname = config.get("repet_env","repet_db") - if host == "" or user == "" or passwd == "" or dbname == "": - if os.environ.get( "REPET_HOST" ) not in [ "", None ]: - host = os.environ.get( "REPET_HOST" ) - if os.environ.get( "REPET_USER" ) not in [ "", None ]: - user = os.environ.get( "REPET_USER" ) - if os.environ.get( "REPET_PW" ) not in [ "", None ]: - passwd = os.environ.get( "REPET_PW" ) - if os.environ.get( "REPET_DB" ) not in [ "", None ]: - dbname = os.environ.get( "REPET_DB" ) - if host == "" or user == "" or passwd == "" or dbname == "": - print "*** Error: missing information about MySQL connection" - sys.exit(1) - - if outFileName == "": - outFileName = inTable - - prg = "mysql" - cmd = prg - cmd += " -h %s" % ( host ) - cmd += " -u %s" % ( user ) - cmd += " -p\"%s\"" % ( passwd ) - cmd += " --database=%s" % ( dbname ) - cmd += " -e\"SELECT * FROM %s" % ( inTable ) - if param != "": - cmd += " %s" % ( param ) - cmd += ";\"" - cmd += " > " - if keepFirstLine == False: - cmd += "%s.tmp" % ( outFileName ) - else: - cmd += "%s" % ( outFileName ) - if verbose > 0: print cmd; sys.stdout.flush() - log = os.system( cmd ) - if log != 0: - print "*** Error: %s returned %i" % ( prg, log ) - sys.exit(1) - - if keepFirstLine == False: - tmpFileName = "%s.tmp" % ( outFileName ) - tmpFile = open( tmpFileName, "r" ) - outFile = open( outFileName, "w" ) - i = 0 - for line in tmpFile: - if i > 0: - outFile.write( line ) - i += 1 - tmpFile.close() - outFile.close() - os.remove( tmpFileName ) - - return 0 - -#---------------------------------------------------------------------------- - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/srptGameXmlMaker.py --- a/commons/tools/srptGameXmlMaker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,283 +0,0 @@ -#!/usr/bin/env python - -import user, os, sys, getopt, ConfigParser -from os import listdir - -def setup_env(): - if "REPET_PATH" in os.environ.keys(): - sys.path.append( os.environ["REPET_PATH"] ) - else: - print "*** Error: no environment variable REPET_PATH ***" - sys.exit(1) -setup_env() - -from pyRepet.sql.RepetDBMySQL import * -from pyRepet.gamexml.Xml_writer import * -from pyRepet.gamexml.computational import * - -#------------------------------------------------------------------------------ - -def help(): - - print "" - print "usage:",sys.argv[0],"[options]" - print "options:" - print " -h: this help" - print " -f: fasta file (required to generate new '.gamexml' files)" - print " -n: annotation tier_name" - print " -g: gamexml file (for Apollo). If it's not mentionned, all '.gamexml' files will be updated with the result file" - print " -l: light gameXML file (without sequence)" - print " -r: result files (require -n)" - print " -R: reverse the query and subject of Blaster results" - print " -s: tier_name of an annotation to remove from a gameXML file" - print " -t: file of table name to use to create the gamexml files (tier name 'tab' format 'tab' table name)" - print " -c: configuration file from TEdenovo or TEannot pipeline" - print " -H: MySQL host (if no configuration file)" - print " -U: MySQL user (if no configuration file)" - print " -P: MySQL password (if no configuration file)" - print " -D: MySQL database (if no configuration file)" - print " -v: verbose (default=0/1/2)" - print "" - -#------------------------------------------------------------------------------ - -def automatisation( result_file, tier_name, reverse, comput ): - - if verbose > 1: - print "Auto update"; sys.stdout.flush() - writer = Xml_writer() - file_liste = [] - liste_comp = [] - liste_comp = listdir('./') - - if result_file != "": - for j in liste_comp: - if writer.file_in_keys( j, comput ): - file_liste = file_liste + [j] - - for i in file_liste: - writer.update_gamexml( i, result_file, tier_name, comput ) - - else: - for j in liste_comp: - if j.find( "gamexml" ) != -1: - writer.parse_gamexml( j ) - writer.verif_name_prog( tier_name ) - writer.write( j ) - if verbose > 1: - print tier_name + " program from " +j +" removed" - -#------------------------------------------------------------------------------ - -def main(): - - f_result = "" - f_gamexml = "" - f_fasta = "" - f_table = "" - tier_name = "" - substract_name = "" - no_seq = 0 - configFileName = "" - host = "" - user = "" - passwd = "" - dbname = "" - verbose = 0 - - try: - options,arguments=getopt.getopt(sys.argv[1:],"hn:f:g:r:s:lRt:c:H:U:P:D:v:",["help","tier_name=","fasta","gamexml","result","substract_program","light","reverse_result","table"]) - except getopt.GetoptError: - help() - sys.exit(1) - if options == []: - help() - sys.exit(1) - for o,a in options: - if o == "-h" or o == "--help": - help() - sys.exit(0) - elif o == "-f" or o == "--fasta": - f_fasta = a - elif o == "-g" or o == "--gamexml": - f_gamexml = a - elif o == "-n" or o == "--tier_name": - tier_name = a - elif o == "-r" or o == "--result": - f_result = a - elif o == "-s" or o == "--subtract_program": - substract_name = a - elif o == "-l" or o == "--light": - no_seq = 1 - elif o == "-R" or o == "--reverse_result": - writer.set_reverse() - elif o == "-t" or o == "--table": - f_table = a - elif o == "-c": - configFileName = a - elif o == "-H": - host = a - elif o == "-U": - user = a - elif o == "-P": - passwd = a - elif o == "-D": - dbname = a - elif o == "-v": - verbose = int(a) - - if tier_name == "" and substract_name == "" and f_result != "": - print "*** Error: option -n required" - help() - sys.exit(1) - - if f_fasta == "" and f_gamexml == "": - print "*** Error: options -g or -f required" - help() - sys.exit(1) - - if substract_name!="" and f_result!="" : - print "Error: option -s and -r together" - help() - sys.exit(1) - - - if verbose > 0: - print "\nbeginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if configFileName != "": - config = ConfigParser.ConfigParser() - config.readfp( open(configFileName) ) - host = config.get("repet_env","repet_host") - user = config.get("repet_env","repet_user") - passwd = config.get("repet_env","repet_pw") - dbname = config.get("repet_env","repet_db") - - if host == "" and os.environ.get( "REPET_HOST" ) != None: - host = os.environ.get( "REPET_HOST" ) - if user == "" and os.environ.get( "REPET_USER" ) != None: - user = os.environ.get( "REPET_USER" ) - if passwd == "" and os.environ.get( "REPET_PW" ) != None: - passwd = os.environ.get( "REPET_PW" ) - if dbname == "" and os.environ.get( "REPET_DB" ) != None: - dbname = os.environ.get( "REPET_DB" ) - - writer = Xml_writer() - - # create the dico - comput = computational() - - # create all the ".gamexml" files (option '-f') - if f_fasta != "": - writer.create_gamexml( f_fasta, f_result, tier_name, comput, no_seq ) - - # - if f_result != "": - if f_gamexml != "": - key = ".".join( f_gamexml.split(".")[:-1] ) - else: - key = "" - format = writer.find_type_file( f_result ) - resFile = open( f_result ) - if format == "path": - comput.load_dico_path_from_file( key, f_result ) - - if f_table != "": - if verbose > 1: - print "parsing file %s... " % ( f_gamexml ); sys.stdout.flush() - writer.parse_gamexml( f_gamexml ) - - if f_gamexml != "": -## key=".".join(f_gamexml.split(".")[:-1]) - key = f_gamexml.split(".")[0] - else: - key = "" - - tfile = open( f_table ) - lines = tfile.readlines() - for l in lines: - if l[0] == "#": - continue - tok = l.split() - #print tok - if len(tok) == 0: - break - tier_name = tok[0] - format = tok[1] - table = tok[2] - alias = "" - if verbose > 1: - print "table: " + table + " (format=" + format + ")" - if len(tok) > 3: - alias = tok[3] - if verbose > 1: - print " alias=" + alias - - if host == "" or user == "" or passwd == "" or dbname == "": - print "*** Error: missing information about MySQL connection" - sys.exit(1) - db = RepetDB( user, host, passwd, dbname ) - - if format == "path": - comput.load_dico_path_from_table( db, key, table, alias ) - writer.update_gamexml_comput( tier_name, comput ) - elif format == "rpath": - comput.load_dico_rpath_from_table( db, key, table, alias ) - elif format == "ipath": - comput.load_dico_ipath_from_table( db, key, table, alias ) - writer.update_gamexml_comput( tier_name, comput ) - elif format == "align": - comput.load_dico_align_from_table( db, key, table, alias ) - writer.update_gamexml_comput( tier_name, comput ) - elif format == "map": - comput.load_dico_map_from_table( db, key, table, alias ) - writer.update_gamexml_comput( tier_name, comput ) - elif format == "rmap": - comput.load_dico_rmap_from_table( db, key, table, alias ) - writer.update_gamexml_comput( tier_name, comput ) - elif format == "set": - comput.load_dico_set_from_table( db, key, table, alias ) - writer.update_gamexml_comput( tier_name, comput ) - elif format == "annot": - comput.load_dico_annot_from_table( db, key, table, alias ) - writer.update_gamexml_annot( table, comput ) - elif format == "annot_set": - comput.load_dico_annotset_from_table( db, key, table, alias ) - writer.update_gamexml_annot( table, comput ) - else: - print "*** Error: unknown format '%s'" % ( format ) - sys.exit(1) - writer.write(f_gamexml) - - db.close() - - # - if f_gamexml == "" and f_result != "" and f_fasta == "": - automatisation( f_result, tier_name, writer.get_reverse(), comput ) - - # update a ".gamexml" file (options '-g' and '-t') - if f_gamexml != "" and f_result != "": - writer.update_gamexml( f_gamexml, f_result, tier_name, comput ) - - # remove a comput - if substract_name != "" and tier_name == "": - if f_gamexml != "": - writer.parse_gamexml( f_gamexml ) - writer.verif_name_prog( substract_name ) - writer.write( f_gamexml ) - if verbose > 1: - print substract_name + " program from " + f_gamexml +" removed" - else: - automatisation( "", substract_name, 0, None ) - - if verbose > 0: - print "%s finished successfully\n" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#------------------------------------------------------------------------------ - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/srptPhyML.py --- a/commons/tools/srptPhyML.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -#!/usr/bin/env python - -import user, os, sys, getopt, exceptions, logging, ConfigParser - -if not os.environ.has_key( "REPET_PATH" ): - print "*** Error: no environment variable REPET_PATH" - sys.exit(1) -sys.path.append( os.environ["REPET_PATH"] ) - -import pyRepet.sql.RepetJobMySQL -import pyRepet.launcher.Launcher - -#----------------------------------------------------------------------------- - -def help(): - - """ - Give the list of the command-line options. - """ - - print - print "usage:",sys.argv[0]," [ options ]" - print "options:" - print " -h: this help" - print " -g: name of the group identifier (same for all the jobs)" - print " -q: name of the query directory" - print " -S: suffix in the query directory (default='*.fa')" - print " -Q: name of the queue (on the cluster)" - print " -d: absolute path to the temporary directory" - print " -C: configuration file from TEdenovo or TEannot pipeline" - print " -t: job table name (default=jobs)" - print " -p: absolute path to project directory (if jobs management via files)" - print " -c: clean (remove job launch files and job stdout)" - print " -v: verbose (default=0/1/2)" - print - -#----------------------------------------------------------------------------- - -def main(): - - """ - This program takes a directory as input and launches MAP on each file in it. - """ - - groupid = "" - queryDir = "" - patternSuffix = "*.fa" - queue = "" - tmpDir = "" - configFileName = "" - jobTable = "jobs" - projectDir = "" - clean = False - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hg:q:S:Q:d:C:t:p:cv:") - except getopt.GetoptError, err: - print str(err) - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-g": - groupid = a - elif o == "-q": - queryDir = a - elif o == "-S": - patternSuffix = a - elif o == "-Q": - queue = a - elif o == "-d": - tmpDir = a - elif o == "-C": - configFileName = a - elif o == "-t": - jobTable = a - elif o == "-p": - projectDir = a - elif o == "-c": - clean = True - elif o == "-v": - verbose = int(a) - - if groupid == "" or queryDir == "": - print "*** Error: missing compulsory options" - help() - sys.exit(1) - - if os.environ["REPET_JOBS"] == "files" and projectDir == "": - print "*** Error: missing compulsory options for jobs management via files" - help() - sys.exit(1) - - if verbose > 0: - print "\nbeginning of %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - #-------------------------------------------------------------------------- - - # create the 'log' file - - logFileName = "%s_pid%s.log" % ( groupid, os.getpid() ) - handler = logging.FileHandler( logFileName ) - formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" ) - handler.setFormatter( formatter ) - logging.getLogger('').addHandler( handler ) - logging.getLogger('').setLevel( logging.DEBUG ) - logging.info( "started" ) - - - # open a connection to the MySQL table - - if configFileName != "": - if not os.path.exists( configFileName ): - print "*** Error: configuration file '%s' doesn't exist" % ( configFileName ) - sys.exit(1) - config = ConfigParser.ConfigParser() - config.readfp( open(configFileName) ) - host = config.get("repet_env","repet_host") - user = config.get("repet_env","repet_user") - passwd = config.get("repet_env","repet_pw") - dbname = config.get("repet_env","repet_db") - else: - host = os.environ["REPET_HOST"] - user = os.environ["REPET_USER"] - passwd = os.environ["REPET_PW"] - dbname = os.environ["REPET_DB"] - - if os.environ["REPET_JOBS"] == "files": - jobdb = pyRepet.sql.RepetJobMySQL.RepetJob( dbname = projectDir + "/" + os.environ["REPET_DB"] ) - elif os.environ["REPET_JOBS"] == "MySQL": - jobdb = pyRepet.sql.RepetJobMySQL.RepetJob( user, host, passwd, dbname ) - else: - print "*** Error: REPET_JOBS is '%s'" % ( os.environ["REPET_JOBS"] ) - sys.exit(1) - - - currentDir = os.getcwd() - if tmpDir == "": - tmpDir = currentDir - - # launch PhyML on each fasta file in queryDir - cL = pyRepet.launcher.Launcher.PhyMlLauncher( jobdb=jobdb, query=queryDir, cdir=currentDir, tmpdir=tmpDir, job_table=jobTable, queue=queue, groupid=groupid, acro="PhyML" ) - cL.run( patternSuffix ) - - # clean - if clean == True: - cL.clean() - - - logging.info( "finished" ) - - if verbose > 0: - print "%s finished successfully\n" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#---------------------------------------------------------------------------- - -if __name__ == '__main__': - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/srptTableOverlap.py --- a/commons/tools/srptTableOverlap.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,319 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import getopt -import logging -import string -import ConfigParser - -from pyRepet.sql.TableAdaptator import * -import pyRepet.sql.RepetDBMySQL -import pyRepet.coord.Map -import pyRepet.coord.Path -import pyRepet.coord.Set - - -def help(): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " -q: query table" - print " -s: subject table" - print " -p: by path" - print " -t: table type comparison: qtype/stype where qtype=[map,set,path] and stype=[path,set,map]" - print " -c: configuration file from TEdenovo or TEannot pipeline" - print " -H: MySQL host (if no configuration file)" - print " -U: MySQL user (if no configuration file)" - print " -P: MySQL password (if no configuration file)" - print " -D: MySQL database (if no configuration file)" - print - - -def pathOverlapByPath( qtable, qtype, stable, stype, db, fout, verbose=0 ): - - if qtype == "path": - db.create_path_index( qtable ) - qtablePathAdaptator = TablePathAdaptator( db, qtable ) - path_num_list = qtablePathAdaptator.getPath_num() - elif qtype == "set": - db.create_set_index( qtable ) - qtableSetAdaptator = TableSetAdaptator( db, qtable ) - path_num_list = qtableSetAdaptator.getSet_num() - else: - string = "unknown query table type: %s" % ( qtype ) - if verbose > 0: - print string - logging.error( string ) - sys.exit(1) - string = "nb of paths in query table: %i" % (len(path_num_list) ) - if verbose > 0: - print string - logging.info( string ) - - if stype == "path": - stablePathAdaptator = TableBinPathAdaptator( db, stable ) -# stablePathAdaptator=TablePathAdaptator(db,stable) - elif stype == "set": - stableSetAdaptator = TableBinSetAdaptator( db, stable ) -# stableSetAdaptator=TableSetAdaptator(db,stable) - else: - string = "unknown subject table type: %s" % ( stype ) - if verbose > 0: - print string - logging.error( string ) - sys.exit(1) - - count = 0 - for path_num in path_num_list: - if qtype == "path": - qlist = qtablePathAdaptator.getPathList_from_num( path_num ) - qlist = pyRepet.coord.Path.path_list_rangeQ2Set( qlist ) - elif qtype == "set": - qlist = qtableSetAdaptator.getSetList_from_num( path_num ) - - qlist.sort() - qmin, qmax = pyRepet.coord.Set.set_list_boundaries( qlist ) - - qmin = qmin - 1 - qmax = qmax + 1 - if stype == "path": - slist = stablePathAdaptator.getPathList_from_qcoord(qlist[0].seqname.split()[0],qmin,qmax) - slist = pyRepet.coord.Path.path_list_rangeQ2Set( slist ) - elif stype == "set": - slist = stableSetAdaptator.getSetList_from_qcoord(qlist[0].seqname.split()[0],qmin,qmax) - - if len(slist) > 0: - print "----------------------------------------" - print "query:" - pyRepet.coord.Set.set_list_show( qlist ) - qlist=pyRepet.coord.Set.set_list_merge( qlist ) - qsize=pyRepet.coord.Set.set_list_size( qlist ) - print "query size=",qsize - - slist_dict = pyRepet.coord.Set.set_list_split( slist ) - subj_names = "" - for i,l in slist_dict.items(): - if subj_names != "": - subj_names += "|" - subj_names += "%d:%s" % (i,l[0].name) - subj_count = len(slist_dict.keys()) - - print "subject:" - pyRepet.coord.Set.set_list_show( slist ) - slist = pyRepet.coord.Set.set_list_merge( slist ) - ssize = pyRepet.coord.Set.set_list_size( slist ) - osize = pyRepet.coord.Set.set_list_overlap_size( qlist, slist ) - - print "subject size=",ssize - print "overlap size=",osize - - fout.write("%d\t%s\t%d\t%s\t%d\t%d\t%d\t%f\t%f\n"\ - %(path_num,qlist[0].name,\ - qsize,\ - subj_names,\ - subj_count,\ - ssize,\ - osize,\ - float(osize)/qsize,\ - float(osize)/ssize)) - else: - print "----------------------------------------" - print "query:" - pyRepet.coord.Set.set_list_show( qlist ) - qlist = pyRepet.coord.Set.set_list_merge( qlist ) - qsize = pyRepet.coord.Set.set_list_size( qlist ) - print "query size=",qsize - print "No match!" - fout.write("%d\t%s\t%d\t-\t0\t0\t0\t0.0\t0.0\n"\ - %(path_num,qlist[0].name,qsize)) - - -def getOverlapAllPaths( qtable, qtype, stable, stype, db, verbose=0 ): - """ - For each query in qtable, compute the overlap between its matches and the matches in stable. - """ - if qtype =="map": - qtableAdaptator = pyRepet.sql.TableAdaptator.TableMapAdaptator( db, qtable ) - elif qtype == "path": - qtableAdaptator = pyRepet.sql.TableAdaptator.TablePathAdaptator( db, qtable ) - elif qtype == "set": - qtableAdaptator = pyRepet.sql.TableAdaptator.TableSetAdaptator( db, qtable ) - else: - string = "unknown query table type: %s" % ( qtype ) - if verbose > 0: - print string - logging.error( string ) - sys.exit(1) - - string = "fetching query table data..." - contigs = qtableAdaptator.getContig_name() - string += " %i contig(s)" % ( len(contigs) ) - if verbose > 0: - print string; sys.stdout.flush() - logging.info( string ) - - if stype == "map": - stableAdaptator = pyRepet.sql.TableAdaptator.TableMapAdaptator( db, stable ) - elif stype == "path": - stableAdaptator = pyRepet.sql.TableAdaptator.TablePathAdaptator( db, stable ) - elif stype == "set": - stableAdaptator = pyRepet.sql.TableAdaptator.TableSetAdaptator( db, stable ) - else: - string = "unknown subject table type: %s" % ( stype ) - if verbose > 0: - print string - logging.error( string ) - sys.exit(1) - - string = "looking for overlaps with subject data..." - if verbose > 0: - print string; sys.stdout.flush() - logging.info( string ) - sum_qsize = 0 - sum_osize = 0 - sum_non_osize = 0 - for c in contigs: - string = "contig '%s': "%(c) - qlist = qtableAdaptator.getSetList_from_contig( c ) - qlist = pyRepet.coord.Set.set_list_merge( qlist ) - slist = stableAdaptator.getSetList_from_contig( c ) - slist = pyRepet.coord.Set.set_list_merge( slist ) - qsize = pyRepet.coord.Set.set_list_size( qlist ) - osize = pyRepet.coord.Set.set_list_overlap_size( qlist, slist ) - sum_osize += osize - sum_qsize += qsize - sum_non_osize += qsize - osize - string += "qsize=%d osize=%d" % ( qsize, osize ) - logging.debug( string ) - if verbose > 0: - print string; sys.stdout.flush() - - string = "summary:" - string += "\ncumulative coverage of the query table: %i nt" % ( sum_qsize ) - string += "\nsize of overlaps with the subject table: %i nt" % ( sum_osize ) - string += "\n proportion of query: %.3f" % ( float(sum_osize)/sum_qsize ) - string += "\nsize of non-overlaps with the subject table: %i nt" % ( sum_non_osize ) - string += "\n proportion of query: %.3f" % ( float(sum_non_osize)/sum_qsize ) - if verbose > 0: - print string; sys.stdout.flush() - logging.info( string ) - - return sum_osize, sum_non_osize, sum_qsize - - -def main (): - """ - This program computes the overlaps between two tables recording spatial coordinates. - """ - qtable = "" - stable = "" - type = "" - by_path = False - configFileName = "" - host = "" - user = "" - passwd = "" - db = "" - verbose = 0 - try: - opts, args = getopt.getopt( sys.argv[1:], "hq:s:t:pc:H:U:P:D:v:" ) - except getopt.GetoptError: - help() - sys.exit(1) - if len(args) != 0: - help() - sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-q": - qtable = a - elif o == "-s": - stable = a - elif o == "-t": - type = a - elif o == "-p": - by_path = True - elif o == "-c": - configFileName = a - elif o == "-H": - host = a - elif o == "-U": - user = a - elif o == "-P": - passwd = a - elif o == "-D": - db = a - elif o == "-v": - verbose = int(a) - if qtable=="" or stable=="" or \ - (configFileName== "" and (host=="" or \ - user=="" or passwd=="" or db=="")): - print "ERROR: missing compulsory options" - help() - sys.exit(1) - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - if configFileName != "": - config = ConfigParser.ConfigParser() - config.readfp( open(configFileName) ) - host = config.get("repet_env","repet_host") - user = config.get("repet_env","repet_user") - passwd = config.get("repet_env","repet_pw") - dbname = config.get("repet_env","repet_db") - - logfilename = qtable + "-" + stable + "-" + str(os.getpid()) + ".log" - handler = logging.FileHandler( logfilename ) - formatter = logging.Formatter("%(asctime)s %(levelname)s: %(message)s") - handler.setFormatter( formatter ) - logging.getLogger('').addHandler(handler) - logging.getLogger('').setLevel(logging.DEBUG) - logging.info("started") - - db = pyRepet.sql.RepetDBMySQL.RepetDB( user, host, passwd, dbname ) - - qtype, stype = type.split("/") - - if not db.exist( qtable ): - if not os.path.exists( qtable ): - msg = "ERROR: neither table nor file '%s'" % ( qtable ) - sys.stderr.write( "%s\n" % msg ) - sys.exit(1) - tmp = qtable.replace(".","_") - db.create_table( db, tmp, qtable, qtype ) - qtable = tmp - if not db.exist( stable ): - if not os.path.exists( stable ): - msg = "ERROR: neither table nor file '%s'" % ( stable ) - sys.stderr.write( "%s\n" % msg ) - sys.exit(1) - tmp = stable.replace(".","_") - db.create_table( db, tmp, stable, qtype ) - stable = tmp - - string = "input tables:" - string += "\nquery table: %s ('%s' format)" % ( qtable, qtype ) - string += "\nsubject table: %s ('%s' format)" % ( stable, stype ) - logging.info( string ) - - if by_path: - fout = open(qtable+"_vs_"+stable+".dat","w") - pathOverlapByPath( qtable, qtype, stable, stype, db, fout, verbose ) - fout.close() - else: - getOverlapAllPaths( qtable, qtype, stable, stype, db, verbose ) - - logging.info("finished") - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tabFileReader.py --- a/commons/tools/tabFileReader.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,600 +0,0 @@ -#!/usr/bin/env python - -###@file -# Read a file recording matches in the 'tab' format (output from Matcher) and return the number of matches between queries and subjects being CC, CI, IC and II. -# A match is said to be CC (for complete-complete) when both query and subject match over x% of their entire respective length. By default, x=95. -# -# usage: tabFileReader.py [ options ] -# options: -# -h: this help -# -m: name of the file recording the matches (format='tab', output from Matcher) -# -q: name of the fasta file recording the queries -# -s: name of the fasta file recording the subjects -# -t: threshold over which the match is 'complete', in % of the seq length (default=95) -# -i: identity below which matches are ignored (default=0) -# -l: length below which matches are ignored (default=0) -# -o: overlap on query and subject below which matches are ignored (default=0) -# -v: verbose (default=0/1) - -import sys -import getopt -from string import * - -import pyRepet.seq.BioseqDB -import pyRepet.util.Stat - -#TODO: remove case changes in headers (4 lower() method calls in this script) - -#---------------------------------------------------------------------------- - -def help(): - print - print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] ) - print "options:" - print " -h: this help" - print " -m: name of the file recording the matches (format='tab', output from Matcher)" - print " -q: name of the fasta file recording the queries" - print " -s: name of the fasta file recording the subjects" - print " -t: coverage threshold over which the match is 'complete' (in %% of the seq length, default=95)" - print " -i: identity below which matches are ignored (default=0)" - print " -l: length below which matches are ignored (default=0)" - print " -o: overlap on query and subject below which matches are ignored (default=0)" - print " -I: identity threshold for 'CC' matches (default=90)" - print " -E: E-value threshold for 'CC' matches (default=1e-10)" - print " -T: coverage threshold for match length on query compare to subject length (default=90)" - print " -v: verbose (default=0/1)" - print - -#---------------------------------------------------------------------------- - -#here are the fields of a '.tab' file: -#[0]: query sequence name -#[1]: whole match start coordinate on the query sequence -#[2]: whole match end coordinate on the query sequence -#[3]: length on the query sequence -#[4]: length in percentage of the query sequence -#[5]: length on the query relative to the subject length in percentage -#[6]: subject sequence name -#[7]: whole match start coordinate on the subject sequence -#[8]: whole match end coordinate on the subject sequence -#[9]: length on the subject sequence -#[10]: length in percentage of the subject sequence -#[11]: BLAST E-value -#[12]: BLAST score -#[13]: identity percentage -#[14]: path - -class tabFileReader( object ): - - def __init__( self, line ): - - columns = line.split("\t") - - self.name_sbj = (columns[6]) - self.length_sbj = int(round(int(columns[9])/float(columns[10]),0)) #length of the subject - self.prct_sbj = float(columns[10]) * 100 #prct_sbj = length of the match on the subject divided by the length of the subject * 100 - if int(columns[7]) < int(columns[8]): - self.start_sbj = int(columns[7]) #start of the match on the subject - self.end_sbj = int(columns[8]) #end of the match on the subject - else: - self.start_sbj = int(columns[8]) - self.end_sbj = int(columns[7]) - self.sbj_dist_ends = int(columns[9]) #length on the subject that matches with the query - - self.name_qry = columns[0] - self.length_qry = int(round(int(columns[3])/float(columns[4]),0)) #length of the query - self.prct_qry = float(columns[4]) * 100 #prct_qry = length of the match on the query divided by the length of the query * 100 - if int(columns[1]) < int(columns[2]): - self.start_qry = int(columns[1]) #start of the match on the query - self.end_qry = int(columns[2]) #end of the match on the query - else: - self.start_qry = int(columns[2]) - self.end_qry = int(columns[1]) - self.qry_dist_ends = int(columns[3]) #length on the query that matches with the subject - - self.length_match = int(columns[3]) - self.prct_matchQryOverSbj = float(columns[5]) * 100 #length on the query relative to the subject length in percentage - self.identity = float(columns[13]) - self.score = int(columns[12]) - self.evalue = float(columns[11]) - - self.sbj2qry = [self.length_sbj,self.prct_sbj,self.start_sbj,self.end_sbj,self.name_qry,self.length_sbj,self.prct_qry,self.start_qry,self.end_qry,self.identity,self.score] - - self.qry2sbj = [self.length_qry,self.prct_qry,self.start_qry,self.end_qry,self.name_sbj,self.length_sbj,self.prct_sbj,self.start_sbj,self.end_sbj,self.identity,self.score] - -#---------------------------------------------------------------------------- - -def make_dico( lMatches ): - """ - Record the matches in two dictionaries which keys are the queries or the subjects. - """ - - Sbj2Qry = {} - Qry2Sbj = {} - - for match in lMatches: - if Sbj2Qry.has_key( match.name_sbj ): - Sbj2Qry[match.name_sbj].append( match ) - else: - Sbj2Qry[match.name_sbj] = [ match ] - if Qry2Sbj.has_key( match.name_qry ): - Qry2Sbj[match.name_qry].append( match ) - else: - Qry2Sbj[match.name_qry] = [ match ] - - return [ Sbj2Qry, Qry2Sbj ] - -#---------------------------------------------------------------------------- - -def find_UniqRedun( list_matchs ): - - list_total_sbj = [];list_total_qry = [] - list_uniq_sbj = [];list_redun_sbj = [] - list_uniq_qry = [];list_redun_qry = [] - - for match in list_matchs: - list_total_sbj.append(match.name_sbj) - list_total_qry.append(match.name_qry) - - for name_sbj in list_total_sbj: - if list_total_sbj.count(name_sbj) == 1: - list_uniq_sbj.append(name_sbj) - else: - if name_sbj not in list_redun_sbj: - list_redun_sbj.append(name_sbj) - - for name_qry in list_total_qry: - if list_total_qry.count(name_qry) == 1: - list_uniq_qry.append(name_qry) - else: - if name_qry not in list_redun_qry: - list_redun_qry.append(name_qry) - - return [ list_uniq_sbj, list_redun_sbj, list_uniq_qry, list_redun_qry ] - -#---------------------------------------------------------------------------- - -def remove( all, sup_sbjqry, sup_sbj, sup_qry, inf_sbjqry ): - - for name_sbj in all.keys(): - - if sup_sbjqry.has_key( name_sbj ) and sup_sbj.has_key( name_sbj ): - del sup_sbj[ name_sbj ] - - if sup_sbjqry.has_key( name_sbj ) and sup_qry.has_key( name_sbj ): - del sup_qry[ name_sbj ] - - if sup_sbjqry.has_key( name_sbj ) and inf_sbjqry.has_key( name_sbj ): - del inf_sbjqry[ name_sbj ] - - if sup_sbj.has_key( name_sbj ) and sup_qry.has_key( name_sbj ): - del sup_qry[ name_sbj ] - - if sup_sbj.has_key( name_sbj ) and inf_sbjqry.has_key( name_sbj ): - del inf_sbjqry[ name_sbj ] - - if sup_qry.has_key( name_sbj ) and inf_sbjqry.has_key( name_sbj ): - del inf_sbjqry[ name_sbj ] - - return [ sup_sbj, sup_qry, inf_sbjqry ] - -#---------------------------------------------------------------------------- - -def write_output( outFile, match_type, Sbj2Qry, dSbj2Cat, Qry2Sbj, dQry2Cat ): - """ - Save the results (subjects in each category and its matches) in a human-readable way. - """ - - if match_type == 'CC': - msg = "Matches with L >= %i%% for subject and query (CC)" % ( thresholdCoverage ) - elif match_type == 'CI': - msg = "Matches with L >= %i%% for subject and L < %i%% for query (CI)" % ( thresholdCoverage, thresholdCoverage ) - elif match_type == 'IC': - msg = "Matches with L < %i%% for subject and L >= %i%% for query (IC)" % ( thresholdCoverage, thresholdCoverage ) - elif match_type == 'II': - msg ="Matches with L < %i%% for subject and query (II)" % ( thresholdCoverage ) - if verbose > 1: - print "%s: %i subjects" % ( msg, len(Sbj2Qry.keys()) ) - outFile.write("\n%s\n" % ( msg ) ) - - for name_sbj in Sbj2Qry.keys(): - matchs = Sbj2Qry[name_sbj] - if len(matchs) == 1: - outFile.write("-> subject %s (%s: %s,%s) matches with query %s (%s: %s,%s): prct_sbj %.3f & prct_qry %.3f (id=%.3f,Eval=%g)\n" % (name_sbj,matchs[0].length_sbj,matchs[0].start_sbj,matchs[0].end_sbj,matchs[0].name_qry,matchs[0].length_qry,matchs[0].start_qry,matchs[0].end_qry,matchs[0].prct_sbj,matchs[0].prct_qry,matchs[0].identity,matchs[0].evalue)) - else: - outFile.write("-> subject %s (%s: %s,%s) matches with %s queries:\n" % (name_sbj,matchs[0].length_sbj,matchs[0].start_sbj,matchs[0].end_sbj,len(matchs))) - for match in matchs: - outFile.write("%s versus %s (%s: %s,%s): prct_sbj %.3f & prct_qry %.3f (id=%.3f,Eval=%g)\n"%(name_sbj,match.name_qry,match.length_qry,match.start_qry,match.end_qry,match.prct_sbj,match.prct_qry,match.identity,match.evalue)) - - tmpList = [] - for name_sbj in Sbj2Qry.keys(): - tmpList.append( name_sbj.split(" ")[0].lower() ) - tmpList.sort() - for name_sbj in tmpList: - outFile.write( name_sbj+"\n" ) - dSbj2Cat[ name_sbj ] = match_type - - tmpList = [] - for name_qry in Qry2Sbj.keys(): - tmpList.append( name_qry.split(" ")[0].lower() ) - tmpList.sort() - for name_qry in tmpList: - outFile.write( name_qry+"\n" ) - dQry2Cat[ name_qry ] = match_type - -#---------------------------------------------------------------------------- - -def writeSubjectCategory( dSbj2Cat ): - """ - Save the category (CC/CI/IC/II/NA) in which each subject has been found. - - @param dSbj2Cat: dictionary which keys are subject names and values the category of that subject - @type dSbj2Cat: dictionary - """ - - # sort the subject names in alphabetical order - lSbjSorted = dSbj2Cat.keys() - lSbjSorted.sort() - - catFile = open( tabFileName + "_sbjCategories.txt", "w" ) - for sbj in lSbjSorted: - string = "%s\t%s\n" % ( sbj, dSbj2Cat[ sbj ] ) - catFile.write( string ) - catFile.close() - -#---------------------------------------------------------------------------- - -def writeQueryCategory( dQry2Cat ): - """ - Save the category (CC/CI/IC/II/NA) in which each query has been found. - - @param dQry2Cat: dictionary which keys are query names and values the category of that query - @type dQry2Cat: dictionary - """ - - # sort the query names in alphabetical order - lQrySorted = dQry2Cat.keys() - lQrySorted.sort() - - catFile = open( tabFileName + "_qryCategories.txt", "w" ) - for qry in lQrySorted: - string = "%s\t%s\n" % ( qry, dQry2Cat[ qry ] ) - catFile.write( string ) - catFile.close() - -#---------------------------------------------------------------------------- - -def main(): - - global tabFileName - tabFileName = "" - qryFileName = "" - sbjFileName = "" - global thresholdCoverage - thresholdCoverage = 95 - minIdentity = 0 - minLength = 0 - minOverlap = 0 - global thresholdIdentity - thresholdIdentity = 90 - global thresholdEvalue - thresholdEvalue = 1e-10 - global thresholdCoverageMatch - thresholdCoverageMatch = 90 - global verbose - verbose = 0 - - try: - opts, args = getopt.getopt(sys.argv[1:],"hm:q:s:t:i:l:I:E:T:o:v:") - except getopt.GetoptError, err: - print str(err); help(); sys.exit(1) - for o,a in opts: - if o == "-h": - help() - sys.exit(0) - elif o == "-m": - tabFileName = a - elif o == "-q": - qryFileName = a - elif o == "-s": - sbjFileName = a - elif o == "-t": - thresholdCoverage = int(a) - elif o == "-i": - minIdentity = float(a) - elif o == "-l": - minLength = int(a) - elif o == "-o": - minOverlap = float(a) - elif o == "-I": - thresholdIdentity = int(a) - elif o == "-E": - thresholdEvalue = float(a) - elif o == "-T": - thresholdCoverageMatch = int(a) - elif o == "-v": - verbose = int(a) - - if tabFileName == "": - msg = "ERROR: missing 'tab' file (-m)" - sys.stderr.write( "%s\n" % msg ) - help() - sys.exit(1) - if qryFileName == "" or sbjFileName == "": - msg = "ERROR: missing 'fasta' files (-q or -s)" - sys.stderr.write( "%s\n" % msg ) - help() - sys.exit(1) - - if verbose > 0: - print "START %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - # 4 categories of matchs: - # type 1 (CC): the length of the match on the subject is >= 95% of the total length of the subject, idem for the query - # type 2 (CI): sbj >= 95% & qry < 95% - # type 3 (IC): sbj < 95% & qry >= 95% - # type 4 (II): sbj & qry < 95% - ListMatches_all = [] - ListMatches_sup_sbjqry = [] - ListMatches_sup_sbj = [] - ListMatches_sup_qry = [] - ListMatches_inf_sbjqry = [] - - qryDB = pyRepet.seq.BioseqDB.BioseqDB( qryFileName ) - nbQry = qryDB.getSize() - if verbose > 0: - print "nb of queries in '%s': %i" % ( qryFileName, nbQry ) - dQry2Cat = {} - for bs in qryDB.db: - dQry2Cat[ bs.header.split(" ")[0].lower() ] = "NA" - - sbjDB = pyRepet.seq.BioseqDB.BioseqDB( sbjFileName ) - nbSbj = sbjDB.getSize() - if verbose > 0: - print "nb of subjects in '%s': %i" % ( sbjFileName, nbSbj ) - dSbj2Cat = {} - for bs in sbjDB.db: - dSbj2Cat[ bs.header.split(" ")[0].lower() ] = "NA" - - tabFile = open( tabFileName ) - nbMatchesInTab = 0 - dSubject2DistinctQueries = {} - dQuery2DistinctSubjects = {} - - # For each match, create a 'tabFileReader' object and record it in a list according to the type of the match - if verbose > 0: - print "parse the 'tab' file..."; sys.stdout.flush() - while True: - line = tabFile.readline() - if line == "": - break - if line[0:10] == "query.name": - continue - nbMatchesInTab += 1 - - match = tabFileReader( line ) - if match.identity < minIdentity: - line = tabFile.readline() - continue - if match.length_match < minLength: - line = tabFile.readline() - continue - if match.prct_qry < minOverlap or match.prct_sbj < minOverlap: - line = tabFile.readline() - continue - ListMatches_all.append( match ) - - # type 1: sbj C & qry C - if match.prct_sbj >= thresholdCoverage and match.prct_qry >= thresholdCoverage: - qsLengthRatio = 100 * match.length_qry / float(match.length_sbj) - if match.identity >= thresholdIdentity \ - and match.evalue <= thresholdEvalue \ - and qsLengthRatio >= thresholdCoverage - 2 \ - and qsLengthRatio <= 100 + (100-thresholdCoverage) + 2 \ - and match.prct_matchQryOverSbj >= thresholdCoverageMatch: - ListMatches_sup_sbjqry.append( match ) - else: - ListMatches_inf_sbjqry.append( match ) - - # type 2: sbj C & qry I - elif match.prct_sbj >= thresholdCoverage and match.prct_qry < thresholdCoverage: - ListMatches_sup_sbj.append( match ) - - # type 3: sbj I & qry C - elif match.prct_qry >= thresholdCoverage and match.prct_sbj < thresholdCoverage: - ListMatches_sup_qry.append( match ) - - # type 4: sbj I & qry I - elif match.prct_qry < thresholdCoverage and match.prct_sbj < thresholdCoverage: - ListMatches_inf_sbjqry.append( match ) - - if not dSubject2DistinctQueries.has_key( match.name_sbj ): - dSubject2DistinctQueries[ match.name_sbj ] = [] - if not match.name_qry in dSubject2DistinctQueries[ match.name_sbj ]: - dSubject2DistinctQueries[ match.name_sbj ].append( match.name_qry ) - if not dQuery2DistinctSubjects.has_key( match.name_qry ): - dQuery2DistinctSubjects[ match.name_qry ] = [] - if not match.name_sbj in dQuery2DistinctSubjects[ match.name_qry ]: - dQuery2DistinctSubjects[ match.name_qry ].append( match.name_sbj ) - - if verbose > 0: - print "parsing done !"; sys.stdout.flush() - print "nb matches in '%s': %i" % ( tabFileName, nbMatchesInTab ) - print "nb matches 'CC': %i" % ( len(ListMatches_sup_sbjqry) ) - if verbose > 1: - for match in ListMatches_sup_sbjqry: - print "\t%s (%.2f%%) - %s (%.2f%%) id=%.2f" % ( match.name_sbj, match.prct_sbj, match.name_qry, match.prct_qry, match.identity ) - print "nb matches 'CI': %i" % ( len(ListMatches_sup_sbj) ) - if verbose > 1: - for match in ListMatches_sup_sbj: - print "\t%s (%.2f%%) - %s (%.2f%%) id=%.2f" % ( match.name_sbj, match.prct_sbj, match.name_qry, match.prct_qry, match.identity ) - print "nb matches 'IC': %i" % ( len(ListMatches_sup_qry) ) - print "nb matches 'II': %i" % ( len(ListMatches_inf_sbjqry) ) - - if nbMatchesInTab == 0: - print "nothing to do" - sys.exit(0) - - # For each type of matchs, record them in 2 dictionaries: Sbj2Qry and Qry2Sbj - D_all = make_dico( ListMatches_all ) - Sbj2Qry_all = D_all[0] - Qry2Sbj_all = D_all[1] - - D_sup_sbjqry = make_dico(ListMatches_sup_sbjqry) - Sbj2Qry_sup_sbjqry = D_sup_sbjqry[0] - Qry2Sbj_sup_sbjqry = D_sup_sbjqry[1] - - D_sup_sbj = make_dico(ListMatches_sup_sbj) - Sbj2Qry_sup_sbj = D_sup_sbj[0] - Qry2Sbj_sup_sbj = D_sup_sbj[1] - - D_sup_qry = make_dico(ListMatches_sup_qry) - Sbj2Qry_sup_qry = D_sup_qry[0] - Qry2Sbj_sup_qry = D_sup_qry[1] - - D_inf_sbjqry = make_dico(ListMatches_inf_sbjqry) - Sbj2Qry_inf_sbjqry = D_inf_sbjqry[0] - Qry2Sbj_inf_sbjqry = D_inf_sbjqry[1] - - - # For each type of matches, find the subjects/queries that are involve in one or several match - list_all = find_UniqRedun(ListMatches_all) - UniqSbj_all = list_all[0] - RedunSbj_all = list_all[1] - UniqQry_all = list_all[2] - RedunQry_all = list_all[3] - - list1 = find_UniqRedun(ListMatches_sup_sbjqry) - UniqSbj_sup_sbjqry = list1[0] - RedunSbj_sup_sbjqry = list1[1] - UniqQry_sup_sbjqry = list1[2] - RedunQry_sup_sbjqry = list1[3] - - list2 = find_UniqRedun(ListMatches_sup_sbj) - UniqSbj_sup_sbj = list2[0] - RedunSbj_sup_sbj = list2[1] - UniqQry_sup_sbj = list2[2] - RedunQry_sup_sbj = list2[3] - - list3 = find_UniqRedun(ListMatches_sup_qry) - UniqSbj_sup_qry = list3[0] - RedunSbj_sup_qry = list3[1] - UniqQry_sup_qry = list3[2] - RedunQry_sup_qry = list3[3] - - list4 = find_UniqRedun(ListMatches_inf_sbjqry) - UniqSbj_inf_sbjqry = list4[0] - RedunSbj_inf_sbjqry = list4[1] - UniqQry_inf_sbjqry = list4[2] - RedunQry_inf_sbjqry = list4[3] - - iStatSbj = pyRepet.util.Stat.Stat() - for subject in dSubject2DistinctQueries.keys(): - iStatSbj.add( len( dSubject2DistinctQueries[ subject ] ) ) - iStatQry = pyRepet.util.Stat.Stat() - for query in dQuery2DistinctSubjects.keys(): - iStatQry.add( len( dQuery2DistinctSubjects[ query ] ) ) - - - # Write the review of the '.tab' file - outFile = open( tabFileName + "_tabFileReader.txt", "w" ) - outFile.write( "Input: %s\n" % ( tabFileName ) ) - - outFile.write( "\n# Number of subjects in '%s': %i\n" % ( sbjFileName, nbSbj ) ) - outFile.write( "# Number of queries in '%s': %i\n" % ( qryFileName, nbQry ) ) - - outFile.write( "\nNumber of matches: %s\n" % (len(ListMatches_all))) - outFile.write( " # Number of different subjects that match: %s (Sn*=%.2f%%)\n" % ( len(Sbj2Qry_all.keys()), 100 * len(Sbj2Qry_all.keys()) / float(nbSbj) ) ) - outFile.write( " Among them, number of different subjects having exactly one match: %s (%.2f%%)\n" % ( len(UniqSbj_all), 100 * len(UniqSbj_all) / float(len(Sbj2Qry_all.keys())) ) ) - outFile.write( " Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_all))) - outFile.write( " Different queries per subject: mean=%.2f sd=%.2f min=%.2f q25=%.2f med=%.2f q75=%.2f max=%.2f\n" % ( iStatSbj.mean(), iStatSbj.sd(), iStatSbj.min, iStatSbj.quantile(0.25), iStatSbj.median(), iStatSbj.quantile(0.75), iStatSbj.max ) ) - outFile.write( " # Number of different queries that match: %s (Sp*=%.2f%%)\n" % ( len(Qry2Sbj_all.keys()), 100 * len(Qry2Sbj_all.keys()) / float(nbQry) ) ) - outFile.write( " Among them, number of different queries having exactly one match: %s (%.2f%%)\n" % ( len(UniqQry_all), 100 * len(UniqQry_all) / float(len(Qry2Sbj_all.keys())) ) ) - outFile.write( " Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_all)) ) - outFile.write( " Different subjects per query: mean=%.2f sd=%.2f min=%.2f q25=%.2f med=%.2f q75=%.2f max=%.2f\n" % ( iStatQry.mean(), iStatQry.sd(), iStatQry.min, iStatQry.quantile(0.25), iStatQry.median(), iStatQry.quantile(0.75), iStatQry.max ) ) - - outFile.write( "\nNumber of matches with L >= %i%% for subject & query: %i\n" % ( thresholdCoverage, len(ListMatches_sup_sbjqry) ) ) - outFile.write( " # Number of different subjects in the 'CC' case: %s (%.2f%%)\n" % ( len(Sbj2Qry_sup_sbjqry), 100 * len(Sbj2Qry_sup_sbjqry) / float(nbSbj) ) ) - outFile.write( " Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_sup_sbjqry))) - outFile.write( " Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_sup_sbjqry))) - outFile.write( " # Number of different queries in the 'CC' case: %s (%.2f%%)\n" % ( len(Qry2Sbj_sup_sbjqry), 100 * len(Qry2Sbj_sup_sbjqry) / float(nbQry) ) ) - outFile.write( " Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_sup_sbjqry))) - outFile.write( " Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_sup_sbjqry))) - - outFile.write( "\nNumber of matches with L >= %i%% for subject and L < %i%% for query: %i\n" % ( thresholdCoverage, thresholdCoverage, len(ListMatches_sup_sbj) ) ) - outFile.write( " Number of different subjects in that case: %s\n" % (len(Sbj2Qry_sup_sbj))) - outFile.write( " Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_sup_sbj))) - outFile.write( " Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_sup_sbj))) - outFile.write( " Number of different queries in that case: %s\n" % (len(Qry2Sbj_sup_sbj))) - outFile.write( " Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_sup_sbj))) - outFile.write( " Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_sup_sbj))) - - outFile.write( "\nNumber of matches with L < %i%% for subject and L >= %i%% for query: %i\n" % ( thresholdCoverage, thresholdCoverage, len(ListMatches_sup_qry) ) ) - outFile.write( " Number of different subjects in that case: %s\n" % (len(Sbj2Qry_sup_qry))) - outFile.write( " Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_sup_qry))) - outFile.write( " Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_sup_qry))) - outFile.write( " Number of different queries in that case: %s\n" % (len(Qry2Sbj_sup_qry))) - outFile.write( " Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_sup_qry))) - outFile.write( " Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_sup_qry))) - - outFile.write( "\nNumber of matches with L < %i%% for subject & query: %i\n" % ( thresholdCoverage, len(ListMatches_inf_sbjqry) ) ) - outFile.write( " Number of different subjects in that case: %s\n" % (len(Sbj2Qry_inf_sbjqry))) - outFile.write( " Among them, number of different subjects having exactly one match: %s\n" % (len(UniqSbj_inf_sbjqry))) - outFile.write( " Among them, number of different subjects having more than one match: %s\n" % (len(RedunSbj_inf_sbjqry))) - outFile.write( " Number of different queries in that case: %s\n" % (len(Qry2Sbj_inf_sbjqry))) - outFile.write( " Among them, number of different queries having exactly one match: %s\n" % (len(UniqQry_inf_sbjqry))) - outFile.write( " Among them, number of different queries having more than one match: %s\n" % (len(RedunQry_inf_sbjqry))) - - - # For the elements already counted in the matches with L >= 95% for subject & query, remove them from the other dictionnaries - rmv_Sbj2Qry = remove( Sbj2Qry_all, Sbj2Qry_sup_sbjqry, Sbj2Qry_sup_sbj, Sbj2Qry_sup_qry, Sbj2Qry_inf_sbjqry ) - rmv_Qry2Sbj = remove( Qry2Sbj_all, Qry2Sbj_sup_sbjqry, Qry2Sbj_sup_sbj, Qry2Sbj_sup_qry, Qry2Sbj_inf_sbjqry ) - - outFile.write("\n\nAfter removal of the subjects/queries already counted in the matches with L >= %i%% for them:\n" % ( thresholdCoverage ) ) - - outFile.write( "\nMatches with L >= %i%% for subject and L < %i%% for query:\n" % ( thresholdCoverage, thresholdCoverage ) ) - outFile.write( " # Number of different subjects in the 'CI' case: %s (%.2f%%)\n" % ( len(rmv_Sbj2Qry[0]), 100*len(rmv_Sbj2Qry[0])/float(nbSbj) ) ) - outFile.write( " # Number of different queries in the 'CI' case: %s (%.2f%%)\n" % ( len(rmv_Qry2Sbj[0]), 100*len(rmv_Qry2Sbj[0])/float(nbQry) ) ) - - outFile.write( "\nMatches with L < %i%% for subject and L >= %i%% for query:\n" % ( thresholdCoverage, thresholdCoverage ) ) - outFile.write( " # Number of different subjects in the 'IC' case: %s (%.2f%%)\n" % (len(rmv_Sbj2Qry[1]), 100*len(rmv_Sbj2Qry[1])/float(nbSbj) ) ) - outFile.write( " # Number of different queries in the 'IC' case: %s (%.2f%%)\n" % (len(rmv_Qry2Sbj[1]), 100*len(rmv_Qry2Sbj[1])/float(nbQry) ) ) - - outFile.write( "\nMatches with L < %i%% for subject & query:\n" % ( thresholdCoverage ) ) - outFile.write( " # Number of different subjects in the 'II' case: %s (%.2f%%)\n" % (len(rmv_Sbj2Qry[2]), 100*len(rmv_Sbj2Qry[2])/float(nbSbj) ) ) - outFile.write( " # Number of different queries in the 'II' case: %s (%.2f%%)\n" % (len(rmv_Qry2Sbj[2]), 100*len(rmv_Qry2Sbj[2])/float(nbQry) ) ) - - outFile.write("\n==========================================================================\n") - - write_output( outFile, 'CC', Sbj2Qry_sup_sbjqry, dSbj2Cat, Qry2Sbj_sup_sbjqry, dQry2Cat ) - - outFile.write("\n==========================================================================\n") - - write_output( outFile, 'CI', rmv_Sbj2Qry[0], dSbj2Cat, rmv_Qry2Sbj[0], dQry2Cat ) - - outFile.write("\n==========================================================================\n") - - write_output( outFile, 'IC', rmv_Sbj2Qry[1], dSbj2Cat, rmv_Qry2Sbj[1], dQry2Cat ) - - outFile.write("\n==========================================================================\n") - - write_output( outFile, 'II', rmv_Sbj2Qry[2], dSbj2Cat, rmv_Qry2Sbj[2], dQry2Cat ) - - outFile.write("\n==========================================================================\n") - - outFile.close() - - writeSubjectCategory( dSbj2Cat ) - writeQueryCategory( dQry2Cat ) - - if verbose > 0: - print "END %s" % (sys.argv[0].split("/")[-1]) - sys.stdout.flush() - - return 0 - -#----------------------------------------------------------------------------------------------------- - -if __name__ == "__main__": - main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/MockFastaForReplaceGreaterThanSymbolInFastaHeader.py --- a/commons/tools/tests/MockFastaForReplaceGreaterThanSymbolInFastaHeader.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -class MockFastaForReplaceGreaterThanSymbolInFastaHeader(object): - def write(self, inFileName): - f = open(inFileName, 'w') - f.write(">sp|P0A2V0|NDVA_AGRT5 Beta-(1-->2)glucan export ATP-binding/permease protein ndvA OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=ndvA PE=3 SV=1\n") - f.write("MTLFQVYTRALRYLTVHKWRVAVVVIANVILAAITIAEPVLFGRIIDAISSGTNVTPILI\n") - f.write("LWAGFGVFNTVAYVAVAREADRLAHGRRATLLTEAFGRIISMPLSWHHLRGTSNALHTLL\n") - f.write("RASETLFGLWLEFMRTHLATFVALVLLIPTAMAMDLRLSFVLIGLGIVYWFIGKWVMGRT\n") - f.write("KDGQASVEEHYHSVFAHVSDSISNVSVLHSYNRIEAETKALKSFTEKLLSAQYPVLDWWA\n") - f.write("FASALNRTASTVSMMIILVIGTVLVKNGELRVGDVIAFIGFANLLIGRLDQMRQFVTQIF\n") - f.write("EARAKLEDFFVLEDAVKEREEPGDARELSNVSGTVEFRNINFGFANTKQGVHDVSFTAKA\n") - f.write("GETVAIVGPTGAGKTTLINLLQRVYDPDSGQILIDGTDISTVTKNSLRNSIATVFQDAGL\n") - f.write("LNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERGNRLSGGERQRI\n") - f.write("AIARAILKNAPILVLDEATSALDVETEARVKAAVDALRKNRTTFIIAHRLSTVRDADLVL\n") - f.write("FLDQGRIIEKGTFDELTQRGGRFTSLLRTSGLLTEDEGQQPRPKAIAS\n") - f.write(">sp|Q694C1|ABC3G_GORGO DNA dC->dU-editing enzyme APOBEC-3G OS=Gorilla gorilla gorilla GN=APOBEC3G PE=2 SV=1\n") - f.write("MTPQFRNTVERMYRDTFSYNFNNRPILSRRNTVWLCYEVKTKDPSRPPLDAKIFRGQVYS\n") - f.write("ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRNVATFLAEDPKVTLTIFV\n") - f.write("ARLYYFWDQDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK\n") - f.write("YYMLLHIMLGEILRHSMDPPTFTSNFNNEHWVRGRHETYLCYEVERLHNDTWVLLNQRRG\n") - f.write("FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLHQDYRVTCFTSWSPCFSCAQEMAKFIS\n") - f.write("NKKHVSLCIFAARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVYHQGCPFQP\n") - f.write("WDGLEEHSQALSGRLQAILQNQGN\n") - f.write(">sp|P0A4M1|ZTOX_ENTFA Zeta-toxin OS=Enterococcus faecalis PE=3 SV=1\n") - f.write("MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAISEETQGN\n") - f.write("VVIIDNDTFKQQHPNFDELVKLYEKDVVKYVTPYSNRMTEAIISRLRDKGYNLVIEGTGR\n") - f.write("TTDVPIQTATMLQAKDYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDI\n") - f.write("VVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLERELNRKVSGKEIQ\n") - f.write("PTLERIEQKMVQNQHQETPEFKAIQQKMESLQPPTPPIPKTPKLPGI\n") - f.close() - -class MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan(object): - def write(self, inFileName): - f = open(inFileName, 'w') - f.write(">sp|P0A2V0|NDVA_AGRT5 Beta-(1 to 2)glucan export ATP-binding/permease protein ndvA OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=ndvA PE=3 SV=1\n") - f.write("MTLFQVYTRALRYLTVHKWRVAVVVIANVILAAITIAEPVLFGRIIDAISSGTNVTPILI\n") - f.write("LWAGFGVFNTVAYVAVAREADRLAHGRRATLLTEAFGRIISMPLSWHHLRGTSNALHTLL\n") - f.write("RASETLFGLWLEFMRTHLATFVALVLLIPTAMAMDLRLSFVLIGLGIVYWFIGKWVMGRT\n") - f.write("KDGQASVEEHYHSVFAHVSDSISNVSVLHSYNRIEAETKALKSFTEKLLSAQYPVLDWWA\n") - f.write("FASALNRTASTVSMMIILVIGTVLVKNGELRVGDVIAFIGFANLLIGRLDQMRQFVTQIF\n") - f.write("EARAKLEDFFVLEDAVKEREEPGDARELSNVSGTVEFRNINFGFANTKQGVHDVSFTAKA\n") - f.write("GETVAIVGPTGAGKTTLINLLQRVYDPDSGQILIDGTDISTVTKNSLRNSIATVFQDAGL\n") - f.write("LNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERGNRLSGGERQRI\n") - f.write("AIARAILKNAPILVLDEATSALDVETEARVKAAVDALRKNRTTFIIAHRLSTVRDADLVL\n") - f.write("FLDQGRIIEKGTFDELTQRGGRFTSLLRTSGLLTEDEGQQPRPKAIAS\n") - f.write(">sp|Q694C1|ABC3G_GORGO DNA dC to dU-editing enzyme APOBEC-3G OS=Gorilla gorilla gorilla GN=APOBEC3G PE=2 SV=1\n") - f.write("MTPQFRNTVERMYRDTFSYNFNNRPILSRRNTVWLCYEVKTKDPSRPPLDAKIFRGQVYS\n") - f.write("ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRNVATFLAEDPKVTLTIFV\n") - f.write("ARLYYFWDQDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK\n") - f.write("YYMLLHIMLGEILRHSMDPPTFTSNFNNEHWVRGRHETYLCYEVERLHNDTWVLLNQRRG\n") - f.write("FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLHQDYRVTCFTSWSPCFSCAQEMAKFIS\n") - f.write("NKKHVSLCIFAARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVYHQGCPFQP\n") - f.write("WDGLEEHSQALSGRLQAILQNQGN\n") - f.write(">sp|P0A4M1|ZTOX_ENTFA Zeta-toxin OS=Enterococcus faecalis PE=3 SV=1\n") - f.write("MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAISEETQGN\n") - f.write("VVIIDNDTFKQQHPNFDELVKLYEKDVVKYVTPYSNRMTEAIISRLRDKGYNLVIEGTGR\n") - f.write("TTDVPIQTATMLQAKDYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDI\n") - f.write("VVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLERELNRKVSGKEIQ\n") - f.write("PTLERIEQKMVQNQHQETPEFKAIQQKMESLQPPTPPIPKTPKLPGI\n") - f.close() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_AlignTEOnGenomeAccordingToAnnotation.py --- a/commons/tools/tests/Test_AlignTEOnGenomeAccordingToAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,304 +0,0 @@ -from commons.core.seq.Bioseq import Bioseq -from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB -from commons.core.sql.DbFactory import DbFactory -from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.coord.Path import Path -import os -import unittest -from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation - -class Test_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase): - - def test_alignBioseqWithNWalign(self): - iBioseq1 = Bioseq("dmel_chr4", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAGTAGAAGAAA") - iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTTCTTCTACCTATTACATACTTTTCAACAAATCTAGCATACCCTTTTACTCTACGAGTA") - iAlignedBioseq1 = Bioseq("dmel_chr4 Score=58 Identity=0.7", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTT-TAGA-AGTACGTTACTAGTAGAAGAAA----------------------------") - iAlignedBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat Score=58 Identity=0.7", "----------------------------TTTCTTCTACCTATTACAT-ACTTTTC-AACAAATCTAGCATACCCTTTTACTCTACGAGTA") - expiAlignedBioseqDB = AlignedBioseqDB() - expiAlignedBioseqDB.add(iAlignedBioseq1) - expiAlignedBioseqDB.add(iAlignedBioseq2) - - iATEOGATA = AlignTEOnGenomeAccordingToAnnotation() - obsiAlignedBioseqDB = iATEOGATA.alignBioseqWithNWalign(iBioseq1, iBioseq2) - - self.assertEquals(expiAlignedBioseqDB, obsiAlignedBioseqDB) - - def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_one_path(self): - iBioseq1 = Bioseq("dmel_chr4", "TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA") - iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC") - iPath = Path() - iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67)) - - seqTable1 = "seqTable1_seq" - seqTable2 = "seqTable2_seq" - pathTable = "pathTable_path" - - iDb = DbFactory.createInstance() - iDb.createTable(seqTable1, "seq", overwrite = True) - iDb.createTable(seqTable2, "seq", overwrite = True) - iDb.createTable(pathTable, "path", overwrite = True) - - iTSA1 = TableSeqAdaptator(iDb, seqTable1) - iTSA2 = TableSeqAdaptator(iDb, seqTable2) - iTPA = TablePathAdaptator(iDb, pathTable) - iTSA1.insert(iBioseq1) - iTSA2.insert(iBioseq2) - iTPA.insert(iPath) - - expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),) - - iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTable, seqTable1, seqTable2) - iATEOGATA.setMergeSamePathId(True) - iATEOGATA.setDbInstance(iDb) - iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable() - - #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator - sqlCmd = "SELECT * FROM %s_align" % pathTable - iDb.execute(sqlCmd) - obsTTuples = iDb.fetchall() - - iDb.dropTable(seqTable1) - iDb.dropTable(seqTable2) - iDb.dropTable(pathTable) - iDb.dropTable("%s_align" % pathTable) - iDb.close() - - self.assertEquals(expTTuples, obsTTuples) - - def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_n_paths(self): - queryTableName = "query_seq" - subjectTableName = "subject_seq" - pathTableName = "table_path" - - iDb = DbFactory.createInstance() - queryFileName = "dummyDmelChr4.fa" - self._writeDummyDmelChr4(queryFileName) - iDb.createTable(queryTableName, "seq", queryFileName, True) - os.remove(queryFileName) - iDb.createTable(subjectTableName, "seq", overwrite = True) - iDb.createTable(pathTableName, "path", overwrite = True) - - iTSA = TableSeqAdaptator(iDb, subjectTableName) - iTPA = TablePathAdaptator(iDb, pathTableName) - iBioseq1 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC") - iBioseq2 = Bioseq("DmelChr4-B-R4-Map5_NoCat", "CCAAAATTGCCCTCTTTCCGCTCGCTCACGCTGAGAGCATAAGAAATCTAAAAATAGAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGTGTGCGTGTTGTGCTAGAAGACTATTTTCGGGCCGAAATCAATTCTGATCGAAAAAACGAATTTACATTGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAATAAAATAATTTTTAAAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTAAAATTTGTTTGTTAAAATCGCCGATCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTTGAAACACTTTTAATGTTAAAAATGACTTAATAAATATACTAAATAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAAAATATGATAACTGTTTATTGCAAAAGTCATATCAAAGACACTAGAATTATTCTAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAAAGTCAAAGAACTTCTAAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACAGTTGTCTGCTATCACTTTATGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTCCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCGAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGGTA") - iBioseq3 = Bioseq("DmelChr4-B-G9-Map3_NoCat", "ACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAATATGATAACTGTTTATTGCAAAAGTAATATCAAAGACACTAGAATAATTCTAATGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCGCACTTCGTGC") - iTSA.insert(iBioseq1) - iTSA.insert(iBioseq2) - iTSA.insert(iBioseq3) - iPath = Path() - iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67)) - iTPA.insert(iPath) - iPath.setFromTuple((28, "dmel_chr4", 280, 1380, "DmelChr4-B-G9-Map3_NoCat", 3, 1100, 0, 7456, 94.400000))#28 => seems to be a join from "long join" - iTPA.insert(iPath) - iPath.setFromTuple((28, "dmel_chr4", 8971, 9459, "DmelChr4-B-G9-Map3_NoCat", 1102, 1590, 0, 758, 96.707800)) - iTPA.insert(iPath) - iPath.setFromTuple((30, "dmel_chr4", 9815, 9826, "DmelChr4-B-G9-Map3_NoCat", 574, 563, 0, 4, 78.162700))#30 => seems to be a join from "matcher" - iTPA.insert(iPath) - iPath.setFromTuple((30, "dmel_chr4", 9957, 10047, "DmelChr4-B-G9-Map3_NoCat", 429, 337, 0, 33, 78.162700)) - iTPA.insert(iPath) - iPath.setFromTuple((30, "dmel_chr4", 10094, 10127, "DmelChr4-B-G9-Map3_NoCat", 290, 256, 0, 13, 78.162700)) - iTPA.insert(iPath) - - expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),\ - (28, "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGCGCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAAT-----------TT-------GTT---------------ATGTTTAATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAA-CACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAATTAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA--AATATGATA---ACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCAAA-CAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGAACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACACATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTACGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATAAGGCAATGATTGTTG----CTTGTGTCCGTCCGCACTTCGTGC", "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCT------CT--CATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAA-----------------TATGATAACT---GT--TT------ATTGCA-AAAGTAATATCAAAGACACTAGAATAATTCTAATG------CTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCG----CACTTCGTGC", 13732, 96.1763),\ - (30, "------------------------------------ACATTTACAT-TTTTTGAATTTGTGGG-------CGTGGCA-GAACGGGCAATAT-GTATGCATA---ATATGTATGCATAATCTCTACCTTCTTGCTTTTATAGTTCCTGAGACCTCGACGTTCATACGGACAGACGAAATATGCGAAA", "ACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGC--TACCGTTTACACATTTATATTTATGTTTAAT-TCTAATTTGTCAATATCAAAGAC-------------------------------------------", 158, 64.835200000000004)) - - iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName) - iATEOGATA.setMergeSamePathId(True) - iATEOGATA.setDbInstance(iDb) - iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable() - - #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator - sqlCmd = "SELECT * FROM %s_align" % pathTableName - iDb.execute(sqlCmd) - obsTTuples = iDb.fetchall() - - iDb.dropTable(queryTableName) - iDb.dropTable(subjectTableName) - iDb.dropTable(pathTableName) - iDb.dropTable("%s_align" % pathTableName) - iDb.close() - - self.assertEquals(expTTuples, obsTTuples) - - def _writeDummyDmelChr4(self, fileName): - with open(fileName, "w") as f: - f.write(">dmel_chr4\n") - f.write("TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA\n") - f.write("TGTTGGTATTAATGGTCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAG\n") - f.write("AATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAG\n") - f.write("AAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTAC\n") - f.write("TTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGCAAAGACACTAGAATAACAAG\n") - f.write("ATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAA\n") - f.write("ATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCT\n") - f.write("TGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAA\n") - f.write("GACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTA\n") - f.write("GGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGC\n") - f.write("GCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAATTTGTTATGTTTA\n") - f.write("ATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTA\n") - f.write("AACACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAAT\n") - f.write("TAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA\n") - f.write("AATATGATAACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGT\n") - f.write("GCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAAT\n") - f.write("ACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATAT\n") - f.write("GTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCA\n") - f.write("AACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGA\n") - f.write("ACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACA\n") - f.write("CATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTC\n") - f.write("GCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCC\n") - f.write("AAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTG\n") - f.write("GTAAAATGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAAAAGAAAGCGTTTTCGA\n") - f.write("CCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGC\n") - f.write("CATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCA\n") - f.write("CAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTG\n") - f.write("TCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCA\n") - f.write("TCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGT\n") - f.write("TCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGC\n") - f.write("TTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTA\n") - f.write("TAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTA\n") - f.write("CGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTAT\n") - f.write("TGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATT\n") - f.write("TTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCT\n") - f.write("TTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTA\n") - f.write("TTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTT\n") - f.write("GGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTC\n") - f.write("CTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGT\n") - f.write("TTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTA\n") - f.write("ACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACC\n") - f.write("GTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCA\n") - f.write("TAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAA\n") - f.write("ACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAA\n") - f.write("AAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCA\n") - f.write("TCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATA\n") - f.write("TCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAA\n") - f.write("AATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATA\n") - f.write("ACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCA\n") - f.write("TCGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACT\n") - f.write("CTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATT\n") - f.write("AATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGT\n") - f.write("ATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTAT\n") - f.write("TCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTA\n") - f.write("ATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGAT\n") - f.write("AGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCC\n") - f.write("GTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTA\n") - f.write("TTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGA\n") - f.write("TCGACTCGCATATTGATGCTGATCAAGAATATTTATATTTTACATGATCGGAAACGCTTC\n") - f.write("ATTGCTCTACGAGTAATGGGTACAATAATTTAAAACAAACATATTAAAAGTATAGCAAAA\n") - f.write("CCCTATCTGAAGGACTAAAATTTTATCGCATTTTAAAATTTGTTGCATTAAAATCTTTGA\n") - f.write("TAACCTTTCGTTGAATTAGGTGCTTCGACTTTTTTTACCCTAAGAACAATTTCGATTTGG\n") - f.write("CATACATTGAAAACGTAGAAACTCAACCCTGCATTCATTCATAGAACTTATAAAGAGCTA\n") - f.write("CATCTTCGAAAATAAAAAAAAGGTTTGTTTTTAAGACTTAATGCGTACAATGTCGCTTTC\n") - f.write("GACATTAGGGTATTGCTAGAATTAATATTCGCTTTGTTGTTTACTTTTCCAAACAAACAT\n") - f.write("AATGGGTAAACCAAAAAAATGGGAAACGTCAGTATTAAGTGCTATCGAAAACGTTTAGAA\n") - f.write("TATGGAGAATCTAGTTGTTATTACCAAAACGCATAAATACTAAGCATATACTAAAACAAA\n") - f.write("ATAGAAAAAGATAATGTTTATTTTAGACTCACCTTAGCAAACAGCAACTTATTCGACGGC\n") - f.write("GAATCTTTTCCAAGTCTGTGCTCTGATGTTAAACAAGCGTCCATAAATGTTTGTGCAATG\n") - f.write("ACACTTAAACAGGAATCAACGCTGTATGTTTTATTTACATCAAATATAAAATCCGGATTT\n") - f.write("TTTATAAAATTAACCCAGAATCGAAGGGGCAAACAATTTGACTTCCAAGCGTGCACAATA\n") - f.write("TCAGTATCAGCAATATCATGGCGTCGCGCAGCTTCATCAAGTAAGTCAAAGAGCCATTTA\n") - f.write("ACGGCAGGTGGCAACTCCTCATTAACAGTTAAAATAATTGAGAAAAAATCATCAACAAAT\n") - f.write("TTTTGTATAGTTCCTTTTGTGGCCAGAAGACGCGTAAGGTAAACTTCTGGTATTGTTTTG\n") - f.write("TTCACCCTGTCATTACAATTATTAACGACATGCGATTGAAATGCTGGTGATCCTCCGGAT\n") - f.write("AACACGGAATTTTTAATGTTCATATAATGATCAGGTATATTGGGCTTAACAAGATGGTAA\n") - f.write("ACCCGGGGCTGCTGCAAACCTGATTCGATATCATTATTAATTATAATATGACTTTGCGAA\n") - f.write("TTGTTTATAAAATAAACTGCAAAAAGGCAAAACAATTAATTAAAAAATTTTTAGATATTG\n") - f.write("GGCTTAGTACTTACAATTGTGGTATGGTGCCGAATTTTGGTTTTTACTGTATGGTATATG\n") - f.write("ATAATTATCATTTTGACGTGCAATTAGTGACATTACTGCAGATTCTTTGACTCCATAATG\n") - f.write("AGCTAATGTGTTAAGGCGCTTCCATCCGTTAACGGTTTTGGTTGTCAAGTCTTCATCTTG\n") - f.write("TAATGTAAGATGACCTCCTCGGCCGTGCCTCCATTCTAAGTCTACTTCGTTTACAGATGG\n") - f.write("CCTCATAGAGAAAGGAGTGTTTTTAAAAATTGCGTCGAGGATTTTAAGCTTAACTTGAGA\n") - f.write("AATGGTATCCCAATCGTTAACGCGACATTGGACTTTTTCATCAAGATCATCTTGTAAAAT\n") - f.write("ATGCTATATTACAACAGAATGGGTAACTTGTTCATGCAGAAGACGTTCTTCTGAAAGGGA\n") - f.write("GTAACGGGCATCGTTGGTTATTGCGTCCACTAAACCCTTTTCAATTTGATGCTTTATTGC\n") - f.write("TTTGAAGAGCAAAAATAAATTTGATCCGGCGTACTCTTTCAGGTAATCGTACATACAAAT\n") - f.write("TGCTAGGTAGTTGGTCAACATTTTTTCAACAACGCTTTCAGTACGCCTTAGCATCAGCTG\n") - f.write("AGGATGTTTGCTGGCAAGTGATTTATCTATCAAACGTAATAAAAGGGACTTCAAAATTTC\n") - f.write("CGTGGCATATTCCATCTTGTTCATTAAAACAACCATTATTAATGAGGCAACGTTAACTCG\n") - f.write("GTCTCTAATAGAAAATGATGAACGTTGAGCTTCTAATGTTTCTATGAACATTAATAAAAA\n") - f.write("ATATTTATTGCCAATCAGTTGTTCAAATTGTACCATAGCTGCGTCATAGTTAGTCTGTGG\n") - f.write("GCTACCTTCACGAAATTTTGGAGAATTTAAAATAGGATGATCTGATACACCAGGGAAAAA\n") - f.write("CACCTTCATAATATAGTTGACGTGATCTAAAGTTGGTATGCCTGTGCTCTCCAAATCTGC\n") - f.write("TGTTAGGTCGGTCATGTCCGTTTGGAGCTCAGCGAATGCCTGTTTACACTCAGAACGTAC\n") - f.write("GTTGCTTTCTAATGTAATCATCTGTATCTGAATACGTTTATACTCGCGTTCTGCTTGTGT\n") - f.write("TGATTTCCTTCTGAATATTATAAGTACAATTACAAAAACAACGACCAGAAGTGCTACCGT\n") - f.write("TAATATGCCGACTAACAAGGCATGTGAGAAAACATAGGGTTTATTTAAATCATACTTAAG\n") - f.write("ATATCCTATTACAAAACGAAGATTTCGACCTACTTTAACGACAACAAGAGGTAAATCAGT\n") - f.write("TGATTGATCCACACCATTTTCATCAGTTGGAAGTGGTTGTTGCTCCGGCGGAATGCATAA\n") - f.write("AAGTTGGTTAAGTGCCAGGCTGGTAATATTGCATTGGGAAGTTCCAATAGTTACATTTAC\n") - f.write("ATCGTACTCATCAGCTGCCAAGTTTAATAGCTCGCCTTCTATGACCAAGCTGTCACCCTT\n") - f.write("GTAGAGTTTAACGCCGTCGTTGGGAAATGGCAAATATTTTGGGTCTGCTAAATAGACAAT\n") - f.write("AGTGCTCCTTATGTCATGAAAATATTTATTCAAGTTTCGAACTAGTTGTACATTGTCCAT\n") - f.write("TACAAAACTTAGTTGTAAGTTAAATTGAGTTTCATGAACCTTAACGAATGTGGTGACGTC\n") - f.write("CATATTATTGTTAACAAAATAGTTGGCTGAAGATCCTGCATTTGTGTATAAGCGAAAAGT\n") - f.write("GTCTCCAAAGTCGGCTCGCCGCTTTTTTCTATCATATTCATTTTTATACCTGGTTTCAGT\n") - f.write("TTGAAACGAAGAATTTTGTAAGTGCAATTCAGTATCCATCTTTCTGTTCGTCTTTTTAAA\n") - f.write("AGTCTCAAATTTTTAATTTACCGGAGGAGATGGACATTCCATTTGATTAGAGTTGATCAC\n") - f.write("CACACAAGATGTTTTATTTACTCTTTCATTGTCATAAAACACTTCTAGTTCAGGTTTTTG\n") - f.write("GTTTTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGTTCAGTGTTTGTT\n") - f.write("GGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATT\n") - f.write("TCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAAC\n") - f.write("TTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGT\n") - f.write("TAGTCTTAATAATACCCGTACTTGTAGAGTAAAAGGGTATGCTAGATTTGTAGAAAAGTA\n") - f.write("TGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGG\n") - f.write("ATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAG\n") - f.write("AGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCG\n") - f.write("ATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACT\n") - f.write("TTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAAT\n") - f.write("ATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGG\n") - f.write("GAAACTCAACCATAACATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAA\n") - f.write("GAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTAT\n") - f.write("ATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCA\n") - f.write("ACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAAT\n") - f.write("GGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGT\n") - f.write("TATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTA\n") - f.write("AGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGT\n") - f.write("CAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCC\n") - f.write("TTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAG\n") - f.write("TCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGG\n") - f.write("CTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAG\n") - f.write("ATATAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATAT\n") - f.write("TTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTCTCTTA\n") - f.write("CATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAA\n") - f.write("ATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTAAAAAATCATATTG\n") - f.write("ATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCG\n") - f.write("TGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACA\n") - f.write("AAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGA\n") - f.write("TCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCT\n") - f.write("TCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGT\n") - f.write("GGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCC\n") - f.write("TGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACT\n") - f.write("TATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAAT\n") - f.write("ATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATT\n") - f.write("TGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATA\n") - f.write("GGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACA\n") - f.write("GAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATT\n") - f.write("TTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTA\n") - f.write("TATTTTCATACGGACGGACATGGCCAGATCAAAGACACTAGAATAACAAGATGCGTAACG\n") - f.write("CCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCT\n") - f.write("CTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTA\n") - f.write("CGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATT\n") - f.write("TGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGAT\n") - f.write("CAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAA\n") - f.write("AATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATG\n") - f.write("ACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATA\n") - f.write("AGGCAATGATTGTTGCTTGTGTCCGTCCGCACTTCGTGCCTCAAGATATGACCAAAACAA\n") - f.write("AGACACTAGAATAATTCTAGTGTCTTTGATGTGACTTTTGCAATAAACAGTTTTCATATT\n") - f.write("TTTATTTATTTTACAAATTTTTATTTTCTACTTCGTATTATTTTTATGAAATATTTATTT\n") - f.write("CTCGATGTAATGTATTCCTTTTGTTATAAGTAGTTATAATAATTTATATTTTACTTCCTT\n") - f.write("CAATATCACAAAATAAATTTCAAGTATGGCTTTATATTAGAATAATTGTCATTAAATTAT\n") - f.write("TCAGCTTGGGACGTGGGAAAAATTAGAGTAGACATGTCTAGTAGACATCGATTCTTAGGT\n") - f.write("GCTTCTGACCGCACGTCGTGCCTCAAGAAATCAATTTCGCATATTTATACCCATTATTTC\n") - f.write("TAGAGTAAAAGGGTATACTACATTCGTTGAAAAGTATGTAACAGGCAGAAGAAAGCGTTT\n") - f.write("CCGACTATATAATGTATAAAGATCAGGATCAACAGCCGAGTCGATCTGGCCATGTCCGTC\n") - f.write("TGTCCGTATGAACGTCGAGGTCTCAGGAACTATAAAAGCAAGAAGGTAGAGATTATGCAT\n") - f.write("ACATATTATGCATACATATTGCCCGTTGACCCATGTTGTCACGCCCACTCTAACGTCCAC\n") - f.write("AAACCGCACAAAACTGCCACGCCCACAAATTCAAAAAATGTAAATGTAATTGACCAAATT\n") - f.write("TAACAAAACTCTAAAAATGTAACTTTGTTTCTTAGATCAAAATTTAGACCAGAAAATCGT\n") - f.write("CTTCATCTTCTAATGTTTTTACTCACACAAGAAAGCAAATTCTATTTTTAGATTTTAAAG\n") - f.write("TACTCCATTTTACGCGAGCGGAGAGAGAGAGCAATTTTGGCCGTCACCAAAAAAGTGTCT\n") - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_CalcCoordCumulLength.py --- a/commons/tools/tests/Test_CalcCoordCumulLength.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -import unittest -import os -import time -from commons.tools.CalcCoordCumulLength import CalcCoordCumulLength -from commons.core.utils.FileUtils import FileUtils -from pyRepet.util.Stat import Stat - - -class Test_CalcCoordCumulLength( unittest.TestCase ): - - def setUp( self ): - self._i = CalcCoordCumulLength() - self._uniqId = time.strftime("%Y%m%d%H%M%S") - - - def tearDown( self ): - self._i = None - self._uniqId = None - - - def test_mergeCoordinates( self ): - inFileName = "dummyInFile_%s" %( self._uniqId ) - inF = open( inFileName, "w" ) - inF.write( "TE1\tchr1\t101\t200\n" ) - inF.write( "TE2\tchr1\t401\t600\n" ) - inF.write( "TE2\tchr1\t451\t500\n" ) - inF.close() - expFileName = "dummyExpFile_%s" %( self._uniqId ) - expF = open( expFileName, "w" ) - expF.write( "TE1\tchr1\t101\t200\n" ) - expF.write( "TE2\tchr1\t401\t600\n" ) - expF.close() - self._i.setInputFileName( inFileName ) - obsFileName = self._i.mergeCoordinates() - self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [ inFileName, expFileName, obsFileName ]: os.remove( f ) - - - def test_getStatsPerChr( self ): - inFileName = "dummyInFile_%s" %( self._uniqId ) - inF = open( inFileName, "w" ) - inF.write( "TE1\tchr1\t101\t200\n" ) - inF.write( "TE2\tchr1\t401\t600\n" ) - inF.write( "TE1\tchr2\t1301\t1600\n" ) - inF.close() - dExp = { "chr1": Stat(), "chr2": Stat() } - dExp["chr1"].add( 200-101+1 ) - dExp["chr1"].add( 600-401+1 ) - dExp["chr2"].add( 1600-1301+1 ) - dObs = self._i.getStatsPerChr( inFileName ) - self.assertEqual( dObs, dExp ) - - - def test_zRunAsScript( self ): - cDir = os.getcwd() - inFileName = "dummyInFile_%s" %( self._uniqId ) - inF = open( inFileName, "w" ) - inF.write( "TE1\tchr1\t101\t200\n" ) - inF.write( "TE2\tchr1\t401\t600\n" ) - inF.write( "TE2\tchr1\t451\t500\n" ) - inF.close() - outFileName = "dummyOutFile_%s" %( self._uniqId ) - cmd = "CalcCoordCumulLength.py" - cmd += " -i %s" % ( inFileName ) - cmd += " -o %s" % ( outFileName ) - cmd += " -v 0" - log = os.system( cmd ) - self.assertTrue( log == 0 ) - - for f in [ inFileName, outFileName ]: os.remove( f ) - os.chdir( cDir ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_ChangeSequenceHeaders.py --- a/commons/tools/tests/Test_ChangeSequenceHeaders.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,428 +0,0 @@ -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -import unittest -import os -import time -from commons.core.utils.FileUtils import FileUtils -from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders - - -class Test_ChangeSequenceHeaders( unittest.TestCase ): - - def setUp( self ): - self._i = ChangeSequenceHeaders() - self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) - - - def tearDown( self ): - self._i = None - self._uniqId = None - - - def test_script_no_input_file( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 1" - cmd += " -p TE" - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertFalse( exitStatus == 0 ) - - os.chdir( cDir ) - - - def test_shortenSequenceHeadersForFastaFile_fasta_script( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( ">DmelChr4-B-G387-MAP16\nATGTACGATGACGATCAG\n" ) - inF.write( ">consensus524\nGTGCGGATGGAACAGT\n" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( ">TE1\nATGTACGATGACGATCAG\n" ) - expF.write( ">TE2\nGTGCGGATGGAACAGT\n" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 1" - cmd += " -p TE" - cmd += " -l %s" % ( linkFile ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - - def test_retrieveInitialSequenceHeaders_fasta_script( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( ">seq2\nATGTACGATGACGATCAG\n" ) - inF.write( ">seq1\nGTGCGGATGGAACAGT\n" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tconsensus524\t1\t18\n" ) - linkF.write( "seq2\tDmelChr4-B-G387-MAP16\t1\t16\n" ) - linkF.write( "seq3\treference2\n" ) - linkF.close() - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( ">DmelChr4-B-G387-MAP16\nATGTACGATGACGATCAG\n" ) - expF.write( ">consensus524\nGTGCGGATGGAACAGT\n" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - def test_retrieveInitialSequenceHeaders_fastaFromClustering_afterLTRHarvest_Blastclust( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( ">BlastclustCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" ) - inF.write( ">BlastclustCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tchunk1 (dbseq-nr 1) [41806,41825]\t1\t18\n" ) - linkF.write( "seq2\tchunk2 (dbseq-nr 6) [41006,41023]\t1\t16\n" ) - linkF.write( "seq3\treference2\n" ) - linkF.close() - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( ">BlastclustCluster1Mb3_chunk2 (dbseq-nr 6) [41006,41023]\nATGTACGATGACGATCAG\n" ) - expF.write( ">BlastclustCluster8Mb4_chunk1 (dbseq-nr 1) [41806,41825]\nGTGCGGATGGAACAGT\n" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - whichCluster = "A" - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -w %s" % ( whichCluster ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - def test_retrieveInitialSequenceHeaders_fastaFromClustering_forClusterConsensus_Blastclust( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( ">BlastclustCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" ) - inF.write( ">BlastclustCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tDHX-incomp_DmelChr4-B-R1-Map4\t1\t18\n" ) - linkF.write( "seq2\tRLX-incomp_DmelChr4-B-R12-Map3_reversed\t1\t16\n" ) - linkF.write( "seq3\treference2\n" ) - linkF.close() - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( ">DHX-incomp_Blc8_DmelChr4-B-R1-Map4\nGTGCGGATGGAACAGT\n" ) - expF.write( ">RLX-incomp_Blc1_DmelChr4-B-R12-Map3_reversed\nATGTACGATGACGATCAG\n" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - whichCluster = "B" - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -w %s" % ( whichCluster ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - def test_retrieveInitialSequenceHeaders_fastaFromClustering_afterLTRHarvest_MCL( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( ">MCLCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" ) - inF.write( ">MCLCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tchunk1 (dbseq-nr 1) [41806,41825]\t1\t18\n" ) - linkF.write( "seq2\tchunk2 (dbseq-nr 6) [41006,41023]\t1\t16\n" ) - linkF.write( "seq3\treference2\n" ) - linkF.close() - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( ">MCLCluster1Mb3_chunk2 (dbseq-nr 6) [41006,41023]\nATGTACGATGACGATCAG\n" ) - expF.write( ">MCLCluster8Mb4_chunk1 (dbseq-nr 1) [41806,41825]\nGTGCGGATGGAACAGT\n" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - whichCluster = "A" - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -w %s" % ( whichCluster ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - def test_retrieveInitialSequenceHeaders_fastaFromClustering_forClusterConsensus_MCL( self ): - cDir = os.getcwd() - - inFile = "dummyInFaFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( ">MCLCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" ) - inF.write( ">MCLCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tDHX-incomp_DmelChr4-B-R1-Map4\t1\t18\n" ) - linkF.write( "seq2\tRLX-incomp_DmelChr4-B-R12-Map3_reversed\t1\t16\n" ) - linkF.write( "seq3\treference2\n" ) - linkF.close() - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( ">DHX-incomp_MCL8_DmelChr4-B-R1-Map4\nGTGCGGATGGAACAGT\n" ) - expF.write( ">RLX-incomp_MCL1_DmelChr4-B-R12-Map3_reversed\nATGTACGATGACGATCAG\n" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - whichCluster = "B" - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f fasta" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -w %s" % ( whichCluster ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - def test_retrieveInitialSequenceHeaders_newick_script( self ): - cDir = os.getcwd() - - inFile = "dummyInFile_%s" % ( self._uniqId ) - inF = open( inFile, "w" ) - inF.write( "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))" ) - inF.close() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\t1360\n" ) - linkF.write( "seq2\tDmelChr4-B-P2.0-MAP3_classII-TIR-comp|1cl-1gr|26copies\n" ) - linkF.write( "seq3\tDmelChr4-B-G20-MAP3_classII-TIR-comp|1cl-1gr|53copies\n" ) - linkF.write( "seq4\tDmelChr4-B-G14-MAP17_classII-TIR-comp|1cl-1gr|41copies\n" ) - linkF.close() - - expFile = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFile, "w" ) - expF.write( "(DmelChr4-B-G14-MAP17_classII-TIR-comp|1cl-1gr|41copies:0.012511,(DmelChr4-B-G20-MAP3_classII-TIR-comp|1cl-1gr|53copies:0.005340,DmelChr4-B-P2.0-MAP3_classII-TIR-comp|1cl-1gr|26copies:0.002201))" ) - expF.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f newick" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - - def test_retrieveInitialSequenceHeadersForAlignFile( self ): - cDir = os.getcwd() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t1000\n" ) - linkF.write( "seq2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t1\t800\n" ) - linkF.close() - - inFile = "dummyAlignFile_%s" % ( self._uniqId ) - inFileHandler = open( inFile, "w" ) - inFileHandler.write( "seq1\t1\t100\tseq2\t110\t11\t1e-38\t254\t98.5\n" ) - inFileHandler.write( "seq2\t11\t110\tseq1\t100\t1\t1e-38\t254\t98.5\n" ) - inFileHandler.close() - - expFile = "dummyExpAlignFile_%s" % ( self._uniqId ) - expFileHandler = open( expFile, "w" ) - expFileHandler.write( "name=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t100\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t110\t11\t1e-38\t254\t98.500000\n" ) - expFileHandler.write( "name=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t11\t110\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t100\t1\t1e-38\t254\t98.500000\n" ) - expFileHandler.close() - - obsFile = "dummyObsAlignFile_%s" % ( self._uniqId ) - - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f align" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - - def test_retrieveInitialSequenceHeadersForPathFile( self ): - cDir = os.getcwd() - - linkFile = "dummyLinkFile_%s" % ( self._uniqId ) - linkF = open( linkFile, "w" ) - linkF.write( "seq1\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t1000\n" ) - linkF.write( "seq2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t1\t800\n" ) - linkF.close() - - inFile = "dummyAlignFile_%s" % ( self._uniqId ) - inFileHandler = open( inFile, "w" ) - inFileHandler.write( "11\tseq1\t1\t100\tseq2\t110\t11\t1e-38\t254\t98.5\n" ) - inFileHandler.write( "2\tseq2\t11\t110\tseq1\t100\t1\t1e-38\t254\t98.5\n" ) - inFileHandler.close() - - expFile = "dummyExpAlignFile_%s" % ( self._uniqId ) - expFileHandler = open( expFile, "w" ) - expFileHandler.write( "11\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t100\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t110\t11\t1e-38\t254\t98.500000\n" ) - expFileHandler.write( "2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t11\t110\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t100\t1\t1e-38\t254\t98.500000\n" ) - expFileHandler.close() - - obsFile = "dummyObsAlignFile_%s" % ( self._uniqId ) - - cmd = "python ../ChangeSequenceHeaders.py" - cmd += " -i %s" % ( inFile ) - cmd += " -f path" - cmd += " -s 2" - cmd += " -l %s" % ( linkFile ) - cmd += " -o %s" % ( obsFile ) - exitStatus = os.system( cmd ) - - self.assertTrue( exitStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ inFile, linkFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_CorrelateTEageWithGCcontent.py --- a/commons/tools/tests/Test_CorrelateTEageWithGCcontent.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils - - -class Test_CorrelateTEageWithGCcontent( unittest.TestCase ): - - def test_zLaunchAsScript( self ): - cDir = os.getcwd() - - coordFile = "dummyPathFile" - coordFileHandler = open( coordFile, "w" ) - coordFileHandler.write( "1\tchr1\t1\t5\tTE1\t1\t5\t0.0\t100\t98.7\n" ) - coordFileHandler.write( "1\tchr1\t11\t20\tTE1\t6\t15\t0.0\t100\t98.7\n" ) - coordFileHandler.write( "2\tchr1\t26\t30\tTE1\t1\t5\t0.0\t100\t96.7\n" ) - coordFileHandler.write( "3\tchr2\t1\t10\tTE2\t1\t10\t0.0\t100\t98.7\n" ) - coordFileHandler.close() - - genomeFile = "dummyGenomeFile" - genomeFileHandler = open( genomeFile, "w" ) - genomeFileHandler.write( ">chr1\n" ) - genomeFileHandler.write( "AGCTGTTTTTAGCAGACGCATTTTTGGAGGTTTT\n" ) - genomeFileHandler.write( ">chr2\n" ) - genomeFileHandler.write( "ATATATATGGTTTTTTTTTT\n" ) - genomeFileHandler.close() - - refseqFile = "dummyRefseqFile" - refseqFileHandler = open( refseqFile, "w" ) - refseqFileHandler.write( ">TE1\nAGCAGCGACGACGACGACGACTTTT\n" ) - refseqFileHandler.write( ">TE2\nAGCAGCGACGACGACGACGACTTTT\n" ) - refseqFileHandler.write( ">TE3\nAGCAGCGACGACGACGACGACTTTT\n" ) - refseqFileHandler.close() - - expFile = "dummyExpFile" - expFileHandler = open( expFile, "w" ) - expFileHandler.write( "copy\tTE\tchr\tlength\tid\tGC\tlengthPerc\n" ) - expFileHandler.write( "1\tTE1\tchr1\t15\t98.70\t%.2f\t%.2f\n" % ( 100 * 9 / 15.0, 100 * 15 / 25.0 ) ) - expFileHandler.write( "2\tTE1\tchr1\t5\t96.70\t%.2f\t%.2f\n" % ( 100 * 4 / 5.0, 100 * 5 / 25.0 ) ) - expFileHandler.write( "3\tTE2\tchr2\t10\t98.70\t%.2f\t%.2f\n" % ( 100 * 2 / 10.0, 100 * 10 / 25.0 ) ) - expFileHandler.close() - - obsFile = "dummyObsFile" - - cmd = "CorrelateTEageWithGCcontent.py" - cmd += " -i %s" % ( coordFile ) - cmd += " -g %s" % ( genomeFile ) - cmd += " -r %s" % ( refseqFile ) - cmd += " -o %s" % ( obsFile ) - cmd += " -v %i" % ( 0 ) - returnStatus = os.system( cmd ) - - self.assertTrue( returnStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ coordFile, genomeFile, refseqFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_AlignTEOnGenomeAccordingToAnnotation.py --- a/commons/tools/tests/Test_F_AlignTEOnGenomeAccordingToAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,122 +0,0 @@ -from commons.core.sql.DbFactory import DbFactory -from commons.core.utils.FileUtils import FileUtils -import subprocess -import os -import unittest -from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation - -class Test_F_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase): - - def test_run_merge_same_paths(self): - pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"] - queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"] - subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"] - pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path" - queryTableName = "testDmelChr4_chr_seq" - subjectTableName = "testDmelChr4_refTEs_seq" - iDb = DbFactory.createInstance() - iDb.createTable(queryTableName, "seq", queryFileName, True) - iDb.createTable(subjectTableName, "seq", subjectFileName, True) - iDb.createTable(pathTableName, "path", pathFileName, True) - expFileName = "%s/Tools/exp%s_merge.alignedSeq" % (os.environ["REPET_DATA"], pathTableName) - - iATOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName, True) - iATOGATA.run() - obsFileName = "obs%s_merge.alignedSeq" % pathTableName - iDb.exportDataToFile("%s_align" % pathTableName, obsFileName) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(obsFileName) - iDb.dropTable(queryTableName) - iDb.dropTable(subjectTableName) - iDb.dropTable(pathTableName) - iDb.dropTable("%s_align" % pathTableName) - iDb.close() - - def test_run_as_script_merge_same_paths(self): - pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"] - queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"] - subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"] - pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path" - queryTableName = "testDmelChr4_chr_seq" - subjectTableName = "testDmelChr4_refTEs_seq" - iDb = DbFactory.createInstance() - iDb.createTable(queryTableName, "seq", queryFileName, True) - iDb.createTable(subjectTableName, "seq", subjectFileName, True) - iDb.createTable(pathTableName, "path", pathFileName, True) - expFileName = "%s/Tools/exp%s_merge.alignedSeq" % (os.environ["REPET_DATA"], pathTableName) - - cmd = "AlignTEOnGenomeAccordingToAnnotation.py -p %s -q %s -s %s -m " % (pathTableName, queryTableName, subjectTableName) - process = subprocess.Popen(cmd, shell = True) - process.communicate() - obsFileName = "obs%s_merge.alignedSeq" % pathTableName - iDb.exportDataToFile("%s_align" % pathTableName, obsFileName) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(obsFileName) - iDb.dropTable(queryTableName) - iDb.dropTable(subjectTableName) - iDb.dropTable(pathTableName) - iDb.dropTable("%s_align" % pathTableName) - iDb.close() - - def test_run_as_script_without_merge(self): - pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"] - queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"] - subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"] - pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path" - queryTableName = "testDmelChr4_chr_seq" - subjectTableName = "testDmelChr4_refTEs_seq" - iDb = DbFactory.createInstance() - iDb.createTable(queryTableName, "seq", queryFileName, True) - iDb.createTable(subjectTableName, "seq", subjectFileName, True) - iDb.createTable(pathTableName, "path", pathFileName, True) - expFileName = "%s/Tools/exp%s.alignedSeq" % (os.environ["REPET_DATA"], pathTableName) - - cmd = "AlignTEOnGenomeAccordingToAnnotation.py -p %s -q %s -s %s" % (pathTableName, queryTableName, subjectTableName) - process = subprocess.Popen(cmd, shell = True) - process.communicate() - obsFileName = "obs%s.alignedSeq" % pathTableName - iDb.exportDataToFile("%s_align" % pathTableName, obsFileName) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(obsFileName) - iDb.dropTable(queryTableName) - iDb.dropTable(subjectTableName) - iDb.dropTable(pathTableName) - iDb.dropTable("%s_align" % pathTableName) - iDb.close() - -# def test_run_as_script_merge_same_paths_old(self): -# pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"] -# queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"] -# subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"] -# pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path" -# queryTableName = "testDmelChr4_chr_seq" -# subjectTableName = "testDmelChr4_refTEs_seq" -# iDb = DbFactory.createInstance() -# iDb.createTable(queryTableName, "seq", queryFileName, True) -# iDb.createTable(subjectTableName, "seq", subjectFileName, True) -# iDb.createTable(pathTableName, "path", pathFileName, True) -# expFileName = "%s/Tools/exp%s_merge_old.alignedSeq" % (os.environ["REPET_DATA"], pathTableName) -# -# cmd = "srptAlignPath.py -m %s -q %s -s %s" % (pathTableName, queryTableName, subjectTableName) -# process = subprocess.Popen(cmd, shell = True) -# process.communicate() -# obsFileName = "obs%s.alignedSeq" % pathTableName -# iDb.exportDataToFile("%s_align" % pathTableName, obsFileName) -# -# self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) -# -# os.remove(obsFileName) -# iDb.dropTable(queryTableName) -# iDb.dropTable(subjectTableName) -# iDb.dropTable(pathTableName) -# iDb.dropTable("%s_align" % pathTableName) -# iDb.close() -# -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_CheckMysqlConnect.py --- a/commons/tools/tests/Test_F_CheckMysqlConnect.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -import unittest -import os -import socket - -class Test_F_CheckMysqlConnect(unittest.TestCase): - - HOST_NAME = "compute-2-46.local" - - def setUp(self): - self._host = socket.gethostname() - self._cmd = "" - - def tearDown(self): - os.remove("testOutputCheckMysqlConnect.txt") - - def test_CheckMysqlConnect_as_script_True(self): - if self.HOST_NAME in self._host: - self._cmd = "CheckMysqlConnect.py -p /share/apps/bin/python > testOutputCheckMysqlConnect.txt" - else: - self._cmd = "CheckMysqlConnect.py > testOutputCheckMysqlConnect.txt" - os.system(self._cmd) - - self.assertFalse(self._isFailedInOutputFile()) - - def test_CheckMysqlConnect_as_script_False(self): - configFile = "%s/repet_tools/tests/config.cfg" % os.environ.get("REPET_PATH") - host = "unknownServer" - self._writeConfig(configFile, host) - - if self.HOST_NAME in self._host: - self._cmd = "CheckMysqlConnect.py -p /share/apps/bin/python -C %s > testOutputCheckMysqlConnect.txt" % configFile - else: - self._cmd = "CheckMysqlConnect.py -C %s > testOutputCheckMysqlConnect.txt " % configFile - os.system(self._cmd) - os.remove(configFile) - - self.assertTrue(self._isFailedInOutputFile()) - - def _isFailedInOutputFile(self): - f = open("testOutputCheckMysqlConnect.txt", "r") - line = f.readline() - - while line: - if "FAILED" in line: - f.close() - return True - line = f.readline() - - f.close() - return False - - def _writeConfig(self, configFileName, repetHost = os.environ.get("REPET_HOST")): - f = open( configFileName, "w" ) - f.write("[repet_env]\n") - f.write("repet_host: %s\n" % repetHost) - f.write("repet_user: %s\n" % os.environ.get("REPET_USER")) - f.write("repet_pw: %s\n" % os.environ.get("REPET_PW")) - f.write("repet_db: %s\n" % os.environ.get("REPET_DB")) - f.write("repet_port: %s\n" % os.environ.get("REPET_PORT")) - f.close() - -if __name__ == "__main__": - unittest.main() - \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_FilterAlign.py --- a/commons/tools/tests/Test_F_FilterAlign.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,168 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import unittest -import os - -class Test_F_FilterAlign(unittest.TestCase): - - def test_as_script(self): - alignFileName = "batch.fa.align" - self._writeAlignFile(alignFileName) - expFileName = "exp.filtered" - self._writeExpFile(expFileName) - obsFileName = "batch.fa.align.filtered" - cmd = "FilterAlign.py" - cmd += " -i %s" % alignFileName - cmd += " -S 100" - cmd += " -v 1" - os.system(cmd) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(alignFileName) - os.remove(expFileName) - os.remove(obsFileName) - - def _writeExpFile(self, fileName): - f = open(fileName, "w") - f.write("chunk09914\t2257\t2722\trefTE_747\t2614\t2169\t0\t249\t77.5463\n") - f.write("chunk09914\t3114\t4494\trefTE_747\t1598\t228\t0\t571\t78.0453\n") - f.write("chunk09914\t2251\t4816\trefTE_759\t173\t2769\t0\t3203\t90.5966\n") - f.write("chunk09914\t3019\t3698\trefTE_764\t49\t735\t0\t343\t78.3912\n") - f.write("chunk09914\t4102\t4530\trefTE_764\t1191\t1603\t0\t154\t83.0601\n") - f.write("chunk09914\t4603\t4864\trefTE_779\t291\t24\t6.5e-39\t135\t80.9917\n") - f.write("chunk09914\t4642\t4909\trefTE_787\t56\t326\t0\t132\t79.0323\n") - f.write("chunk09914\t5086\t6724\trefTE_787\t532\t2194\t0\t218\t71.4668\n") - f.write("chunk09914\t6180\t6594\trefTE_812\t2516\t2949\t1.6e-32\t125\t72.5441\n") - f.write("chunk09914\t2349\t2723\trefTE_818\t1034\t663\t0\t347\t80.0539\n") - f.write("chunk09914\t2412\t2727\trefTE_818\t1169\t1482\t0\t278\t78.5942\n") - f.write("chunk09914\t3853\t5302\trefTE_828\t3133\t1713\t0\t417\t77.8644\n") - f.write("chunk09914\t5486\t6724\trefTE_828\t1715\t454\t0\t584\t73.8655\n") - f.write("chunk09914\t849\t1203\trefTE_838\t83\t449\t0\t493\t95.7386\n") - f.write("chunk09914\t3355\t4471\trefTE_861\t2024\t3183\t0\t260\t77.1289\n") - f.write("chunk09914\t2263\t4696\trefTE_866\t19\t2476\t0\t3136\t91.1287\n") - f.write("chunk09914\t4803\t5747\trefTE_866\t2479\t3429\t0\t1352\t93.1217\n") - f.write("chunk09914\t4134\t4702\trefTE_880\t1685\t1129\t7.8e-35\t126\t80.7851\n") - f.write("chunk09914\t3598\t4029\trefTE_904\t666\t1122\t0\t414\t84.7418\n") - f.write("chunk09914\t3887\t4480\trefTE_904\t1030\t1635\t0\t384\t82.6087\n") - f.write("chunk09914\t2257\t2722\trefTE_908\t1005\t551\t0\t240\t78.5377\n") - f.write("chunk09914\t6180\t6594\trefTE_914\t1420\t987\t8.6e-30\t125\t72.5441\n") - f.write("chunk09914\t4144\t6724\trefTE_931\t3801\t1202\t0\t1057\t74.7937\n") - f.write("chunk09914\t848\t1204\trefTE_966\t370\t1\t0\t522\t98.0282\n") - f.write("chunk09914\t854\t1145\trefTE_966\t5130\t4829\t0\t411\t95.8763\n") - f.write("chunk09914\t4142\t4487\trefTE_969\t455\t130\t4.2039e-45\t161\t81.1881\n") - f.write("chunk09914\t848\t1218\trefTE_980\t1182\t814\t0\t431\t92.1127\n") - f.write("chunk09914\t4093\t4489\trefTE_999\t5850\t5485\t3.6e-39\t142\t81.0651\n") - f.write("chunk09914\t2257\t2722\trefTE_1006\t2472\t2025\t0\t257\t77.4193\n") - f.write("chunk09914\t3755\t4491\trefTE_1006\t941\t230\t0\t188\t80.0948\n") - f.write("chunk09914\t5060\t6724\trefTE_1006\t7451\t5776\t0\t711\t72.3792\n") - f.write("chunk09914\t2251\t3361\trefTE_1015\t7278\t8364\t0\t1514\t86.8087\n") - f.write("chunk09914\t2780\t6724\trefTE_1015\t1\t3962\t0\t5370\t91.9552\n") - f.write("chunk09914\t3383\t4672\trefTE_1015\t8150\t9445\t0\t1746\t92.1217\n") - f.write("chunk09914\t6228\t6594\trefTE_1018\t5554\t5920\t6.2e-22\t106\t73.3138\n") - f.close() - - def _writeAlignFile(self, fileName): - f = open(fileName, "w") - f.write("chunk09914\t5038\t5133\trefTE_745\t288\t389\t1.3e-15\t38\t86.747\n") - f.write("chunk09914\t6415\t6574\trefTE_745\t605\t761\t1.3e-15\t76\t78.9116\n") - f.write("chunk09914\t2257\t2722\trefTE_747\t2614\t2169\t3.8e-165\t249\t77.5463\n") - f.write("chunk09914\t3114\t4494\trefTE_747\t1598\t228\t3.8e-165\t571\t78.0453\n") - f.write("chunk09914\t2251\t4816\trefTE_759\t173\t2769\t0\t3203\t90.5966\n") - f.write("chunk09914\t3019\t3698\trefTE_764\t49\t735\t3.4e-133\t343\t78.3912\n") - f.write("chunk09914\t4102\t4530\trefTE_764\t1191\t1603\t3.4e-133\t154\t83.0601\n") - f.write("chunk09914\t4640\t4702\trefTE_764\t1676\t1738\t3.4e-133\t39\t86.2069\n") - f.write("chunk09914\t1436\t1549\trefTE_779\t749\t628\t3.9e-33\t38\t75.7009\n") - f.write("chunk09914\t3992\t4156\trefTE_779\t958\t743\t2.6e-34\t42\t85.4305\n") - f.write("chunk09914\t4050\t4229\trefTE_779\t782\t602\t6.5e-39\t57\t82.6923\n") - f.write("chunk09914\t4430\t4499\trefTE_779\t1029\t952\t1.2e-33\t39\t83.3333\n") - f.write("chunk09914\t4603\t4864\trefTE_779\t291\t24\t6.5e-39\t135\t80.9917\n") - f.write("chunk09914\t4642\t4909\trefTE_787\t56\t326\t4e-86\t132\t79.0323\n") - f.write("chunk09914\t5086\t6724\trefTE_787\t532\t2194\t4e-86\t218\t71.4668\n") - f.write("chunk09914\t4689\t4718\trefTE_812\t828\t855\t1.6e-32\t37\t92.8571\n") - f.write("chunk09914\t6178\t6204\trefTE_812\t1111\t1138\t1.6e-32\t36\t92.5926\n") - f.write("chunk09914\t6180\t6594\trefTE_812\t2516\t2949\t1.6e-32\t125\t72.5441\n") - f.write("chunk09914\t2349\t2723\trefTE_818\t1034\t663\t2e-97\t347\t80.0539\n") - f.write("chunk09914\t2412\t2727\trefTE_818\t1169\t1482\t1.1e-73\t278\t78.5942\n") - f.write("chunk09914\t3315\t3420\trefTE_818\t423\t318\t2e-97\t41\t74\n") - f.write("chunk09914\t3339\t3429\trefTE_818\t153\t49\t1.7e-96\t38\t82.5581\n") - f.write("chunk09914\t3853\t5302\trefTE_828\t3133\t1713\t1.6e-281\t417\t77.8644\n") - f.write("chunk09914\t5486\t6724\trefTE_828\t1715\t454\t1.6e-281\t584\t73.8655\n") - f.write("chunk09914\t2593\t2700\trefTE_831\t905\t798\t1.2e-15\t85\t75\n") - f.write("chunk09914\t849\t1203\trefTE_838\t83\t449\t2.6e-138\t493\t95.7386\n") - f.write("chunk09914\t5276\t5639\trefTE_842\t725\t1094\t1.7e-16\t47\t71.8563\n") - f.write("chunk09914\t6223\t6594\trefTE_842\t1689\t2058\t1.7e-16\t70\t73.8602\n") - f.write("chunk09914\t6180\t6594\trefTE_844\t3220\t2788\t3e-19\t97\t71.5013\n") - f.write("chunk09914\t6415\t6593\trefTE_847\t3137\t2959\t2e-15\t85\t74.4186\n") - f.write("chunk09914\t4691\t4762\trefTE_852\t2829\t2755\t1.9e-21\t36\t82.0895\n") - f.write("chunk09914\t6172\t6594\trefTE_852\t1201\t770\t1.9e-21\t97\t71.2121\n") - f.write("chunk09914\t2441\t2723\trefTE_861\t995\t1282\t3.9e-54\t78\t75.3906\n") - f.write("chunk09914\t3323\t3437\trefTE_861\t1683\t1811\t3.9e-54\t36\t81.3084\n") - f.write("chunk09914\t3355\t4471\trefTE_861\t2024\t3183\t3.9e-54\t260\t77.1289\n") - f.write("chunk09914\t4602\t4701\trefTE_861\t3281\t3372\t3.9e-54\t39\t85.7143\n") - f.write("chunk09914\t360\t470\trefTE_864\t2853\t2962\t6.3e-17\t38\t77.2277\n") - f.write("chunk09914\t4200\t4472\trefTE_864\t3062\t3320\t6.3e-17\t81\t75.2066\n") - f.write("chunk09914\t2594\t2736\trefTE_865\t3\t145\t1.3e-26\t62\t71.7391\n") - f.write("chunk09914\t3531\t3622\trefTE_865\t727\t810\t1.3e-26\t38\t80\n") - f.write("chunk09914\t4025\t4484\trefTE_865\t2086\t2534\t1.3e-26\t79\t78.7179\n") - f.write("chunk09914\t2263\t4696\trefTE_866\t19\t2476\t0\t3136\t91.1287\n") - f.write("chunk09914\t4803\t5747\trefTE_866\t2479\t3429\t0\t1352\t93.1217\n") - f.write("chunk09914\t646\t733\trefTE_870\t3379\t3466\t6.1e-19\t96\t79.5455\n") - f.write("chunk09914\t6272\t6716\trefTE_875\t2153\t1701\t3.7e-13\t77\t73.7624\n") - f.write("chunk09914\t646\t737\trefTE_877\t3412\t3502\t2.2e-18\t94\t82.2222\n") - f.write("chunk09914\t3596\t3756\trefTE_880\t2230\t2079\t7.8e-35\t53\t79.2857\n") - f.write("chunk09914\t4090\t4521\trefTE_880\t1702\t1261\t4.1e-24\t90\t81.3699\n") - f.write("chunk09914\t4134\t4702\trefTE_880\t1685\t1129\t7.8e-35\t126\t80.7851\n") - f.write("chunk09914\t2569\t2725\trefTE_885\t789\t935\t6.6e-18\t73\t76.9231\n") - f.write("chunk09914\t2583\t2699\trefTE_885\t118\t1\t4.4e-17\t90\t81.25\n") - f.write("chunk09914\t3507\t3758\trefTE_885\t1631\t1887\t6.6e-18\t49\t77.6786\n") - f.write("chunk09914\t3598\t4029\trefTE_904\t666\t1122\t3e-117\t414\t84.7418\n") - f.write("chunk09914\t3841\t3924\trefTE_904\t1044\t1130\t3.1e-11\t60\t82.2785\n") - f.write("chunk09914\t3887\t4480\trefTE_904\t1030\t1635\t3.9e-108\t384\t82.6087\n") - f.write("chunk09914\t4660\t4708\trefTE_904\t1763\t1813\t3e-117\t40\t79.5918\n") - f.write("chunk09914\t2257\t2722\trefTE_908\t1005\t551\t3.9e-62\t240\t78.5377\n") - f.write("chunk09914\t4689\t4718\trefTE_914\t3130\t3103\t8.6e-30\t37\t92.8571\n") - f.write("chunk09914\t6180\t6594\trefTE_914\t1420\t987\t8.6e-30\t125\t72.5441\n") - f.write("chunk09914\t4691\t4755\trefTE_930\t2120\t2187\t2.3e-14\t39\t86.6667\n") - f.write("chunk09914\t6172\t6506\trefTE_930\t3738\t4087\t2.3e-14\t71\t72.293\n") - f.write("chunk09914\t3755\t3945\trefTE_931\t4127\t3947\t0\t45\t79.3939\n") - f.write("chunk09914\t4144\t6724\trefTE_931\t3801\t1202\t0\t1057\t74.7937\n") - f.write("chunk09914\t4692\t4772\trefTE_962\t2382\t2453\t1.5e-16\t39\t85.0746\n") - f.write("chunk09914\t6178\t6560\trefTE_962\t3929\t4309\t1.5e-16\t79\t70.5882\n") - f.write("chunk09914\t848\t1204\trefTE_966\t370\t1\t4e-147\t522\t98.0282\n") - f.write("chunk09914\t854\t1145\trefTE_966\t5130\t4829\t1.5e-115\t411\t95.8763\n") - f.write("chunk09914\t1139\t1203\trefTE_966\t4770\t4681\t1.5e-115\t38\t87.5\n") - f.write("chunk09914\t646\t734\trefTE_967\t4583\t4671\t4.8e-16\t87\t76.4045\n") - f.write("chunk09914\t3565\t3698\trefTE_969\t1106\t990\t4.3e-45\t53\t79.646\n") - f.write("chunk09914\t4142\t4487\trefTE_969\t455\t130\t4.3e-45\t161\t81.1881\n") - f.write("chunk09914\t848\t1218\trefTE_980\t1182\t814\t6.8e-120\t431\t92.1127\n") - f.write("chunk09914\t4691\t4762\trefTE_986\t3059\t3133\t3.3e-21\t36\t82.0895\n") - f.write("chunk09914\t6172\t6594\trefTE_986\t4689\t5120\t3.3e-21\t97\t71.2121\n") - f.write("chunk09914\t149\t280\trefTE_987\t3872\t3721\t2.8e-18\t38\t79.2\n") - f.write("chunk09914\t4689\t4769\trefTE_987\t3186\t3102\t2.8e-18\t37\t83.5616\n") - f.write("chunk09914\t6178\t6594\trefTE_987\t1600\t1188\t2.8e-18\t77\t72.0317\n") - f.write("chunk09914\t4108\t4241\trefTE_991\t2079\t2237\t1.2e-12\t62\t82.1705\n") - f.write("chunk09914\t4602\t4701\trefTE_991\t2535\t2634\t1.2e-12\t43\t78.022\n") - f.write("chunk09914\t3596\t3757\trefTE_999\t6434\t6307\t3.6e-39\t52\t85.124\n") - f.write("chunk09914\t4093\t4489\trefTE_999\t5850\t5485\t3.6e-39\t142\t81.0651\n") - f.write("chunk09914\t4348\t4702\trefTE_999\t5619\t5295\t5.9e-13\t54\t79.7251\n") - f.write("chunk09914\t4541\t4805\trefTE_1002\t3207\t2973\t6.8e-27\t57\t85.5769\n") - f.write("chunk09914\t6178\t6723\trefTE_1002\t1494\t946\t6.8e-27\t96\t75.7764\n") - f.write("chunk09914\t4085\t4179\trefTE_1004\t3933\t4033\t1.5e-17\t47\t80\n") - f.write("chunk09914\t4690\t4718\trefTE_1004\t4126\t4153\t1.5e-17\t38\t92.8571\n") - f.write("chunk09914\t6262\t6594\trefTE_1004\t5242\t5574\t1.5e-17\t65\t70.2265\n") - f.write("chunk09914\t2257\t2722\trefTE_1006\t2472\t2025\t2.5e-134\t257\t77.4193\n") - f.write("chunk09914\t3134\t3382\trefTE_1006\t1450\t1199\t2.9e-118\t45\t75.7991\n") - f.write("chunk09914\t3331\t3661\trefTE_1006\t1468\t1146\t2.5e-134\t98\t78.2313\n") - f.write("chunk09914\t3755\t4491\trefTE_1006\t941\t230\t2.5e-134\t188\t80.0948\n") - f.write("chunk09914\t5060\t6724\trefTE_1006\t7451\t5776\t3.8e-204\t711\t72.3792\n") - f.write("chunk09914\t2670\t2723\trefTE_1009\t6642\t6591\t7.1e-18\t39\t86\n") - f.write("chunk09914\t3328\t3647\trefTE_1009\t5826\t5508\t7.1e-18\t84\t75\n") - f.write("chunk09914\t6\t130\trefTE_1011\t3884\t3994\t1.6e-11\t38\t76.6355\n") - f.write("chunk09914\t4690\t4741\trefTE_1011\t4997\t5046\t1.6e-11\t37\t91.1111\n") - f.write("chunk09914\t6180\t6716\trefTE_1011\t6676\t7235\t1.6e-11\t55\t71.2274\n") - f.write("chunk09914\t2251\t3361\trefTE_1015\t7278\t8364\t0\t1514\t86.8087\n") - f.write("chunk09914\t2780\t6724\trefTE_1015\t1\t3962\t0\t5370\t91.9552\n") - f.write("chunk09914\t3383\t4672\trefTE_1015\t8150\t9445\t0\t1746\t92.1217\n") - f.write("chunk09914\t6228\t6594\trefTE_1018\t5554\t5920\t6.2e-22\t106\t73.3138\n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_GFF3Maker.py --- a/commons/tools/tests/Test_F_GFF3Maker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,707 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbMySql import DbMySql -from commons.tools.GFF3Maker import GFF3Maker - -class Test_F_GFF3Maker(unittest.TestCase): - - def setUp(self): - self._projectName = "projectName" - self._iDb = DbMySql() - self._tablesFileName = "annotation_tables.txt" - self._fastaFileName = "%s_chr.fa" % self._projectName - self._fastaTableName = "%s_chr_seq" % self._projectName - self._writeFastaFile(self._fastaFileName) - self._iDb.createTable(self._fastaTableName, "seq", self._fastaFileName, True) - self._inputFileName = "%s_chr_allTEs_nr_noSSR_join.pathOrSet" % self._projectName - self._expGFFFileName = "explm_SuperContig_29_v2.gff3" - self._obsGFFFileName = "lm_SuperContig_29_v2.gff3" - self._obsGFFEmptyFileName = "lm_SuperContig_30_v2.gff3" - - def tearDown(self): - self._iDb.dropTable(self._fastaTableName) - self._iDb.dropTable(self._inputTableName) - self._iDb.close() - os.remove(self._obsGFFFileName) - os.remove(self._expGFFFileName) - os.remove(self._fastaFileName) - os.remove(self._tablesFileName) - os.remove(self._inputFileName) - - def test_run_as_script_path_with_seq_withAllFiles(self): - self._writeTablesFile("path") - self._writePathFile(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - self._writeExpPathGFFFile(self._expGFFFileName) - expGFFEmptyFileName = "explm_SuperContig_30_v2.gff3" - self._writeExpEmptyPathGFFFileWithSeq(expGFFEmptyFileName) - - cmd = "GFF3Maker.py -t %s -f %s -w -a -p"% (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expGFFEmptyFileName, self._obsGFFEmptyFileName)) - - os.remove(expGFFEmptyFileName) - os.remove(self._obsGFFEmptyFileName) - - def test_run_as_script_path_without_seq_withAllFiles(self): - self._writeTablesFile("path") - self._writePathFile(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - self._writeExpPathGFFFile_without_seq(self._expGFFFileName) - expGFFEmptyFileName = "explm_SuperContig_30_v2.gff3" - self._writeExpEmptyPathGFFFile(expGFFEmptyFileName) - - cmd = "GFF3Maker.py -t %s -f %s -a -p" % (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expGFFEmptyFileName, self._obsGFFEmptyFileName)) - - os.remove(expGFFEmptyFileName) - os.remove(self._obsGFFEmptyFileName) - - def test_run_without_seq(self): - self._writeTablesFile("path") - self._writePathFile(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - self._writeExpPathGFFFile_without_seq(self._expGFFFileName) - - iGFF3Maker = GFF3Maker() - iGFF3Maker.setTablesFileName(self._tablesFileName) - iGFF3Maker.setInFastaName(self._fastaTableName) - iGFF3Maker.setAreMatchPartCompulsory(True) - iGFF3Maker.run() - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName)) - - def test_run_without_seq_and_match_part_not_compulsory(self): - self._writeTablesFile("path") - self._writePathFile(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - self._writeExpPathGFFFile_without_seq_and_match_part_not_comulsory(self._expGFFFileName) - - iGFF3Maker = GFF3Maker() - iGFF3Maker.setTablesFileName(self._tablesFileName) - iGFF3Maker.setInFastaName(self._fastaTableName) - iGFF3Maker.run() - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName)) - - def test_run_as_script_pathReversed(self): - self._writeTablesFile("path") - self._writePathFileReverse(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - self._writeExpPathGFFFileReversed(self._expGFFFileName) - - cmd = "GFF3Maker.py -t %s -f %s -w -p" % (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName)) - - def test_run_as_script_set(self): - self._writeTablesFile("set") - self._writeSetFile(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_set" % self._projectName - self._iDb.createTable(self._inputTableName, "set", self._inputFileName, True) - self._writeExpSetGFFFile(self._expGFFFileName) - - cmd = "GFF3Maker.py -t %s -f %s -w -p " % (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName)) - - def test_run_as_script_setReversed(self): - self._writeTablesFile("set") - self._writeSetFileReverse(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_set" % self._projectName - self._iDb.createTable(self._inputTableName, "set", self._inputFileName, True) - self._writeExpSetGFFFileReversed(self._expGFFFileName) - - cmd = "GFF3Maker.py -t %s -f %s -w -p " % (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName)) - - def test_run_as_script_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8(self): - self._writeTablesFile("path") - self._writePathFile_withClassif(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - - self._writeClassifFile("input.classif") - inputClassifTableName = "%s_classif" % self._projectName - self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True) - - self._expGFFFileName = "explm_SuperContig_30_v2.gff3" - self._obsGFFFileName = "lm_SuperContig_30_v2.gff3" - self._writeExpPathGFFFile_without_seq_withClassif(self._expGFFFileName) - - cmd = "GFF3Maker.py -t %s -f %s -i %s -p" % (self._tablesFileName, self._fastaTableName, inputClassifTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - - os.remove("input.classif") - os.remove("lm_SuperContig_29_v2.gff3") - self._iDb.dropTable(inputClassifTableName) - - def test_run_as_script_path_without_seq_withAllFilesWithTargetLength(self): - fastaFileName = "genome.fa" - self._writeFastaFileExtended(fastaFileName) - self._iDb.createTable(self._fastaTableName, "seq", fastaFileName, True) - os.remove(fastaFileName) - - self._writeTablesFile_withTESeqTables("path") - - self._writePathFile(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - - inFileName2 = "%s_chr_bankBLRtx.path" % self._projectName - self._writePathFile2(inFileName2) - bankPathTableName = "%s_chr_bankBLRtx_path" % self._projectName - self._iDb.createTable(bankPathTableName, "path", inFileName2, True) - os.remove(inFileName2) - - refTEsFastaFileName = "%s_refTEs.fa" % self._projectName - self._writeRefTEsSeqFile(refTEsFastaFileName) - refTESeqTableName = "%s_refTEs_seq" % self._projectName - self._iDb.createTable(refTESeqTableName, "seq", refTEsFastaFileName, True) - os.remove(refTEsFastaFileName) - - bankBLRtxFastaFileName = "dummyRepbase.fa" - self._writeBankBLRtxSeqFile(bankBLRtxFastaFileName) - bankBLRtxTableName = "%s_bankBLRtx_nt_seq" % self._projectName - self._iDb.createTable(bankBLRtxTableName, "seq", bankBLRtxFastaFileName, True) - os.remove(bankBLRtxFastaFileName) - - self._expGFFFileName = "explm_SuperContig_29_v2.gff3" - expSeq2GFFFileName = "expChr1.gff3" - self._obsGFFFileName = "lm_SuperContig_29_v2.gff3" - obsSeq2GFFFileName = "chr1.gff3" - self._writeExpPathGFFFile_without_seq_withTargetLength_seq1(self._expGFFFileName) - self._writeExpPathGFFFile_without_seq_withTargetLength_seq2(expSeq2GFFFileName) - - cmd = "GFF3Maker.py -t %s -f %s -p" % (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expSeq2GFFFileName, obsSeq2GFFFileName)) - - os.remove(expSeq2GFFFileName) - os.remove(obsSeq2GFFFileName) - self._iDb.dropTable(refTESeqTableName) - self._iDb.dropTable(bankBLRtxTableName) - self._iDb.dropTable(bankPathTableName) - - def test_run_as_script_split_file_by_annotation_method(self): - fastaFileName = "dummyDmelChr4.fa" - self._writeFastaFile_DmelChr4(fastaFileName) - self._iDb.createTable(self._fastaTableName, "seq", fastaFileName, True) - os.remove(fastaFileName) - - self._writeTablesFile_withTESeqTables("path") - - self._writePathFile_refTEs_annotation(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - - inFileName2 = "%s_chr_bankBLRtx.path" % self._projectName - self._writePathFile_bankBLRtx_annotation(inFileName2) - bankPathTableName = "%s_chr_bankBLRtx_path" % self._projectName - self._iDb.createTable(bankPathTableName, "path", inFileName2, True) - os.remove(inFileName2) - - refTEsFastaFileName = "%s_refTEs.fa" % self._projectName - self._writeRefTEsSeqFile(refTEsFastaFileName) - refTESeqTableName = "%s_refTEs_seq" % self._projectName - self._iDb.createTable(refTESeqTableName, "seq", refTEsFastaFileName, True) - os.remove(refTEsFastaFileName) - - bankBLRtxFastaFileName = "dummyRepbase.fa" - self._writeBankBLRtxSeqFile(bankBLRtxFastaFileName) - bankBLRtxTableName = "%s_bankBLRtx_nt_seq" % self._projectName - self._iDb.createTable(bankBLRtxTableName, "seq", bankBLRtxFastaFileName, True) - os.remove(bankBLRtxFastaFileName) - - self._expGFFFileName = "expdmel_chr4_Annot1.gff3" - expGFFFileName2 = "expdmel_chr1_Annot1.gff3" - expGFFFileName3 = "expdmel_chr4_Annot2.gff3" - self._obsGFFFileName = "dmel_chr4_Annot1.gff3" - obsGFFFileName2 = "dmel_chr1_Annot1.gff3" - obsGFFFileName3 = "dmel_chr4_Annot2.gff3" - self._writeExpPathGFFFile_split_file1(self._expGFFFileName) - self._writeExpPathGFFFile_split_file2(expGFFFileName2) - self._writeExpPathGFFFile_split_file3(expGFFFileName3) - - cmd = "GFF3Maker.py -t %s -f %s -s -p" % (self._tablesFileName, self._fastaTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expGFFFileName2, obsGFFFileName2)) - self.assertTrue(FileUtils.are2FilesIdentical(expGFFFileName3, obsGFFFileName3)) - - os.remove(expGFFFileName2) - os.remove(expGFFFileName3) - os.remove(obsGFFFileName2) - os.remove(obsGFFFileName3) - self._iDb.dropTable(refTESeqTableName) - self._iDb.dropTable(bankBLRtxTableName) - self._iDb.dropTable(bankPathTableName) - - def test_run_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8_withIdenticalMatches(self): - self._writeTablesFile("path") - self._writePathFile_withClassif_withIdenticalMatches(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - - self._writeClassifFile("input.classif") - inputClassifTableName = "%s_classif" % self._projectName - self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True) - - self._expGFFFileName = "explm_SuperContig_30_v2.gff3" - self._obsGFFFileName = "lm_SuperContig_30_v2.gff3" - self._writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self._expGFFFileName) - - iGFF3Maker = GFF3Maker() - iGFF3Maker.setTablesFileName(self._tablesFileName) - iGFF3Maker.setInFastaName(self._fastaTableName) - iGFF3Maker.setClassifTable(inputClassifTableName) - iGFF3Maker.setDoMergeIdenticalMatches(True) - iGFF3Maker.setAreMatchPartCompulsory(True) - iGFF3Maker.run() - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - - os.remove("input.classif") - os.remove("lm_SuperContig_29_v2.gff3") - self._iDb.dropTable(inputClassifTableName) - - def test_run_as_script_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8_withIdenticalMatches(self): - self._writeTablesFile("path") - self._writePathFile_withClassif_withIdenticalMatches(self._inputFileName) - self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName - self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True) - - self._writeClassifFile("input.classif") - inputClassifTableName = "%s_classif" % self._projectName - self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True) - - self._expGFFFileName = "explm_SuperContig_30_v2.gff3" - self._obsGFFFileName = "lm_SuperContig_30_v2.gff3" - self._writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self._expGFFFileName) - - cmd = "GFF3Maker.py -t %s -f %s -i %s -m -p" % (self._tablesFileName, self._fastaTableName, inputClassifTableName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName)) - - os.remove("input.classif") - os.remove("lm_SuperContig_29_v2.gff3") - self._iDb.dropTable(inputClassifTableName) - - def _writeRefTEsSeqFile(self, inFileName): - with open(inFileName, "w") as f: - f.write(">DTX-incomp_DmelChr4-L-B1-Map3\n") - f.write("ATCGATCGTT\n") - f.write(">DTX-incomp_DmelChr4-B-P0.0-Map3\n") - f.write("GCTAGCTA\n") - - def _writeBankBLRtxSeqFile(self, inFileName): - with open(inFileName, "w") as f: - f.write(">PROTOP_B:classII:TIR\n") - f.write("ATCGATCGTT\n") - f.write(">DMRT1C:classI:?\n") - f.write("GCTAGCTA\n") - f.write(">BATUMI_I:classI:LTR_retrotransposon\n") - f.write("GCTAATGGCATA\n") - - def _writeExpPathGFFFile_without_seq_withTargetLength_seq1(self, inFileName): - with open(inFileName, "w") as f: - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;TargetLength=10;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;TargetLength=10;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;TargetLength=8\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - - def _writeExpPathGFFFile_without_seq_withTargetLength_seq2(self, inFileName): - with open(inFileName, "w") as f: - f.write("##gff-version 3\n") - f.write("##sequence-region chr1 1 18\n") - f.write("chr1\tprojectName_REPET_TEs\tmatch\t1\t100\t0.0\t-\t.\tID=ms1_chr1_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 85 228;TargetLength=10;Identity=30.56\n") - f.write("chr1\tprojectName_REPET_TEs\tmatch_part\t1\t100\t1e-20\t-\t.\tID=mp1-1_chr1_PROTOP_B:classII:TIR;Parent=ms1_chr1_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 85 228;Identity=30.56\n") - f.write("chr1\tprojectName_REPET_TEs\tmatch\t100\t1000\t0.0\t-\t.\tID=ms2_chr1_DMRT1C:classI:?;Target=DMRT1C:classI:? 85 228;TargetLength=8;Identity=30.56\n") - f.write("chr1\tprojectName_REPET_TEs\tmatch_part\t100\t1000\t1e-30\t-\t.\tID=mp2-1_chr1_DMRT1C:classI:?;Parent=ms2_chr1_DMRT1C:classI:?;Target=DMRT1C:classI:? 85 228;Identity=30.56\n") - - def _writeExpPathGFFFile_split_file1(self, inFileName): - with open(inFileName, 'w') as f: - f.write("##gff-version 3\n") - f.write("##sequence-region dmel_chr4 1 18\n") - f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4630\t4889\t0.0\t+\t.\tID=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 232 512;TargetLength=8\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4630\t4704\t0.0\t+\t.\tID=mp21-1_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 232 312;Identity=84.4417\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4837\t4889\t0.0\t+\t.\tID=mp21-2_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 456 512;Identity=84.4417\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4364\t4611\t0.0\t+\t.\tID=ms6_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;TargetLength=10;Identity=91.24\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4364\t4611\t0.0\t+\t.\tID=mp6-1_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms6_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;Identity=91.24\n" % self._projectName) - - def _writeExpPathGFFFile_split_file2(self, inFileName): - with open(inFileName, 'w') as f: - f.write("##gff-version 3\n") - f.write("##sequence-region dmel_chr1 1 25\n") - f.write("dmel_chr1\t%s_REPET_TEs\tmatch\t4364\t4611\t0.0\t+\t.\tID=ms35_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;TargetLength=10;Identity=91.24\n" % self._projectName) - f.write("dmel_chr1\t%s_REPET_TEs\tmatch_part\t4364\t4611\t0.0\t+\t.\tID=mp35-1_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms35_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;Identity=91.24\n" % self._projectName) - - def _writeExpPathGFFFile_split_file3(self, inFileName): - with open(inFileName, 'w') as f: - f.write("##gff-version 3\n") - f.write("##sequence-region dmel_chr4 1 18\n") - f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t3143\t4364\t0.0\t-\t.\tID=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 24 2206;TargetLength=8\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3143\t3361\t0.0\t-\t.\tID=mp66-1_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1988 2206;Identity=89.7202\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3345\t3410\t0.0\t-\t.\tID=mp66-2_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1654 1719;Identity=54.55\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3448\t3572\t0.0\t-\t.\tID=mp66-3_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1495 1619;Identity=77.3433\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3564\t3693\t0.0\t-\t.\tID=mp66-4_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1380 1509;Identity=83.7306\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3705\t3857\t0.0\t-\t.\tID=mp66-5_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 539 691;Identity=84.5762\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3861\t3992\t0.0\t-\t.\tID=mp66-6_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 403 534;Identity=67.1422\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3985\t4106\t0.0\t-\t.\tID=mp66-7_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 290 411;Identity=76.612\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4102\t4248\t0.0\t-\t.\tID=mp66-8_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 139 285;Identity=75.3027\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4236\t4364\t0.0\t-\t.\tID=mp66-9_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 24 152;Identity=66.6657\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4412\t4889\t0.0\t-\t.\tID=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 553 1082;TargetLength=10\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4412\t4501\t5e-108\t-\t.\tID=mp27-1_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 993 1082;Identity=91.3066\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4483\t4652\t9e-146\t-\t.\tID=mp27-2_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 821 990;Identity=86.5572\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4672\t4775\t9e-146\t-\t.\tID=mp27-3_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 684 787;Identity=88.8013\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4782\t4889\t9e-141\t-\t.\tID=mp27-4_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 553 661;Identity=53.7067\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4917\t5195\t0.0\t+\t.\tID=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7030 7303;TargetLength=12\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4917\t5007\t2e-144\t+\t.\tID=mp141-1_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Parent=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7030 7120;Identity=94.1756\n" % self._projectName) - f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4976\t5195\t2e-144\t+\t.\tID=mp141-2_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Parent=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7087 7303;Identity=82.2343\n" % self._projectName) - - def _writeClassifFile(self, inputFileName): - f = open(inputFileName, "w") - f.write("PotentialHostGene-chim_fTest05105818-B-G11-Map20\t1240\t+\tPotentialChimeric\tNA\tPotentialHostGene\tNA\tCI=100; coding=(HG_BLRn: FBtr0089196_Dmel_r4.3: 95.65%); other=(TE_BLRtx: PROTOP:classII:TIR: 12.03%, PROTOP_A:classII:TIR: 49.14%; TermRepeats: termTIR: 49; SSRCoverage=0.25<0.75)\n") - f.write("DTX-comp-chim_fTest05105818-B-G7-Map3_reversed\t1944\t-\tPotentialChimeric\tII\tTIR\tcomplete\tCI=33; coding=(TE_BLRtx: PROTOP:classII:TIR: 12.77%, PROTOP_A:classII:TIR: 25.16%, PROTOP_A:classII:TIR: 100.00%); struct=(TElength: <700bps; TermRepeats: termTIR: 844); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 29.48%; SSRCoverage=0.24<0.75)\n") - f.write("DTX-incomp_fTest05105818-B-G9-Map3_reversed\t1590\t-\tok\tII\tTIR\tincomplete\tCI=33; coding=(TE_BLRtx: PROTOP:classII:TIR: 10.92%, PROTOP:classII:TIR: 11.03%, PROTOP_A:classII:TIR: 55.20%); struct=(TElength: >700bps); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60%; SSRCoverage=0.21<0.75)\n") - f.write("DTX-incomp_fTest05105818-B-P0.0-Map3\t1042\t.\tok\tII\tTIR\tincomplete\tCI=50; coding=(TE_BLRtx: PROTOP:classII:TIR: 17.39%, PROTOP_A:classII:TIR: 22.17%); struct=(TElength: >700bps; TermRepeats: termTIR: 50); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 47.22%; SSRCoverage=0.25<0.75)\n") - f.write("DTX-comp_fTest05105818-B-P1.0-Map9_reversed\t1137\t-\tok\tII\tTIR\tcomplete\tCI=50; coding=(TE_BLRtx: PROTOP:classII:TIR: 6.70%, PROTOP_A:classII:TIR: 66.43%, PROTOP_B:classII:TIR: 6.42%); struct=(TElength: >700bps; TermRepeats: termTIR: 52); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 51.19%; SSRCoverage=0.22<0.75)\n") - f.write("RLX-incomp_fTest05105818-B-R12-Map3_reversed\t2284\t-\tok\tI\tLTR\tincomplete\tCI=28; coding=(TE_BLRtx: ROOA_I:classI:LTR_retrotransposon: 27.57%, ROOA_LTR:classI:LTR_retrotransposon: 94.56%; TE_BLRx: BEL11_AGp:classI:LTR_retrotransposon: 19.47%, BEL2-I_Dmoj_1p:classI:LTR_retrotransposon: 11.49%); struct=(TElength: >700bps); other=(SSRCoverage=0.07<0.75)\n") - f.write("DTX-incomp_fTest05105818-B-R19-Map4\t705\t+\tok\tII\tTIR\tincomplete\tCI=66; coding=(TE_BLRtx: TC1-2_DM:classII:TIR: 42.70%; TE_BLRx: TC1-2_DMp:classII:TIR: 41.18%); struct=(TElength: >700bps); other=(SSRCoverage=0.14<0.75)\n") - f.write("DHX-incomp_fTest05105818-B-R1-Map4\t2367\t.\tok\tII\tHelitron\tincomplete\tCI=20; coding=(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00%, DNAREP1_DYak:classII:Helitron: 9.08%); struct=(TElength: >700bps); other=(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52%; SSRCoverage=0.18<0.75)\n") - f.write("noCat_fTest05105818-B-R2-Map6\t4638\t.\tok\tnoCat\tnoCat\tNA\tCI=NA; coding=(HG_BLRn: FBtr0089179_Dmel_r4.3: 73.65%); struct=(SSRCoverage=0.05<0.75)\n") - f.write("PotentialHostGene-chim_fTest05105818-B-R4-Map5_reversed\t1067\t-\tPotentialChimeric\tNA\tPotentialHostGene\tNA\tCI=100; coding=(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%); other=(TE_BLRtx: PROTOP:classII:TIR: 13.06%, PROTOP_A:classII:TIR: 37.47%; SSRCoverage=0.27<0.75)\n") - f.write("DTX-incomp_fTest05105818-B-R9-Map3_reversed\t714\t-\tok\tII\tTIR\tincomplete\tCI=66; coding=(TE_BLRtx: TC1_DM:classII:TIR: 40.88%; TE_BLRx: Tc1-1_TCa_1p:classII:TIR: 30.18%, Tc1-3_FR_1p:classII:TIR: 9.97%); struct=(TElength: >700bps); other=(SSRCoverage=0.08<0.75)\n") - f.close() - - def _writePathFile_withClassif(self,inFileName): - f = open(inFileName,'w') - f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030\t228\t85\t1e-40\t84\t30.56\n') - f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030\t522\t229\t1e-40\t106\t23.99\n') - f.write('3\tlm_SuperContig_30_v2\t78081\t78088\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n') - f.write('3\tlm_SuperContig_30_v2\t78089\t78588\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n') - f.write('4\tlm_SuperContig_30_v2\t88031\t88080\tDTX-incomp_fTest05105818-B-G1-Map3\t370\t420\t3e-23\t101\t31.89\n') - f.write('5\tlm_SuperContig_30_v2\t108588\t108081\tDTX-incomp_fTest05105818-B-G9-Map3_reversed\t590\t820\t3e-24\t101\t32.89\n') - f.write('6\tlm_SuperContig_30_v2\t118081\t118588\tPotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed\t154\t289\t3e-25\t101\t33.89\n') - f.write('7\tlm_SuperContig_30_v2\t288031\t288080\tnoCat_Blc22_fTest05105818-B-R2-Map6\t1900\t2090\t3e-26\t101\t34.89\n') - f.close() - - def _writeExpPathGFFFile_without_seq_withClassif(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_30_v2 1 120\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t78081\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;TargetDescription=CI:20 coding:(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00% | DNAREP1_DYak:classII:Helitron: 9.08%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52% SSRCoverage:0.18<0.75)\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78088\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209;Identity=30.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78089\t78588\t3e-22\t+\t.\tID=mp3-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350;Identity=35.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t88031\t88080\t0.0\t+\t.\tID=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t88031\t88080\t3e-23\t+\t.\tID=mp4-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t108081\t108588\t0.0\t-\t.\tID=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;TargetDescription=CI:33 coding:(TE_BLRtx: PROTOP:classII:TIR: 10.92% | PROTOP:classII:TIR: 11.03% | PROTOP_A:classII:TIR: 55.20%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60% SSRCoverage:0.21<0.75);Identity=32.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t108081\t108588\t3e-24\t-\t.\tID=mp5-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Parent=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;Identity=32.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t118081\t118588\t0.0\t+\t.\tID=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;TargetDescription=CI:100 coding:(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%) other:(TE_BLRtx: PROTOP:classII:TIR: 13.06% | PROTOP_A:classII:TIR: 37.47% SSRCoverage:0.27<0.75);Identity=33.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t118081\t118588\t3e-25\t+\t.\tID=mp6-1_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Parent=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;Identity=33.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms7_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Target=noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090;TargetDescription=CI:NA coding:(HG_BLRn: FBtr0089179_Dmel_r4.3: 73.65%) struct:(SSRCoverage:0.05<0.75);Identity=34.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp7-1_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Parent=ms7_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Target=noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090;Identity=34.89\n") - - f.close() - - def _writePathFile_withClassif_withIdenticalMatches(self,inFileName): - f = open(inFileName,'w') - f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030\t228\t85\t1e-40\t84\t30.56\n') - f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030\t522\t229\t1e-40\t106\t23.99\n') - f.write('3\tlm_SuperContig_30_v2\t78081\t78088\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n') - f.write('3\tlm_SuperContig_30_v2\t78089\t78588\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n') - f.write('4\tlm_SuperContig_30_v2\t88031\t88080\tDTX-incomp_fTest05105818-B-G1-Map3\t370\t420\t3e-23\t101\t31.89\n') - f.write('5\tlm_SuperContig_30_v2\t108588\t108081\tDTX-incomp_fTest05105818-B-G9-Map3_reversed\t590\t820\t3e-24\t101\t32.89\n') - f.write('6\tlm_SuperContig_30_v2\t118081\t118588\tPotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed\t154\t289\t3e-25\t101\t33.89\n') - - f.write('7\tlm_SuperContig_30_v2\t288031\t288080\tnoCat_Blc22_fTest05105818-B-R2-Map6\t1900\t2090\t3e-26\t101\t34.89\n') - f.write('8\tlm_SuperContig_30_v2\t288031\t288080\tDTX-incomp_fTest05105818-B-P0.0-Map3\t100\t190\t3e-26\t101\t39.89\n') - f.write('9\tlm_SuperContig_30_v2\t288031\t288080\tRLX-incomp_fTest05105818-B-R12-Map3_reversed\t1100\t1290\t3e-26\t101\t40.89\n') - f.write('10\tlm_SuperContig_30_v2\t288031\t288080\tPotentialHostGene-chim_fTest05105818-B-G11-Map20\t990\t1890\t3e-26\t101\t38.09\n') - - f.write('11\tlm_SuperContig_30_v2\t288031\t288080\tDTX-incomp_fTest05105818-B-G1-Map3\t990\t1890\t3e-26\t301\t38.09\n') - - f.write('12\tlm_SuperContig_30_v2\t388031\t388080\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n') - f.write('12\tlm_SuperContig_30_v2\t388081\t388380\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n') - - f.write('13\tlm_SuperContig_30_v2\t388031\t388080\tDTX-incomp_fTest05105818-B-P0.0-Map3\t119\t309\t3e-21\t101\t30.89\n') - f.write('13\tlm_SuperContig_30_v2\t388081\t388380\tDTX-incomp_fTest05105818-B-P0.0-Map3\t250\t450\t3e-22\t101\t35.89\n') - f.close() - - def _writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_30_v2 1 120\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t78081\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;TargetDescription=CI:20 coding:(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00% | DNAREP1_DYak:classII:Helitron: 9.08%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52% SSRCoverage:0.18<0.75)\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78088\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209;Identity=30.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78089\t78588\t3e-22\t+\t.\tID=mp3-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350;Identity=35.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t88031\t88080\t0.0\t+\t.\tID=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t88031\t88080\t3e-23\t+\t.\tID=mp4-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t108081\t108588\t0.0\t-\t.\tID=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;TargetDescription=CI:33 coding:(TE_BLRtx: PROTOP:classII:TIR: 10.92% | PROTOP:classII:TIR: 11.03% | PROTOP_A:classII:TIR: 55.20%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60% SSRCoverage:0.21<0.75);Identity=32.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t108081\t108588\t3e-24\t-\t.\tID=mp5-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Parent=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;Identity=32.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t118081\t118588\t0.0\t+\t.\tID=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;TargetDescription=CI:100 coding:(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%) other:(TE_BLRtx: PROTOP:classII:TIR: 13.06% | PROTOP_A:classII:TIR: 37.47% SSRCoverage:0.27<0.75);Identity=33.89\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t118081\t118588\t3e-25\t+\t.\tID=mp6-1_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Parent=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;Identity=33.89\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms10_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Target=PotentialHostGene-chim_fTest05105818-B-G11-Map20 990 1890;OtherTargets=RLX-incomp_fTest05105818-B-R12-Map3_reversed 1100 1290, DTX-incomp_fTest05105818-B-P0.0-Map3 100 190, noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp10-1_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Parent=ms10_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Target=PotentialHostGene-chim_fTest05105818-B-G11-Map20 990 1890\n") - - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms11_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 990 1890;Identity=38.09\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp11-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms11_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 990 1890;Identity=38.09\n") - - #TODO: - #Should this case really occur : If merging multiple match-parts, the current behaviour needs to be fixed to get correct subject start/end coordinates - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t388031\t388380\t0.0\t+\t.\tID=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;OtherTargets=DTX-incomp_fTest05105818-B-P0.0-Map3 119 309\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t388031\t388080\t3e-21\t+\t.\tID=mp12-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209\n") - f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t388081\t388380\t3e-22\t+\t.\tID=mp12-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350\n") - f.close() - - def _writeTablesFile_withTESeqTables(self, tableType): - tableFile = open( self._tablesFileName, "w" ) - string = "%s_REPET_TEs\t%s\t%s_chr_allTEs_nr_noSSR_join_%s\t%s_refTEs_seq\n" % (self._projectName, tableType, self._projectName, tableType, self._projectName) - tableFile.write(string) - string = "%s_REPET_TEs\t%s\t%s_chr_bankBLRtx_%s\t%s_bankBLRtx_nt_seq\n" % (self._projectName, tableType, self._projectName, tableType, self._projectName) - tableFile.write(string) - tableFile.close() - - def _writeTablesFile(self, tableType): - tableFile = open( self._tablesFileName, "w" ) - string = "%s_REPET_TEs\t%s\t%s_chr_allTEs_nr_noSSR_join_%s\n" % (self._projectName, tableType, self._projectName, tableType) - tableFile.write(string) - tableFile.close() - - def _writePathFile(self,inFileName): - f = open(inFileName,'w') - f.write('1\tlm_SuperContig_29_v2\t193781\t194212\tDTX-incomp_DmelChr4-L-B1-Map3\t228\t85\t1e-40\t84\t30.56\n') - f.write('2\tlm_SuperContig_29_v2\t192832\t193704\tDTX-incomp_DmelChr4-L-B1-Map3\t522\t229\t1e-40\t106\t23.99\n') - f.write('3\tlm_SuperContig_29_v2\t78031\t78080\tDTX-incomp_DmelChr4-B-P0.0-Map3\t19\t209\t3e-21\t101\t30.89\n') - f.write('3\tlm_SuperContig_29_v2\t78081\t78588\tDTX-incomp_DmelChr4-B-P0.0-Map3\t19\t209\t3e-21\t101\t30.89\n') - f.close() - - def _writePathFile2(self,inFileName): - f = open(inFileName,'w') - f.write('1\tchr1\t1\t100\tPROTOP_B:classII:TIR\t228\t85\t1e-20\t84\t30.56\n') - f.write('2\tchr1\t100\t1000\tDMRT1C:classI:?\t228\t85\t1e-30\t84\t30.56\n') - f.close() - - def _writePathFile_refTEs_annotation(self,inFileName): - f = open(inFileName,'w') - f.write('6\tdmel_chr4\t4364\t4611\tDTX-incomp_DmelChr4-L-B1-Map3\t854\t1150\t0\t1475\t91.24\n') - f.write('21\tdmel_chr4\t4630\t4704\tDTX-incomp_DmelChr4-B-P0.0-Map3\t232\t312\t0\t65\t84.4417\n') - f.write('21\tdmel_chr4\t4837\t4889\tDTX-incomp_DmelChr4-B-P0.0-Map3\t456\t512\t0\t46\t84.4417\n') - f.write('35\tdmel_chr1\t4364\t4611\tDTX-incomp_DmelChr4-L-B1-Map3\t854\t1150\t0\t1475\t91.24\n') - f.close() - - def _writePathFile_bankBLRtx_annotation(self,inFileName): - f = open(inFileName, 'w') - f.write('27\tdmel_chr4\t4412\t4501\tPROTOP_B:classII:TIR\t1082\t993\t5e-108\t702\t91.3066\n') - f.write('27\tdmel_chr4\t4483\t4652\tPROTOP_B:classII:TIR\t990\t821\t9e-146\t707\t86.5572\n') - f.write('27\tdmel_chr4\t4672\t4775\tPROTOP_B:classII:TIR\t787\t684\t9e-146\t707\t88.8013\n') - f.write('27\tdmel_chr4\t4782\t4889\tPROTOP_B:classII:TIR\t661\t553\t9e-141\t356\t53.7067\n') - f.write('66\tdmel_chr4\t3143\t3361\tDMRT1C:classI:?\t2206\t1988\t0\t1878\t89.7202\n') - f.write('66\tdmel_chr4\t3345\t3410\tDMRT1C:classI:?\t1719\t1654\t0\t313\t54.55\n') - f.write('66\tdmel_chr4\t3448\t3572\tDMRT1C:classI:?\t1619\t1495\t0\t1252\t77.3433\n') - f.write('66\tdmel_chr4\t3564\t3693\tDMRT1C:classI:?\t1509\t1380\t0\t1565\t83.7306\n') - f.write('66\tdmel_chr4\t3705\t3857\tDMRT1C:classI:?\t691\t539\t0\t1252\t84.5762\n') - f.write('66\tdmel_chr4\t3861\t3992\tDMRT1C:classI:?\t534\t403\t0\t1565\t67.1422\n') - f.write('66\tdmel_chr4\t3985\t4106\tDMRT1C:classI:?\t411\t290\t0\t1252\t76.612\n') - f.write('66\tdmel_chr4\t4102\t4248\tDMRT1C:classI:?\t285\t139\t0\t1565\t75.3027\n') - f.write('66\tdmel_chr4\t4236\t4364\tDMRT1C:classI:?\t152\t24\t0\t1565\t66.6657\n') - f.write('141\tdmel_chr4\t4917\t5007\tBATUMI_I:classI:LTR_retrotransposon\t7030\t7120\t2e-144\t984\t94.1756\n') - f.write('141\tdmel_chr4\t4976\t5195\tBATUMI_I:classI:LTR_retrotransposon\t7087\t7303\t2e-144\t2098\t82.2343\n') - f.close() - - def _writePathFileReverse(self,inFileName): - f = open(inFileName,'w') - f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)\t228\t85\t1e-40\t84\t30.56\n') - f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)\t522\t229\t1e-40\t106\t23.99\n') - f.write('3\tlm_SuperContig_29_v2\t78080\t78031\txnc164_090 related to multidrug resistance protein\t19\t209\t3e-21\t101\t30.89\n') - f.write('3\tlm_SuperContig_29_v2\t78588\t78081\txnc164_090 related to multidrug resistance protein\t19\t209\t3e-21\t101\t30.89\n') - f.close() - - def _writeSetFile(self,inFileName): - f = open(inFileName,'w') - f.write('1\tset1\tlm_SuperContig_29_v2\t193781\t194212\n') - f.write('2\tset2\tlm_SuperContig_29_v2\t192832\t193704\n') - f.write('3\tset3\tlm_SuperContig_29_v2\t78031\t78080\n') - f.write('3\tset3\tlm_SuperContig_29_v2\t78081\t78588\n') - f.close() - - def _writeSetFileReverse(self,inFileName): - f = open(inFileName,'w') - f.write('1\tset1\tlm_SuperContig_29_v2\t193781\t194212\n') - f.write('2\tset2\tlm_SuperContig_29_v2\t192832\t193704\n') - f.write('3\tset3\tlm_SuperContig_29_v2\t78080\t78031\n') - f.write('3\tset3\tlm_SuperContig_29_v2\t78588\t78081\n') - f.close() - - def _writeExpEmptyPathGFFFile(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_30_v2 1 120\n") - f.close() - - def _writeExpPathGFFFile(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.write("##FASTA\n") - self._writeSeq1(f) - f.close() - - def _writeExpEmptyPathGFFFileWithSeq(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_30_v2 1 120\n") - f.write("##FASTA\n") - self._writeSeq2(f) - f.close() - - def _writeExpPathGFFFile_without_seq(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.close() - - def _writeExpPathGFFFile_without_seq_and_match_part_not_comulsory(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n") - f.close() - - def _writeExpPathGFFFileReversed(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Parent=ms1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 85 228;Identity=30.56\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Parent=ms2_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 229 522;Identity=23.99\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t-\t.\tID=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t-\t.\tID=mp3-1_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Parent=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209;Identity=30.89\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t-\t.\tID=mp3-2_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Parent=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209;Identity=30.89\n") - f.write("##FASTA\n") - self._writeSeq1(f) - f.close() - - def _writeExpSetGFFFile(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t+\t.\tID=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t0.0\t+\t.\tID=mp1-1_lm_SuperContig_29_v2_set1;Parent=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t+\t.\tID=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t0.0\t+\t.\tID=mp2-1_lm_SuperContig_29_v2_set2;Parent=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 558\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t0.0\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 50\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t0.0\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 508\n") - f.write("##FASTA\n") - self._writeSeq1(f) - f.close() - - def _writeExpSetGFFFileReversed(self, inFileName): - f = open(inFileName, 'w') - f.write("##gff-version 3\n") - f.write("##sequence-region lm_SuperContig_29_v2 1 120\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t+\t.\tID=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t0.0\t+\t.\tID=mp1-1_lm_SuperContig_29_v2_set1;Parent=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t+\t.\tID=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t0.0\t+\t.\tID=mp2-1_lm_SuperContig_29_v2_set2;Parent=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t-\t.\tID=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 558\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t0.0\t-\t.\tID=mp3-1_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 50\n") - f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t0.0\t-\t.\tID=mp3-2_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 508\n") - f.write("##FASTA\n") - self._writeSeq1(f) - f.close() - - def _writeFastaFile(self, inFileName): - f = open(inFileName,'w') - self._writeSeq2(f) - self._writeSeq1(f) - f.close() - - def _writeFastaFileExtended(self, inFileName): - f = open(inFileName,'w') - self._writeSeq2(f) - self._writeSeq1(f) - f.write(">chr1\n") - f.write("CTAAGCTGCGCTATGTAG\n") - f.close() - - def _writeSeq1(self, f): - f.write('>lm_SuperContig_29_v2\n') - f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n') - f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n') - - def _writeSeq2(self, f): - f.write('>lm_SuperContig_30_v2\n') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') - f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') - - def _writeFastaFile_DmelChr4(self, inFileName): - f = open(inFileName,'w') - f.write(">dmel_chr4\n") - f.write("CTAAGCTGCGCTATGTAG\n") - f.write(">dmel_chr1\n") - f.write("CGTAACGCTAGCGCTTATAGTGAGC\n") - f.close() - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_GameXmlMaker.py --- a/commons/tools/tests/Test_F_GameXmlMaker.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,281 +0,0 @@ -import unittest -import os -import glob -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbFactory import DbFactory -from commons.tools.GameXmlMaker import GameXmlMaker - - -class Test_F_GameXmlMaker(unittest.TestCase): - - def setUp(self): - pass - - - def tearDown(self): - FileUtils.removeFilesByPattern("*gamexml") - - - def test_run_as_script_step1(self): - fastaFileName = "input.fa" - self._writeFastaFile(fastaFileName) - - cmd = "GameXmlMaker.py -f %s " % fastaFileName - os.system(cmd) - - lObsGameXmlNew = glob.glob("*.gamexml") - self._writeStep1ExpectedXmls() - self.assertTrue(len(lObsGameXmlNew) > 0) - for obsGameXmlNew in lObsGameXmlNew: - expGameXmlNew = "exp_%s" % obsGameXmlNew - self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew)) - - os.remove(fastaFileName) - - def test_run_as_script_step2(self): - self._tableFileName = "annotation_tables.txt" - - self._writeStep2InputTableFile() - self._writeStep2InputXmls() - self._writeStep2InputPathFile() - self._writeStep2InputSetFile() - self._writeStep2InputMapFile() - self._createStep2Tables() - - lObsGameXmlNew = glob.glob("*.gamexml") - - cmd = "GameXmlMaker.py -t %s " % self._tableFileName - os.system(cmd) - - self._writeStep2ExpXmls() - - self.assertTrue(len(lObsGameXmlNew) > 0) - for obsGameXmlNew in lObsGameXmlNew: - expGameXmlNew = "exp_%s" % obsGameXmlNew - self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew)) - - os.remove("Test_F_GameXmlMaker_path.path") - os.remove("Test_F_GameXmlMaker_set.set") - os.remove("Test_F_GameXmlMaker_chk_map.map") - - os.remove(self._tableFileName) - os.system("ListAndDropTables.py -d Test_F_GameXmlMaker") - - def test_run_step2(self): - self._tableFileName = "annotation_tables.txt" - - self._writeStep2InputTableFile() - self._writeStep2InputXmls() - self._writeStep2InputPathFile() - self._writeStep2InputSetFile() - self._writeStep2InputMapFile() - self._createStep2Tables() - - lObsGameXmlNew = glob.glob("*.gamexml") - - iGameXmlMaker = GameXmlMaker(tablesFileName = self._tableFileName) - iGameXmlMaker.run() - self._writeStep2ExpXmls() - self.assertTrue(len(lObsGameXmlNew) > 0) - for obsGameXmlNew in lObsGameXmlNew: - expGameXmlNew = "exp_%s" % obsGameXmlNew - self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew)) - - os.remove("Test_F_GameXmlMaker_path.path") - os.remove("Test_F_GameXmlMaker_set.set") - os.remove("Test_F_GameXmlMaker_chk_map.map") - - os.remove(self._tableFileName) - os.system("ListAndDropTables.py -d Test_F_GameXmlMaker") - - def _writeFastaFile(self, inFileName): - f = open(inFileName,'w') - f.write('>seq1\n') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') - f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') - f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA\n') - f.write('>seq2\n') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') - f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') - f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n') - f.write('>seq3\n') - f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n') - f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n') - f.write('>seq4\n') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n') - f.write('CAGGAATCATGAAGGGTACGACTGTTCG\n') - f.close() - - def _writeStep1ExpectedXmls(self): - f = open("exp_seq1.gamexml", 'w') - f.write('seq1') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA') - f.write('seq11165') - f.close() - f = open("exp_seq2.gamexml", 'w') - f.write('seq2') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT') - f.write('seq21180') - f.close() - f = open("exp_seq3.gamexml", 'w') - f.write('seq3') - f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA') - f.write('seq31120') - f.close() - f = open("exp_seq4.gamexml", 'w') - f.write('seq4') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG') - f.write('seq4188') - f.close() - - def _createStep2Tables(self): - iDb = DbFactory.createInstance() - iDb.createTable("Test_F_GameXmlMaker_set", "set", "Test_F_GameXmlMaker_set.set", True) - iDb.createTable("Test_F_GameXmlMaker_chk_map", "map", "Test_F_GameXmlMaker_chk_map.map", True) - iDb.createTable("Test_F_GameXmlMaker_path", "path", "Test_F_GameXmlMaker_path.path", True) - iDb.close() - - def _writeStep2InputXmls(self): - f = open("seq1.gamexml", 'w') - f.write('seq1') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA') - f.write('seq11165') - f.close() - f = open("seq2.gamexml", 'w') - f.write('seq2') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT') - f.write('seq21180') - f.close() - f = open("seq3.gamexml", 'w') - f.write('seq3') - f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA') - f.write('seq31120') - f.close() - f = open("seq4.gamexml", 'w') - f.write('seq4') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG') - f.write('seq4188') - f.close() - - def _writeStep2InputPathFile(self): - f = open("Test_F_GameXmlMaker_path.path", 'w') - f.write("1\tseq1\t1\t10\tTE1\t1\t10\t0\t550\t80.7\n") - f.write("2\tseq1\t15\t50\tTE1\t12\t47\t0\t770\t90.8\n") - f.write("2\tseq1\t55\t70\tTE1\t50\t65\t0\t5410\t97.7\n") - f.write("3\tseq1\t75\t80\tTE2\t10\t15\t0\t8710\t60.0\n") - f.write("4\tseq2\t1\t10\tTE2\t20\t30\t0\t5410\t75.7\n") - f.write("5\tseq3\t1\t120\tTE2\t450\t550\t0\t5410\t75.7\n") - f.close() - - def _writeStep2InputSetFile(self): - f = open("Test_F_GameXmlMaker_set.set", 'w') - f.write("1\tseq1\tseq1\t1\t10\n") - f.write("2\tseq1\tseq1\t15\t50\n") - f.write("3\tseq1\tseq1\t75\t80\n") - f.write("4\tseq2\tseq2\t1\t10\n") - f.write("5\tseq3\tseq3\t1\t120\n") - f.close() - - def _writeStep2InputMapFile(self): - f = open("Test_F_GameXmlMaker_chk_map.map", 'w') - f.write("chunk1\tseq1\t1\t200000\n") - f.write("chunk2\tseq1\t190001\t390000\n") - f.write("chunk3\tseq3\t380001\t580000\n") - f.write("chunk4\tseq4\t570001\t770000\n") - f.write("chunk5\tseq5\t760001\t960000\n") - f.write("chunk6\tseq6\t950001\t1150000\n") - f.write("chunk7\tseq7\t1140001\t1281640\n") - f.close() - - def _writeStep2ExpXmls(self): - f = open("exp_seq1.gamexml", 'w') - f.write('seq1') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA') - f.write('seq11165') - f.write('Test_F_GameXmlMaker_pathdbTE1::1') - f.write('110') - f.write('11080.7TE1::2') - f.write('155012') - f.write('4790.85570') - f.write('506597.7TE2::3') - f.write('75801015') - f.write('60.0') - f.write('Test_F_GameXmlMaker_setdb') - f.write('seq1::1') - f.write('110') - f.write('-1-1') - f.write('0') - f.write('seq1::2') - f.write('1550') - f.write('-1-1') - f.write('0') - f.write('seq1::3') - f.write('7580') - f.write('-1-1') - f.write('0') - f.write('Test_F_GameXmlMaker_chk_mapdb') - f.write('chunk1::-1') - f.write('1200000') - f.write('-1-1') - f.write('0') - f.write('chunk2::-1') - f.write('190001390000') - f.write('-1-10') - f.close() - - f = open("exp_seq2.gamexml", 'w') - f.write('seq2') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT') - f.write('seq21180') - f.write('Test_F_GameXmlMaker_pathdbTE2::4') - f.write('110') - f.write('2030') - f.write('75.7') - f.write('Test_F_GameXmlMaker_setdbseq2::4') - f.write('110') - f.write('-1-1') - f.write('0') - f.write('Test_F_GameXmlMaker_chk_mapdb') - f.close() - - f = open("exp_seq3.gamexml", 'w') - f.write('seq3') - f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA') - f.write('seq31120') - f.write('Test_F_GameXmlMaker_pathdbTE2::5') - f.write('1120') - f.write('450550') - f.write('75.7') - f.write('Test_F_GameXmlMaker_setdbseq3::5') - f.write('1120') - f.write('-1-1') - f.write('0') - f.write('Test_F_GameXmlMaker_chk_mapdb') - f.write('chunk3::-1') - f.write('380001580000') - f.write('-1-1') - f.write('0') - f.close() - - f = open("exp_seq4.gamexml", 'w') - f.write('seq4') - f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG') - f.write('seq4188') - f.write('Test_F_GameXmlMaker_pathdb') - f.write('Test_F_GameXmlMaker_setdb') - f.write('Test_F_GameXmlMaker_chk_mapdb') - f.write('chunk4::-1') - f.write('570001770000') - f.write('-1-1') - f.write('0') - f.close() - - def _writeStep2InputTableFile(self): - f = open(self._tableFileName,'w') - f.write("Test_F_GameXmlMaker_path\tpath\tTest_F_GameXmlMaker_path\n") - f.write("Test_F_GameXmlMaker_set\tset\tTest_F_GameXmlMaker_set\n") - f.write("Test_F_GameXmlMaker_chk_map\tmap\tTest_F_GameXmlMaker_chk_map") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_GetMultiAlignAndPhylogenyPerTErefSeq.py --- a/commons/tools/tests/Test_F_GetMultiAlignAndPhylogenyPerTErefSeq.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,147 +0,0 @@ -import subprocess -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbMySql import DbMySql -from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq -from shutil import rmtree -from glob import glob - -class Test_F_GetMultAlignAndPhylogenyPerTErefSeq(unittest.TestCase): - - def setUp(self): - self._verbosity = 3 - - self._testPrefix = 'Test_GMAAPperTErefSeq_' - self._configFileName = "%sConfig.cfg" % self._testPrefix - self._iDb = DbMySql() - - self.inPathTableName = "%sDmelChr4_chr_allTEs_nr_noSSR_join_path" % (self._testPrefix) - self.inPathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"] - self._iDb.createTable(self.inPathTableName, "path", self.inPathFileName, True) - - self.RefTETableName = "%sDmelChr4_refTEs" % (self._testPrefix) - self.RefTEFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"] - self._iDb.createTable(self.RefTETableName, "seq", self.RefTEFileName, True) - - self.genomeTableName = "%sDmelChr4_chr" % (self._testPrefix) - self.genomeFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"] - self._iDb.createTable(self.genomeTableName, "seq", self.genomeFileName, True) - - try: - os.makedirs(self._testPrefix) - except:pass - os.chdir(self._testPrefix) - self._writeConfigFile() - -# self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"] -# self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"] -# self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"] -# self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"] -# self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"] -# self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"] - - -# inputFastaFileName = "input_TEannot_refTEs.fa" -# os.symlink(self._expFastaFileName_Copy, inputFastaFileName) - -# self._tableName = "Dummy_Atha_refTEs_seq" -# self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True) -# os.remove(inputFastaFileName) -# -# self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0] -# self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0] -# self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0] -# self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0] -# self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0] -# self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0] - - def tearDown(self): -# self._iDb.dropTable(self.inPathTableName) -# self._iDb.dropTable(self.RefTETableName) -# self._iDb.dropTable(self.genomeTableName) -# self._iDb.close() - - os.chdir("..") -# try: -# rmtree(self._testPrefix) -# except:pass - - -# def test_run_step1(self): -# iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, configFileName=self._configFileName, step=1, verbosity=self._verbosity) -# iGMAAPperTErefSeq.run() -# -# copiesFiles = glob("*_copies.fa") -# self.assertTrue(len(copiesFiles) > 0) -# self.assertTrue(os.stat("DmelChr4-B-R9-Map3_NoCat_copies.fa")[6] != 0)#check if file is empty -# -# def test_run_step1Step2Map(self): -# iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity) -# iGMAAPperTErefSeq.run() -# iGMAAPperTErefSeq.step = 2 -# iGMAAPperTErefSeq.run() -# -# self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0) -# -# def test_run_step1Step2RefAlign(self): -# iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="RefAlign", configFileName=self._configFileName, step=1, verbosity=self._verbosity) -# iGMAAPperTErefSeq.run() -# iGMAAPperTErefSeq.step = 2 -# iGMAAPperTErefSeq.run() -# -# self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_refalign.fa_aln")[6] != 0) - - def test_run_step1Step2Step3Map(self): - iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity) - iGMAAPperTErefSeq.run() - iGMAAPperTErefSeq.step = 2 - iGMAAPperTErefSeq.run() - iGMAAPperTErefSeq.step = 3 - iGMAAPperTErefSeq.run() - - self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0) - - def _writeConfigFile(self): - f = open(self._configFileName, "w") - f.write("[repet_env]\n") - f.write("repet_host: %s\n" % os.environ["REPET_HOST"]) - f.write("repet_user: %s\n" % os.environ["REPET_USER"]) - f.write("repet_pw: %s\n" % os.environ["REPET_PW"]) - f.write("repet_db: %s\n" % os.environ["REPET_DB"]) - f.write("repet_port: %s\n" % os.environ["REPET_PORT"]) - f.write("repet_job_manager: SGE\n") - f.close() - - -# def test_run_as_script_step1Step2Map(self): -# #cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -m 'Map' -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName) -# cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName) -# subprocess.call(cmd, shell = True) -# -# cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 2 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName) -# subprocess.call(cmd, shell = True) -# -# self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0) - - -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag)) - -# def test_run_as_script_step2(self): -# cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName) -# print cmd -# subprocess.call(cmd, shell = True) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag)) - -if __name__ == "__main__": - unittest.main() diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_GetSpecificTELibAccordingToAnnotation.py --- a/commons/tools/tests/Test_F_GetSpecificTELibAccordingToAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -import subprocess -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbMySql import DbMySql -from commons.tools.GetSpecificTELibAccordingToAnnotation import GetSpecificTELibAccordingToAnnotation - -class Test_F_GetSpecificTELibAccordingToAnnotation(unittest.TestCase): - - def setUp(self): - self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"] - self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"] - self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"] - self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"] - self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"] - self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"] - - self._inFileName = "%s/Tools/GiveInfoTeAnnotFile.txt" % os.environ["REPET_DATA"] - inputFastaFileName = "input_TEannot_refTEs.fa" - os.symlink(self._expFastaFileName_Copy, inputFastaFileName) - self._iDb = DbMySql() - self._tableName = "Dummy_Atha_refTEs_seq" - self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True) - os.remove(inputFastaFileName) - - self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0] - self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0] - self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0] - self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0] - self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0] - self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0] - - def tearDown(self): - self._iDb.dropTable(self._tableName) - self._iDb.close() - os.remove(self._obsFileName_FullLengthCopy) - os.remove(self._obsFileName_Copy) - os.remove(self._obsFileName_FullLengthFrag) - os.remove(self._obsFastaFileName_FullLengthCopy) - os.remove(self._obsFastaFileName_Copy) - os.remove(self._obsFastaFileName_FullLengthFrag) - - def test_run(self): - iGetTELib = GetSpecificTELibAccordingToAnnotation(self._inFileName) - iGetTELib.setTableName(self._tableName) - iGetTELib.run() - - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag)) - - def test_run_as_script(self): - cmd = "GetSpecificTELibAccordingToAnnotation.py -i %s -t %s -v 4" % (self._inFileName, self._tableName) - subprocess.call(cmd, shell = True) - - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py --- a/commons/tools/tests/Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ -import os -import unittest -from commons.core.utils.FileUtils import FileUtils - -CURRENT_DIR = os.getcwd() - -class Test_F_HmmOutput2alignAndTransformCoordInNtAndFilterScores_script(unittest.TestCase): - - def setUp(self): - self._inputFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/test_hmmpfam_output" - self._outputFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmpfam_output.align" - self._prg = "HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py" - self._inputFile2 = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest" - self._consensusFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/ConsensusTestFile_nt.fsa" - self._inputFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput" - self._outputFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscan_output.align" - self._expectedFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput.align" - os.chdir(CURRENT_DIR) - - def testHmmpfamOuput2align(self): - cmd = self._prg - cmd += " -i %s" % ( self._inputFile ) - cmd += " -o %s" % ( self._outputFile ) - os.system( cmd ) - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._inputFile + ".align", self._outputFile)) - self._clean() - - def testHmmpfamOuput2align_clean_option(self): - os.system( "cp " + self._inputFile + " " + self._inputFile + "bis" ) - cmd = self._prg - cmd += " -i %s" % ( self._inputFile + "bis" ) - cmd += " -o %s" % ( self._outputFile ) - cmd += " -c" - os.system( cmd ) - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue( FileUtils.are2FilesIdentical( self._inputFile + ".align", self._outputFile) ) - self.assertFalse( FileUtils.isRessourceExists( self._inputFile + "bis" ) ) - self._clean() - - def testHmmpfamOutput2alignAndTransformCoordInNtAndFilterScores(self): - cmd = self._prg - cmd += " -i %s" % ( self._inputFile2 ) - cmd += " -o %s" % ( self._outputFile ) - cmd += " -T %s" % ( self._consensusFile ) - os.system( cmd ) - self._expectedFile = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/PostPostProcessTestFiltered.align" - self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile)) - self._clean() - - def testHmmscanOuput2align(self): - cmd = self._prg - cmd += " -i %s" % ( self._inputFileScan ) - cmd += " -o %s" % ( self._outputFileScan ) - cmd += " -p hmmscan" - os.system( cmd ) - self.assertTrue(FileUtils.isRessourceExists(self._outputFileScan)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFileScan)) - self._cleanScan() - - def testHmmscanOuput2align_clean_option(self): - os.system( "cp " + self._inputFileScan + " " + self._inputFileScan + "bis" ) - cmd = self._prg - cmd += " -i %s" % ( self._inputFileScan + "bis" ) - cmd += " -o %s" % ( self._outputFileScan ) - cmd += " -c -p hmmscan" - os.system( cmd ) - self.assertTrue( FileUtils.are2FilesIdentical( self._expectedFile, self._outputFileScan) ) - self.assertFalse( FileUtils.isRessourceExists( self._inputFileScan + "bis" ) ) - self._cleanScan() - - def testHmmscanOutput2alignAndTransformCoordInNtAndFilterScores(self): - self._inputFileScan2 = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/hmmscanOutput" - self._consensusFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/repetHmmscan.fa" - self._expectedFileScan = os.environ["REPET_PATH"] + "/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/hmmscanTransformedExpected.align" - cmd = self._prg - cmd += " -i %s" % ( self._inputFileScan2 ) - cmd += " -o %s" % ( self._outputFileScan ) - cmd += " -T %s" % ( self._consensusFileScan ) - cmd += " -p hmmscan" - os.system( cmd ) - self.assertTrue(FileUtils.isRessourceExists(self._outputFileScan)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFileScan, self._outputFileScan)) - self._cleanScan() - - def _clean(self): - os.system( "rm " + self._outputFile ) - - def _cleanScan(self): - os.system( "rm " + self._outputFileScan ) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_LaunchBlaster.py --- a/commons/tools/tests/Test_F_LaunchBlaster.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import unittest -import os -import glob -from commons.tools.LaunchBlaster import LaunchBlaster - -class Test_F_LaunchBlaster(unittest.TestCase): - - def setUp(self): - self._inFileName = "DmelChr4.fa" - inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName) - try: - os.remove(self._inFileName) - except: - pass - os.symlink(inFilePath, self._inFileName) - self._iLaunchBlaster = LaunchBlaster(self._inFileName) - self._iLaunchBlaster.setDoAllByall(True) - self._iLaunchBlaster.setVerbosity(4) - - def tearDown(self): - try: - FileUtils.removeFilesByPattern("%s*" % self._inFileName) - os.remove("formatdb.log") - except: - pass - - def test_run_as_class_1_file(self): - expFileName = "%s/Tools/DmelChr4.align" % os.environ["REPET_DATA"] - obsFileName = "%s.align" % self._inFileName - - self._iLaunchBlaster.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - def test_run_as_class_1_file_changed_params(self): - expFileName = "DmelChr4.align" - with open(expFileName, "w") as fh: - fh.write("dmel_chr4\t691910\t692326\tdmel_chr4\t700019\t700435\t0\t827\t100\n") - obsFileName = "%s.align" % self._inFileName - - self._iLaunchBlaster.setIdentity(100) - self._iLaunchBlaster.setCPU(4) - self._iLaunchBlaster.setDoClean(True) - self._iLaunchBlaster.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(expFileName) - self.assertTrue(glob.glob("*fa_cut*") == []) - self.assertTrue(glob.glob("*Nstretch*") == []) - self.assertTrue(glob.glob("*seq_treated*") == []) - self.assertTrue(glob.glob("*.log") == []) - - def test_run_as_script_1bank_1file(self): - inputFileName = "chunks.fa" - with open(inputFileName, "w") as f: - f.write(">chunk1\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - expFileName = "exp.align" - with open(expFileName, "w") as f: - f.write("chunk1\t1\t120\tdmel_chr4\t1\t120\t2e-64\t238\t100\n") - obsFileName = "%s.align" % inputFileName - - cmd = "LaunchBlaster.py -q %s -s %s -e 0.1 -a" % (inputFileName, self._inFileName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - FileUtils.removeFilesByPattern("%s*" % inputFileName) - os.remove(expFileName) - - def test_run_as_script_1bank_1file_withoutABA(self): - queryFileName = "chunks.fa" - with open(queryFileName, "w") as f: - f.write(">chunk1\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - subjectFileName = "genome.fa" - with open(subjectFileName, "w") as f: - f.write(">chunk1\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - f.write(">chunk2\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - expFileName = "exp.align" - with open(expFileName, "w") as f: - f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n") - f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n") - obsFileName = "%s.align" % queryFileName - - cmd = "LaunchBlaster.py -q %s -s %s -e 0.1" % (queryFileName, subjectFileName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - FileUtils.removeFilesByPattern("%s*" % queryFileName) - FileUtils.removeFilesByPattern("%s*" % subjectFileName) - os.remove(expFileName) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_LaunchBlasterInParallel.py --- a/commons/tools/tests/Test_F_LaunchBlasterInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,116 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import unittest -import os -import shutil -from commons.tools.LaunchBlasterInParallel import LaunchBlasterInParallel - -class Test_F_LaunchBlasterInParallel(unittest.TestCase): - - CLUSTER_HOST = "compute-2-46.local" - - def setUp(self): - self._inFilePath = "%s/Tools/DmelChr4_chunks.fa" % os.environ["REPET_DATA"] - self._configFileName = "TE.cfg" - self._outputFileName = "out.align.not_over" - - def tearDown(self): - try: - os.remove(self._outputFileName) - os.remove(self._configFileName) - except: - pass - - def test_run_as_script_1bank_1file_withoutABA(self): - self._outputFileName = "out.align" - os.mkdir("tmp") - os.chdir("tmp") - queryFileName = "chunks.fa" - with open(queryFileName, "w") as f: - f.write(">chunk1\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - os.chdir("..") - subjectFileName = "genome.fa" - with open(subjectFileName, "w") as f: - f.write(">chunk1\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - f.write(">chunk2\n") - f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n") - f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n") - expFileName = "expected" - with open(expFileName, "w") as f: - f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n") - f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n") - self._writeConfig(0.1) - - cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s/%s -C %s -o %s" % (os.getcwd(), os.getcwd(), subjectFileName, self._configFileName, self._outputFileName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - FileUtils.removeFilesByPattern("*.param") - shutil.rmtree("tmp") - os.remove(subjectFileName) - os.remove(expFileName) - - def test_run_as_script_1bank_2_batches(self): - os.mkdir("tmp") - os.chdir("tmp") - os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa") - os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa") - os.chdir("..") - - expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"] - self._writeConfig() - - cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s -a -o %s -C %s" % (os.getcwd(), self._inFilePath, self._outputFileName, self._configFileName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - FileUtils.removeFilesByPattern("*.param") - shutil.rmtree("tmp") - - def test_run_1bank_1bank_2_batches(self): - os.mkdir("tmp") - os.chdir("tmp") - os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa") - os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa") - os.chdir("..") - - expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"] - self._writeConfig() - - iLaunchBlaster = LaunchBlasterInParallel(configFileName = self._configFileName, outFileName = self._outputFileName) - iLaunchBlaster.setDoAllByall(True) - iLaunchBlaster.setVerbosity(4) - iLaunchBlaster.setQueryDirectory("%s/tmp" % os.getcwd()) - iLaunchBlaster.setSubjectFilePath(self._inFilePath) - iLaunchBlaster.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName)) - FileUtils.removeFilesByPattern("*.param") - shutil.rmtree("tmp") - - def _writeConfig(self, eValue = 1e-300): - with open(self._configFileName, "w") as fh: - fh.write("[jobs]\n") - if os.getenv("HOSTNAME") == self.CLUSTER_HOST: - fh.write("resources: test\n") - else: - fh.write("resources:\n") - fh.write("tmpDir:\n") - fh.write("copy: no\n") - fh.write("clean: yes\n") - fh.write("\n") - fh.write("[prepare_data]\n") - fh.write("chunk_length: 200000\n") - fh.write("chunk_overlap: 10000\n") - fh.write("\n") - fh.write("[alignment]\n") - fh.write("blast: ncbi\n") - fh.write("Evalue: %s\n" % eValue) - fh.write("length: 100\n") - fh.write("identity: 90\n") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_LaunchMatcherInParallel.py --- a/commons/tools/tests/Test_F_LaunchMatcherInParallel.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,88 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -import shutil -import unittest -import os -from commons.tools.LaunchMatcherInParallel import LaunchMatcherInParallel - -class Test_F_LaunchMatcherInParallel(unittest.TestCase): - - CLUSTER_HOST = "compute-2-46.local" - - def setUp(self): - self._configFileName = "TE.cfg" - self._writeConfig() - - def tearDown(self): - FileUtils.removeFilesByPattern("DmelChr4*") - os.remove(self._configFileName) - - def test_run_as_class_1_seq(self): - inFileName = "DmelChr4.align" - fastaFileName = "DmelChr4.fa" - inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName) - inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName) - os.symlink(inFilePath, inFileName) - os.symlink(inFastaPath, fastaFileName) - expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"] - expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"] - - obsPathFileName = "%s.match.path" % inFileName - obsTabFileName = "%s.match.tab" % inFileName - - iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName) - iLaunchMatcherInParallel.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName)) - - def test_run_as_class_n_seq_less_jobs_than_n(self): - inFileName = "DmelChr4_dummy.align" - fastaFileName = "DmelChr4.fa" - inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName) - inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName) - os.symlink(inFilePath, inFileName) - os.symlink(inFastaPath, fastaFileName) - expPathFileName = "%s/Tools/DmelChr4_dummy.align.match.path" % os.environ["REPET_DATA"] - expTabFileName = "%s/Tools/DmelChr4_dummy.align.match.tab" % os.environ["REPET_DATA"] - - obsPathFileName = "%s.match.path" % inFileName - obsTabFileName = "%s.match.tab" % inFileName - - iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName, doClean=True) - iLaunchMatcherInParallel.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName)) - - def test_run_as_class_n_seq_less_jobs_than_n_not_merged_results(self): - inFileName = "DmelChr4_dummy.align" - fastaFileName = "DmelChr4.fa" - inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], inFileName) - inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], fastaFileName) - os.symlink(inFilePath, inFileName) - os.symlink(inFastaPath, fastaFileName) - - iLaunchMatcherInParallel = LaunchMatcherInParallel(align=inFileName, queryFileName=fastaFileName, subjectFileName=fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True, config=self._configFileName, maxFileSize=100, mergeResults=False) - iLaunchMatcherInParallel.run() - - baseFileName = os.path.splitext(inFileName)[0] - lExpMatchFileNames = ["%s_1.align.match.path" % baseFileName, "%s_2.align.match.path" % baseFileName, "%s_3.align.match.path" % baseFileName] - lExpTabFileNames = ["%s_1.align.match.tab" % baseFileName, "%s_2.align.match.tab" % baseFileName, "%s_3.align.match.tab" % baseFileName] - for i in range(0,3): - self.assertTrue(FileUtils.isRessourceExists("tmpMatcher/%s" % lExpMatchFileNames[i])) - self.assertTrue(FileUtils.isRessourceExists("tmpMatcher/%s" % lExpTabFileNames[i])) - shutil.rmtree("tmpMatcher") - - def _writeConfig(self): - with open(self._configFileName, "w") as fh: - fh.write("[jobs]\n") - if os.getenv("HOSTNAME") == self.CLUSTER_HOST: - fh.write("resources: test\n") - else: - fh.write("resources:\n") - fh.write("tmpDir:\n") - fh.write("copy: no\n") - fh.write("clean: yes\n") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_MergeMatchsFiles.py --- a/commons/tools/tests/Test_F_MergeMatchsFiles.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,302 +0,0 @@ -import os -import unittest -from commons.core.utils.FileUtils import FileUtils -from commons.tools.MergeMatchsFiles import MergeMatchsFiles - - -class Test_F_MergeMatchsFiles(unittest.TestCase): - - def test_run_set(self): - inFileName1 = "test1.set" - inFileName2 = "test2.set" - self._writeSetFiles(inFileName1, inFileName2) - iMMF = MergeMatchsFiles("set", "out") - iMMF.run() - obsFileName = "out.set" - expFileName = "exp.set" - self._writeExpSetFile(expFileName) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(expFileName) - os.remove(obsFileName) - - def test_run_align(self): - inFileName1 = "test1.align" - inFileName2 = "test2.align" - self._writeAlignFiles(inFileName1, inFileName2) - iMMF = MergeMatchsFiles("align", "out") - iMMF.run() - obsFileName = "out.align" - expFileName = "exp.align" - self._writeExpAlignFile(expFileName) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(expFileName) - os.remove(obsFileName) - - def test_run_align_allByAll(self): - inFileName1 = "test1.align" - inFileName2 = "test2.align" - self._writeAlignFiles(inFileName1, inFileName2) - iMMF = MergeMatchsFiles("align", "out", True) - iMMF.run() - obsFileName = "out.align" - expFileName = "exp.align" - self._writeExpAlignFile_allByAll(expFileName) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(expFileName) - os.remove(obsFileName) - - def test_run_path(self): - inFileName1 = "test1.path" - inFileName2 = "test2.path" - self._writePathFiles(inFileName1, inFileName2) - iMMF = MergeMatchsFiles("path", "out") - iMMF.run() - obsFileName = "out.path" - expFileName = "exp.path" - self._writeExpPathFile(expFileName) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(expFileName) - os.remove(obsFileName) - - def test_run_tab(self): - inFileName1 = "test1.tab" - inFileName2 = "test2.tab" - self._writeTabFiles(inFileName1, inFileName2) - iMMF = MergeMatchsFiles("tab", "out") - iMMF.run() - obsFileName = "out.tab" - expFileName = "exp.tab" - self._writeExpTabFile(expFileName) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(expFileName) - os.remove(obsFileName) - - def _writeSetFiles(self, fileName1, fileName2): - f = open(fileName1, "w") - f.write("1\t(TCTAT)3\tchunk006\t295\t309\n") - f.write("2\t(A)33\tchunk006\t679\t711\n") - f.write("3\t(G)16\tchunk006\t731\t746\n") - f.write("4\t(GAG)9\tchunk006\t903\t929\n") - f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n") - f.close() - f = open(fileName2, "w") - f.write("1\t(CCACT)3\tchunk011\t101\t116\n") - f.write("2\t(TATATA)7\tchunk011\t316\t357\n") - f.write("3\t(AT)22\tchunk011\t323\t366\n") - f.close() - - def _writeExpSetFile(self, fileName): - f = open(fileName, "w") - f.write("1\t(TCTAT)3\tchunk006\t295\t309\n") - f.write("2\t(A)33\tchunk006\t679\t711\n") - f.write("3\t(G)16\tchunk006\t731\t746\n") - f.write("4\t(GAG)9\tchunk006\t903\t929\n") - f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n") - f.write("6\t(CCACT)3\tchunk011\t101\t116\n") - f.write("7\t(TATATA)7\tchunk011\t316\t357\n") - f.write("8\t(AT)22\tchunk011\t323\t366\n") - f.close() - - def _writeAlignFiles(self, fileName1, fileName2): - f = open(fileName1, "w") - f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n") - f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n") - f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n") - f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n") - f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n") - f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n") - f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n") - f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n") - f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n") - f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n") - f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n") - f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n") - f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n") - f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n") - f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n") - f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n") - f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n") - f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n") - f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n") - f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n") - f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n") - f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n") - f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n") - f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n") - f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n") - f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n") - f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n") - f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n") - f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n") - f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n") - f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n") - f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n") - f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n") - f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n") - f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n") - f.close() - f = open(fileName2, "w") - f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n") - f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n") - f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n") - f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n") - f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n") - f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n") - f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n") - f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n") - f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n") - f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n") - f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n") - f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n") - f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n") - f.close() - - def _writeExpAlignFile_allByAll(self, fileName): - f = open(fileName, "w") - f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.360000\n") - f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.160000\n") - f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.290000\n") - f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.630000\n") - f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.560000\n") - f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.180000\n") - f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.590000\n") - f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.360000\n") - f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.110000\n") - f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.620000\n") - f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.520000\n") - f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.630000\n") - f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.740000\n") - f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.140000\n") - f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.800000\n") - f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.510000\n") - f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.280000\n") - f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.270000\n") - f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.080000\n") - f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.480000\n") - f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.950000\n") - f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.420000\n") - f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.770000\n") - f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.190000\n") - f.close() - - def _writeExpAlignFile(self, fileName): - f = open(fileName, "w") - f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n") - f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n") - f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n") - f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n") - f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n") - f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n") - f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n") - f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n") - f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n") - f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n") - f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n") - f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n") - f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n") - f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n") - f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n") - f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n") - f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n") - f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n") - f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n") - f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n") - f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n") - f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n") - f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n") - f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n") - f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n") - f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n") - f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n") - f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n") - f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n") - f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n") - f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n") - f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n") - f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n") - f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n") - f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n") - f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n") - f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n") - f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n") - f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n") - f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n") - f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n") - f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n") - f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n") - f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n") - f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n") - f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n") - f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n") - f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n") - f.close() - - def _writePathFiles(self, fileName1, fileName2): - f = open(fileName1, "w") - f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n") - f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n") - f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n") - f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n") - f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n") - f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n") - f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n") - f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n") - f.close() - f = open(fileName2, "w") - f.write("1\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n") - f.write("2\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n") - f.write("3\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n") - f.write("4\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n") - f.write("5\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n") - f.write("6\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n") - f.close() - - def _writeExpPathFile(self, fileName): - f = open(fileName, "w") - f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n") - f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n") - f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n") - f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n") - f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n") - f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n") - f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n") - f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n") - f.write("9\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n") - f.write("10\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n") - f.write("11\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n") - f.write("12\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n") - f.write("13\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n") - f.write("14\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n") - f.close() - - def _writeTabFiles(self, fileName1, fileName2): - f = open(fileName1, "w") - f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") - f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n") - f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n") - f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n") - f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n") - f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n") - f.close() - f = open(fileName2, "w") - f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") - f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t1\n") - f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t2\n") - f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t3\n") - f.close() - - def _writeExpTabFile(self, fileName): - f = open(fileName, "w") - f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") - f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n") - f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n") - f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n") - f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n") - f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n") - f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t6\n") - f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t7\n") - f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t8\n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_PostAnalyzeTELib.py --- a/commons/tools/tests/Test_F_PostAnalyzeTELib.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,294 +0,0 @@ -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbFactory import DbFactory -from commons.tools.PostAnalyzeTELib import PostAnalyzeTELib -import subprocess -import unittest -import os - - -class Test_F_PostAnalyzeTELib(unittest.TestCase): - - def setUp(self): - self._expStatFileName = "expStats.tab" - self._obsStatFileName = "" - self._genomeSize = 1281640 - self._pathTableName = "dummyDmelChr4_chr_allTEs_nr_noSSR_join_path" - self._seqTableName = "dummyDmelChr4_denovoLibTEs_seq" - - def tearDown(self): - try: - os.remove(self._expStatFileName) - except: pass - try: - os.remove(self._obsStatFileName) - except: pass - - def test_run_analysis1(self): - libFileName = "TElib.fa" - self._writeInputFasta_analysis1(libFileName) - expClusterFileName = "expClusters.tab" - self._writeExpClusterFile_analysis1(expClusterFileName) - expGlobalStatFileName = "expGlobalStats.txt" - self._writeExpGlobalStats_analysis1(expGlobalStatFileName) - self._writeExpStatsFile_analysis1(self._expStatFileName) - obsClusterFileName = "TElib.tab" - obsGlobalStatFileName = "TElib.globalStatsPerCluster.txt" - self._obsStatFileName = "TElib.statsPerCluster.tab" - - iPATEL = PostAnalyzeTELib(analysis=1, fastaFileName=libFileName, doClean=True) - iPATEL.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expClusterFileName, obsClusterFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName)) - - os.remove(libFileName) - os.remove(expClusterFileName) - os.remove(expGlobalStatFileName) - os.remove(obsClusterFileName) - os.remove(obsGlobalStatFileName) - - def test_run_as_script_analysis1(self): - libFileName = "TElib.fa" - with open(libFileName, "w") as f: - f.write(">transib2\n") - f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n") - f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n") - f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTC\n") - f.write(">transib3\n") - f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n") - f.write("TGAAACTCGTCAGCGTCGTTTCCAAGTCCT\n") - f.write(">transib4\n") - f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n") - f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n") - f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCAT\n") - f.write("AAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n") - expClusterFileName = "expClusters.tab" - with open(expClusterFileName, "w") as f: - f.write("transib4 \n") - f.write("transib2 \n") - f.write("transib3 \n") - with open(self._expStatFileName, "w") as f: - f.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n") - f.write("1\t1\t238\t238\t238\t238\n") - f.write("2\t1\t178\t178\t178\t178\n") - f.write("3\t1\t90\t90\t90\t90\n") - expGlobalStatFileName = "expGlobalStats.txt" - with open(expGlobalStatFileName, "w") as f: - f.write("nb of clusters: 3\n") - f.write("nb of clusters with 1 sequence: 3\n") - f.write("nb of clusters with 2 sequences: 0\n") - f.write("nb of clusters with >2 sequences: 0 (0 sequences)\n") - f.write("nb of sequences: 3\n") - f.write("nb of sequences in the largest cluster: 1\n") - f.write("nb of sequences in the smallest cluster: 1\n") - f.write("size of the smallest sequence: 90\n") - f.write("size of the largest sequence: 238\n") - f.write("average sequences size: 168\n") - f.write("median sequences size: 178\n") - obsClusterFileName = "TElib.tab" - obsGlobalStatFileName = "TElib.globalStatsPerCluster.txt" - self._obsStatFileName = "TElib.statsPerCluster.tab" - - cmd = "PostAnalyzeTELib.py -i %s -L 98 -S 95 -b -c -v 3" % libFileName - process = subprocess.Popen(cmd, shell = True) - process.communicate() - - self.assertTrue(FileUtils.are2FilesIdentical(expClusterFileName, obsClusterFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName)) - - os.remove(libFileName) - os.remove(expClusterFileName) - os.remove(expGlobalStatFileName) - os.remove(obsClusterFileName) - os.remove(obsGlobalStatFileName) - - def test_run_analysis2(self): - clusterFileName = "ConsensusClusters.tab" - self._writeClusterFile_analysis2(clusterFileName) - self._writeExpStatsFile_analysis2(self._expStatFileName) - self._obsStatFileName = "ConsensusClusters.classifStatsPerCluster.tab" - - iPATEL = PostAnalyzeTELib(analysis=2, clusterFileName=clusterFileName, verbosity=3) - iPATEL.run() - print "exp: %s, obs: %s" % (self._expStatFileName, self._obsStatFileName) - self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName)) - - os.remove(clusterFileName) - - def test_run_analysis3(self): - iDb = DbFactory.createInstance() - iDb.createTable(self._pathTableName, "path", "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ['REPET_DATA'], True) - iDb.createTable(self._seqTableName, "seq", "%s/TEannot/DmelChr4_denovoLibTEs.fa" % os.environ['REPET_DATA'], True) - - expGlobalStatFileName = "expGlobalStats.txt" - self._writeExpGlobalStats_analysis3(expGlobalStatFileName) - self._writeExpStatsFile_analysis3(self._expStatFileName) - obsGlobalStatFileName = "%s.globalAnnotStatsPerTE.txt" % self._pathTableName - self._obsStatFileName = "%s.annotStatsPerTE.tab" % self._pathTableName - - iPATEL = PostAnalyzeTELib(analysis=3, pathTableName=self._pathTableName, seqTableName=self._seqTableName, genomeSize=self._genomeSize) - iPATEL.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expGlobalStatFileName, obsGlobalStatFileName)) - self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName)) - - iDb.dropTable(self._pathTableName) - iDb.dropTable(self._seqTableName) - iDb.close() - os.remove(expGlobalStatFileName) - os.remove(obsGlobalStatFileName) - - def test_run_analysis4(self): - iDb = DbFactory.createInstance() - iDb.createTable(self._pathTableName, "path", "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ['REPET_DATA'], True) - iDb.createTable(self._seqTableName, "seq", "%s/TEannot/DmelChr4_denovoLibTEs.fa" % os.environ['REPET_DATA'], True) - - clusterFileName = "clusters.tab" - self._writeClusterFile_analysis4(clusterFileName) - self._writeExpStatsFile_analysis4(self._expStatFileName) - self._obsStatFileName = "%s.annotStatsPerCluster.tab" % self._pathTableName - - iPATEL = PostAnalyzeTELib(analysis=4, clusterFileName=clusterFileName, pathTableName=self._pathTableName, seqTableName=self._seqTableName, genomeSize=self._genomeSize) - iPATEL.run() - - self.assertTrue(FileUtils.are2FilesIdentical(self._expStatFileName, self._obsStatFileName)) - - iDb.dropTable(self._pathTableName) - iDb.dropTable(self._seqTableName) - iDb.close() - os.remove(clusterFileName) - - def _writeInputFasta_analysis1(self, fileName): - with open(fileName, "w") as f: - f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n") - f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n") - f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n") - f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n") - f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n") - f.write(">DTX-incomp_DmelChr4-B-R10-Map3\n") - f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n") - f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n") - f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n") - f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n") - f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n") - f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n") - f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n") - f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n") - - def _writeExpClusterFile_analysis1(self, fileName): - with open(fileName, "w") as f: - f.write("DTX-incomp_DmelChr4-B-R10-Map3 DTX-incomp_DmelChr4-B-R9-Map3_reversed \n") - f.write("PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed \n") - - def _writeExpStatsFile_analysis1(self, fileName): - #TODO: header in option ? - with open(fileName, "w") as f: - f.write("cluster\tsequencesNb\tsizeOfSmallestSeq\tsizeOfLargestSeq\taverageSize\tmedSize\n") - f.write("1\t2\t240\t240\t240\t240\n") - f.write("2\t1\t180\t180\t180\t180\n") - - def _writeExpGlobalStats_analysis1(self, fileName): - #TODO: file or STDOUT ? - with open(fileName, "w") as f: - f.write("nb of clusters: 2\n") - f.write("nb of clusters with 1 sequence: 1\n") - f.write("nb of clusters with 2 sequences: 1\n") - f.write("nb of clusters with >2 sequences: 0 (0 sequences)\n") - f.write("nb of sequences: 3\n") - f.write("nb of sequences in the largest cluster: 2\n") - f.write("nb of sequences in the smallest cluster: 1\n") - f.write("size of the smallest sequence: 180\n") - f.write("size of the largest sequence: 240\n") - f.write("average sequences size: 220\n") - f.write("median sequences size: 240\n") - - def _writeClusterFile_analysis2(self, fileName): - with open(fileName, "w") as f: - f.write("DTX-incomp_DmelChr4-B-R9-Map3_reversed\tDTX-incomp_DmelChr4-B-R10-Map3_reversed\tPotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n") - f.write("DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\tDTX-incomp_Blc1_DmelChr4-B-R10-Map3\n") - f.write("DXX-comp_DmelChr4-B-R9-Map3\tDTX-comp_DmelChr4-B-R10-Map3_reversed\tDTX-incomp_DmelChr4-B-R10-Map3_reversed\tnoCat_DmelChr4-B-G1-Map3\tnoCat_DmelChr4-B-R1-Map4\n") - f.write("RXX-MITE_DmelChr4-B-G7-Map3\tRXX-MITE_DmelChr4-B-G5-Map3\tRXX-MITE_DmelChr4-B-G2-Map3\tRXX-MITE_DmelChr4-B-G23-Map3\tRXX-MITE_DmelChr4-B-G6-Map3\n") - - def _writeExpStatsFile_analysis2(self, fileName): - #TODO: header in option ? - with open(fileName, "w") as f: - f.write("cluster\tnoCat\tPotentialChimeric\tcomp\tincomp\tclassifs (nbTEs)\n") - f.write("1\t0\t1\t0\t2\tDTX (2)\tPotentialHostGene (1)\n") - f.write("2\t0\t0\t0\t2\tDTX (2)\n") - f.write("3\t2\t0\t2\t1\tDTX (2)\tDXX (1)\n") - f.write("4\t0\t0\t0\t0\tMITE (5)\n") - - def _writeExpStatsFile_analysis3(self, fileName): - #TODO: header in option ? - with open(fileName, "w") as f: - f.write("TE\tlength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tmeanLgth\tmeanLgthPerc\n") - f.write("DmelChr4-B-G1-Map3_NoCat\t542\t3701\t12\t4\t10\t4\t95.72\t370.10\t68.28\n") - f.write("DmelChr4-B-G11-Map20_classII-TIR-incomp\t1240\t8216\t27\t0\t22\t0\t88.80\t375.00\t30.24\n") - f.write("DmelChr4-B-G7-Map3_classII-TIR-incomp\t1944\t15212\t49\t1\t42\t1\t89.44\t382.36\t19.67\n") - f.write("DmelChr4-B-G9-Map3_NoCat\t1590\t11564\t24\t0\t21\t1\t92.03\t550.67\t34.63\n") - f.write("DmelChr4-B-P0.0-Map3_classII-TIR-incomp\t1042\t4001\t13\t3\t11\t3\t85.11\t366.36\t35.16\n") - f.write("DmelChr4-B-R1-Map4_NoCat\t2367\t66031\t484\t0\t361\t0\t77.84\t182.91\t7.73\n") - f.write("DmelChr4-B-R12-Map3_NoCat\t2284\t4938\t3\t2\t3\t2\t99.26\t1646.00\t72.07\n") - f.write("DmelChr4-B-R19-Map4_NoCat\t705\t3328\t10\t3\t10\t3\t88.51\t332.80\t47.21\n") - f.write("DmelChr4-B-R2-Map6_NoCat\t4638\t20539\t34\t2\t29\t3\t80.93\t708.24\t15.27\n") - f.write("DmelChr4-B-R4-Map5_NoCat\t1067\t7292\t35\t1\t28\t1\t86.50\t260.54\t24.42\n") - f.write("DmelChr4-B-R9-Map3_NoCat\t714\t5453\t19\t2\t16\t2\t81.18\t340.81\t47.73\n") - - def _writeExpGlobalStats_analysis3(self, fileName): - with open(fileName, "w") as f: - f.write("nb of sequences: 11\n") - f.write("nb of matched sequences: 11\n") - f.write("cumulative coverage: 150275 bp\n") - f.write("coverage percentage: 11.73%\n") - f.write("\n") - f.write("total nb of TE fragments: 710\n") - f.write("total nb full-length fragments: 18 (2.54%)\n") - f.write("total nb of TE copies: 553\n") - f.write("total nb full-length copies: 20 (3.62%)\n") - f.write("families with full-length fragments: 8 (72.73%)\n") - f.write(" with only one full-length fragment: 2\n") - f.write(" with only two full-length fragments: 3\n") - f.write(" with only three full-length fragments: 2\n") - f.write(" with more than three full-length fragments: 1\n") - f.write("families with full-length copies: 9 (81.82%)\n") - f.write(" with only one full-length copy: 3\n") - f.write(" with only two full-length copies: 2\n") - f.write(" with only three full-length copies: 3\n") - f.write(" with more than three full-length copies: 1\n") - f.write("mean of median identity of all families: 88.30 +- 8.33\n") - f.write("mean of median length percentage of all families: 30.83 +- 32.30\n") - - def _writeClusterFile_analysis4(self, fileName): - with open(fileName, "w") as f: - f.write("1\tDmelChr4-B-R1-Map4_NoCat\tDmelChr4-B-R2-Map6_NoCat\tDmelChr4-B-R4-Map5_NoCat\n") - f.write("2\tDmelChr4-B-G7-Map3_classII-TIR-incomp\tDmelChr4-B-P0.0-Map3_classII-TIR-incomp\n") - - def _writeExpStatsFile_analysis4(self, fileName): - with open(fileName, "w") as f: - f.write("Cluster\tcovg\tfrags\tcopies\n") - f.write("1\t93862\t553\t418\n") - f.write("2\t19213\t62\t53\n") - - def _writeConfigFile(self, configFileName): - with open(configFileName, "w") as fHandle: - fHandle.write("[repet_env]\n") - fHandle.write("repet_host: %s\n" % os.environ["REPET_HOST"]) - fHandle.write("repet_user: %s\n" % os.environ["REPET_USER"]) - fHandle.write("repet_pw: %s\n" % os.environ["REPET_PW"]) - fHandle.write("repet_db: %s\n" % os.environ["REPET_DB"]) - fHandle.write("repet_port: 3306\n") - fHandle.write("[analysis1]\n") - fHandle.write("fasta_name: %s\n" % self._expStatFileName) - - fHandle.write("[analysis2]\n") - fHandle.write("clusterFileName: %s\n" % self._expStatFileName) - - fHandle.write("[analysis3]\n") - fHandle.write("pathTableName: %s\n" % self._pathTableName) - fHandle.write("seqTableName: %s\n" % self._seqTableName) - fHandle.write("genomeSize: %s\n" % self._genomeSize) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_ReplaceGreaterThanSymbolInFastaHeader.py --- a/commons/tools/tests/Test_F_ReplaceGreaterThanSymbolInFastaHeader.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.tools.tests.MockFastaForReplaceGreaterThanSymbolInFastaHeader import MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan,\ - MockFastaForReplaceGreaterThanSymbolInFastaHeader -from commons.tools.replaceGreaterThanSymbolInFastaHeaderProgramLauncher import replaceGreaterThanSymbolInFastaHeaderProgramLauncher - -class Test_F_ReplaceGreaterThanSymbolInHeader(unittest.TestCase): - - - def test_run(self): - inputFileName = "dummy_fasta.fsa" - mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader() - mockInput.write(inputFileName) - - expFileName = "exp_dummy_fasta.preprocessed.fsa" - mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan() - mockInput.write(expFileName) - - obsFileName = "dummy_fasta.preprocessed.fasta" - rgtspl = replaceGreaterThanSymbolInFastaHeaderProgramLauncher() - rgtspl.setInputFile(inputFileName) - rgtspl.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(inputFileName) - os.remove(expFileName) - os.remove(obsFileName) - - def test_run_as_script(self): - inputFileName = "dummy_fasta.fsa" - mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader() - mockInput.write(inputFileName) - - expFileName = "exp_dummy_fasta.preprocessed.fsa" - mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan() - mockInput.write(expFileName) - - obsFileName = "dummy_fasta.preprocessed.fasta" - - cmd2Launch = "replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py -i " + inputFileName - os.system(cmd2Launch) - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(inputFileName) - os.remove(expFileName) - os.remove(obsFileName) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_RetrieveInitHeaders.py --- a/commons/tools/tests/Test_F_RetrieveInitHeaders.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -from commons.core.sql.DbMySql import DbMySql -from commons.core.sql.TablePathAdaptator import TablePathAdaptator -from commons.core.coord.PathUtils import PathUtils -from commons.core.utils.FileUtils import FileUtils -import os -import unittest - -class Test_F_RetrieveInitHeaders(unittest.TestCase): - - def setUp(self): - self._iDb = DbMySql() - - def tearDown(self): - self._iDb.close() - - def test_run_as_script_rename_subject_and_clean_table(self): - shortHLinkFileName = "dummy.shortHlink" - self._writeShortHLinkFile(shortHLinkFileName) - pathTableName = "dummyInput_path" - self._createPathTable(pathTableName) - expFileName = "exp.path" - self._writeExpFile(expFileName) - obsTableName = "dummyOutput_path" - - cmd = "RetrieveInitHeaders.py -i %s -l %s -o %s -s -c -v 1" % (pathTableName, shortHLinkFileName, obsTableName) - os.system(cmd) - - self.assertTrue(self._iDb.doesTableExist(obsTableName)) - self.assertFalse(self._iDb.doesTableExist(pathTableName)) - obsFileName = "obs.path" - iTPA = TablePathAdaptator(self._iDb, obsTableName) - lPaths = iTPA.getListOfAllPaths() - PathUtils.writeListInFile(lPaths, obsFileName) - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - os.remove(shortHLinkFileName) - os.remove(expFileName) - os.remove(obsFileName) - self._iDb.dropTable(obsTableName) - - def _writeShortHLinkFile(self, fileName): - f = open(fileName, "w") - f.write("refTE_1\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t1\t5388\n") - f.write("refTE_2\tPaphi_v2-B-R2469-Map20_classI-LTR-comp\t1\t6385\n") - f.write("refTE_3\tPaphi_v2-B-R8543-Map9_classI-LTR-comp\t1\t7148\n") - f.write("refTE_4\tPaphi_v2-B-R33384-Map4_classI-LTR-incomp\t1\t262\n") - f.write("refTE_5\tPaphi_v2-B-P73.1298-Map3_classI-LTR-incomp\t1\t389\n") - f.write("refTE_6\tPaphi_v2-B-R36143-Map3_classI-LTR-incomp\t1\t393\n") - f.write("refTE_7\tPaphi_v2-B-R35261-Map5_classI-LTR-incomp\t1\t408\n") - f.write("refTE_8\tPaphi_v2-B-R12434-Map4_classI-LTR-incomp\t1\t420\n") - f.write("refTE_9\tPaphi_v2-B-R20580-Map4_classI-LTR-incomp\t1\t426\n") - f.write("refTE_10\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t1\t441\n") - f.close() - - def _createPathTable(self, tableName): - fileName = "dummy.path" - f = open(fileName, "w") - f.write("7615\tchunk0030\t188432\t188611\trefTE_1\t5386\t5208\t0\t174\t97.23\n") - f.write("86375\tchunk0372\t155816\t157157\trefTE_1\t2213\t3575\t0\t843\t62.89\n") - f.write("88018\tchunk0381\t52141\t53500\trefTE_1\t2191\t3575\t0\t860\t63.3\n") - f.write("110377\tchunk0473\t117281\t117518\trefTE_1\t3966\t3716\t0\t230\t97.05\n") - f.write("39621\tchunk0169\t123563\t124003\trefTE_10\t1\t441\t0\t439\t99.55\n") - f.write("544710\tchunk2778\t62387\t62625\trefTE_10\t100\t327\t0\t165\t69.09\n") - f.write("601761\tchunk4780\t441\t559\trefTE_10\t5\t123\t0\t119\t100\n") - f.write("17589\tchunk0071\t58591\t59763\trefTE_2\t5139\t6384\t0\t1150\t98.12\n") - f.write("21050\tchunk0087\t186576\t186812\trefTE_2\t3636\t3891\t0\t232\t98.31\n") - f.close() - self._iDb.createTable(tableName, "path", fileName, True) - os.remove(fileName) - - def _writeExpFile(self, fileName): - f = open(fileName, "w") - f.write("7615\tchunk0030\t188432\t188611\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t5386\t5208\t0\t174\t97.230000\n") - f.write("86375\tchunk0372\t155816\t157157\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t2213\t3575\t0\t843\t62.890000\n") - f.write("88018\tchunk0381\t52141\t53500\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t2191\t3575\t0\t860\t63.300000\n") - f.write("110377\tchunk0473\t117281\t117518\tPaphi_v2-B-R11932-Map16_classI-LTR-comp\t3966\t3716\t0\t230\t97.050000\n") - f.write("39621\tchunk0169\t123563\t124003\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t1\t441\t0\t439\t99.550000\n") - f.write("544710\tchunk2778\t62387\t62625\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t100\t327\t0\t165\t69.090000\n") - f.write("601761\tchunk4780\t441\t559\tPaphi_v2-B-R5129-Map3_classI-LTR-incomp\t5\t123\t0\t119\t100.000000\n") - f.write("17589\tchunk0071\t58591\t59763\tPaphi_v2-B-R2469-Map20_classI-LTR-comp\t5139\t6384\t0\t1150\t98.120000\n") - f.write("21050\tchunk0087\t186576\t186812\tPaphi_v2-B-R2469-Map20_classI-LTR-comp\t3636\t3891\t0\t232\t98.310000\n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_SplicerFromAnnotation.py --- a/commons/tools/tests/Test_F_SplicerFromAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -import unittest -import os -from commons.core.sql.DbMySql import DbMySql -from commons.core.utils.FileUtils import FileUtils -#from commons.tools.SplicerFromAnnotation import SplicerFromAnnotation - -class Test_F_SplicerFromAnnotation(unittest.TestCase): - - def setUp(self): - self._inFastaFileName = "%s/Tools/Splicer_inputFile.fa" % os.environ["REPET_DATA"] - self._outFastaFileName = "%s/Tools/Splicer_outputSplicedFile.fa.splice" % os.environ["REPET_DATA"] - self._refTEseqFileName = "%s/Tools/Splicer_refTEs_seq.fa" % os.environ["REPET_DATA"] - self.configFileName = "TEdenovo.cfg" - self._writeConfigFile() - self.pathFileName = "annotations_path" - self._writePathFile() - self._iDb = DbMySql(cfgFileName = self.configFileName) - self._tableName = "Splicer_inputFile_chr_allTEs_nr_noSSR_join_path" - self._iDb.createTable(self._tableName, "path", self.pathFileName, True) - self._tableName_refTEseq = "Splicer_inputFile_refTEs_seq" - self._iDb.createTable(self._tableName_refTEseq, "seq", self._refTEseqFileName, True) - - def tearDown(self): - self._iDb.dropTable(self._tableName) - self._iDb.dropTable(self._tableName_refTEseq) - self._iDb.dropTable("Splicer_inputFile_annotationIdentitySup80_path") - self._iDb.dropTable("Splicer_inputFile_annotationToSplice_path") - self._iDb.close() - os.remove("annotations_path") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.globalAnnotStatsPerTE.txt") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.fa") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.fa") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_OneCopyAndMore.txt") - os.remove("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_OneCopyAndMore.fa") - os.remove("Splicer_inputFile_annotationToSplice_path.path") - os.remove(self.configFileName) -# os.remove(self.obsOutSplicedFastaFileName) - - def test_run_as_script_FLC(self): - expOutSplicedFastaFileName = "%s/Tools/Splicer_outputSplicedFile_FLC.fa.splice" % os.environ["REPET_DATA"] - self.obsOutSplicedFastaFileName = "Splicer_inputFile_FLC.fa.splice" - self._writeConfigFile() - self._writePathFile() - cmd = 'SplicerFromAnnotation.py -i %s -C %s -o %s -v 2' % (self._inFastaFileName,self.configFileName, self.obsOutSplicedFastaFileName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(expOutSplicedFastaFileName, self.obsOutSplicedFastaFileName)) - - def test_run_as_script_FLF(self): - expOutSplicedFastaFileName = "%s/Tools/Splicer_outputSplicedFile_FLF.fa.splice" % os.environ["REPET_DATA"] - self.obsOutSplicedFastaFileName = "Splicer_inputFile_FLF.fa.splice" - self._writeConfigFile() - self._writePathFile() - cmd = 'SplicerFromAnnotation.py -i %s -t 3 -C %s -o %s -v 2' % (self._inFastaFileName,self.configFileName, self.obsOutSplicedFastaFileName) - os.system(cmd) - - self.assertTrue(FileUtils.are2FilesIdentical(expOutSplicedFastaFileName, self.obsOutSplicedFastaFileName)) - - def _writeConfigFile(self): - f = open(self.configFileName, "w") - f.write("[repet_env]\n") - f.write("repet_version: 2.0\n") - f.write("repet_host: %s\n" % os.environ["REPET_HOST"]) - f.write("repet_user: %s\n" % os.environ["REPET_USER"]) - f.write("repet_pw: %s\n" % os.environ["REPET_PW"]) - f.write("repet_db: %s\n" % os.environ["REPET_DB"]) - f.write("repet_port: %s\n" % os.environ["REPET_PORT"]) - f.write("repet_job_manager: %s\n" % os.environ["REPET_JOB_MANAGER"]) - f.close() - - def _writePathFile(self): - f = open(self.pathFileName, "w") - f.write("1\tA_contig00012\t2853\t3530\tRLX-comp_3b_Itr1_v2-L-B1064-Map1_reversed\t8127\t8803\t0\t648\t95.7227\n") - f.write("3\tA_contig00012\t3531\t6064\tRLX-incomp_3b_Itr1_v2-L-B450-Map1\t3207\t709\t0\t2166\t85.4973\n") - f.write("4\tA_contig00012\t1\t1542\tDTX-incomp_3b_Itr1_v2-L-B1836-Map1\t673\t2218\t0\t1460\t94.7437\n") - f.write("4\tA_contig00012\t1523\t2849\tDTX-incomp_3b_Itr1_v2-L-B1836-Map1\t2385\t3693\t0\t1086\t81.9079\n") - f.write("23\tA_contig00033\t10551\t10668\tRLX-comp_3b_Itr1_v2-L-B2275-Map1\t668\t784\t1.3e-11\t97\t82.8571\n") - f.write("24\tA_contig00033\t7649\t7753\tRLX-comp_3b_Itr1_v2-L-B1105-Map1\t5349\t5453\t1.4e-13\t82\t78.5714\n") - f.write("25\tA_contig00033\t2998\t3243\tRLX-comp_3b_Itr1_v2-L-B757-Map1\t4422\t4659\t1.2e-12\t201\t81.8182\n") - f.write("26\tA_contig00033\t30462\t30502\tRLX-comp_3b_Itr1_v2-L-B389-Map1_reversed\t1548\t1509\t0\t38\t95.12\n") - f.write("26\tA_contig00033\t30462\t30504\tRLX-comp_3b_Itr1_v2-L-B389-Map1_reversed\t1548\t1505\t0\t41\t94.8026\n") - f.write("28\tA_contig00033\t6826\t7046\tRLX-comp_3b_Itr1_v2-L-B381-Map1\t5655\t5443\t0\t170\t77.3196\n") - f.write("30\tA_contig00033\t11712\t11818\tRLX-comp_3b_Itr1_v2-L-B108-Map1_reversed\t7782\t7682\t0\t80\t75\n") - f.write("31\tA_contig00033\t17122\t17221\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t9987\t9889\t0\t75\t75.2187\n") - f.write("32\tA_contig00033\t19069\t19131\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t8261\t8325\t2.8e-14\t45\t71.345\n") - f.write("33\tA_contig00033\t19343\t19375\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t8229\t8197\t0\t29\t86.6953\n") - f.write("34\tA_contig00033\t20411\t20783\tRLX-comp-chim_3b_Itr1_v2-L-B410-Map1_reversed\t7558\t7186\t0\t314\t84.4327\n") - f.write("35\tA_contig00033\t6346\t6541\tRLX-incomp-chim_3b_Itr1_v2-L-B359-Map1_reversed\t10604\t10416\t1.9e-24\t163\t83.2536\n") - f.write("36\tA_contig00033\t16757\t17121\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t8290\t7930\t0\t282\t77.5216\n") - f.write("37\tA_contig00033\t17222\t18658\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t7243\t5796\t0\t1094\t76.1977\n") - f.write("38\tA_contig00033\t19132\t19342\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5780\t5567\t0\t191\t90.9524\n") - f.write("39\tA_contig00033\t19409\t19455\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5558\t5512\t0\t38\t82.9787\n") - f.write("39\tA_contig00033\t19416\t19441\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5551\t5526\t0\t24\t96.15\n") - f.write("40\tA_contig00033\t19641\t20410\tDTX-incomp-chim_3b_Itr1_v2-L-B171-Map1_reversed\t5533\t4749\t0\t651\t84.55\n") - f.write("41\tA_contig00033\t19475\t19640\tDTX-incomp-chim_3b_Itr1_v2-L-B151-Map1_reversed\t9514\t9708\t0\t127\t76.7025\n") - f.write("42\tA_contig00033\t3244\t3364\tDTX-incomp_3b_Itr1_v2-L-B1836-Map1\t2536\t2405\t6.8e-23\t95\t78.8462\n") - f.write("43\tA_contig00033\t19376\t19408\tRLX-comp_3b_Itr1_v2-L-B1517-Map1\t705\t733\t1.1e-11\t27\t80.4348\n") - f.write("43\tA_contig00033\t19456\t19474\tRLX-comp_3b_Itr1_v2-L-B1517-Map1\t775\t790\t1.1e-11\t15\t80.4348\n") - f.write("44\tA_contig00033\t5494\t5583\tRIX-incomp-chim_3b_Itr1_v2-L-B121-Map1\t7419\t7507\t4.9e-11\t68\t76.1905\n") - f.write("45\tA_contig00033\t10810\t11031\tRLX-comp_3b_Itr1_v2-L-B2073-Map1\t3079\t3297\t1e-17\t171\t77.2021\n") - f.write("46\tA_contig00033\t11253\t11406\tRLX-comp_3b_Itr1_v2-L-B1616-Map1\t1726\t1569\t0\t120\t78.2609\n") - f.write("47\tA_contig00033\t11407\t11508\tRLX-comp_3b_Itr1_v2-L-B351-Map1_reversed\t10133\t10039\t0\t79\t77.8689\n") - f.write("48\tA_contig00033\t3673\t3719\tRLX-comp_3b_Itr1_v2-L-B228-Map1_reversed\t13011\t12966\t0\t37\t78.629\n") - f.write("49\tA_contig00033\t3959\t4055\tRLX-comp_3b_Itr1_v2-L-B134-Map1_reversed\t1917\t2010\t5.5e-24\t74\t77.2727\n") - f.write("50\tA_contig00033\t30505\t37270\tRLX-comp_3b_Itr1_v2-L-B124-Map1\t14149\t7383\t0\t6365\t94.0818\n") - f.write("51\tA_contig00033\t8859\t9079\tRLX-incomp_3b_Itr1_v2-L-B2010-Map1_reversed\t390\t603\t1.9e-11\t171\t77.6596\n") - f.write("52\tA_contig00033\t9080\t9140\tRLX-incomp_3b_Itr1_v2-L-B1720-Map1_reversed\t1393\t1460\t0\t49\t80.8333\n") - f.write("53\tA_contig00033\t12386\t12435\tRLX-incomp_3b_Itr1_v2-L-B1706-Map1\t2678\t2725\t1.3e-25\t40\t81.1765\n") - f.write("54\tA_contig00033\t5052\t5096\tRLX-incomp_3b_Itr1_v2-L-B77-Map2_reversed\t5445\t5402\t6.1e-13\t37\t84.507\n") - f.write("55\tA_contig00033\t14485\t16756\tRLX-incomp_3b_Itr1_v2-L-B965-Map1\t4566\t6848\t0\t1881\t82.8154\n") - f.write("57\tA_contig00033\t10229\t10370\tRLX-incomp_3b_Itr1_v2-L-B502-Map1_reversed\t8598\t8438\t0\t109\t77.2727\n") - f.write("59\tA_contig00033\t2457\t2617\tRLX-incomp_3b_Itr1_v2-L-B405-Map1\t4742\t4910\t0\t129\t80.2721\n") - f.write("60\tA_contig00033\t8071\t8183\tRLX-incomp_3b_Itr1_v2-L-B109-Map1\t4413\t4529\t0\t97\t86.5979\n") - f.write("61\tA_contig00033\t12867\t14362\tRXX-LARD-chim_3b_Itr1_v2-L-B1998-Map1_reversed\t1465\t3000\t0\t1283\t85.8025\n") - f.write("62\tA_contig00033\t90\t256\tRXX-LARD-chim_3b_Itr1_v2-L-B1928-Map1\t905\t717\t2.5e-38\t128\t76.875\n") - f.write("63\tA_contig00033\t5097\t5249\tRXX-LARD-chim_3b_Itr1_v2-L-B1928-Map1\t4158\t4017\t4e-36\t127\t83.3333\n") - f.write("64\tA_contig00033\t8689\t8796\tRXX-LARD-chim_3b_Itr1_v2-L-B1905-Map1\t5584\t5469\t5.04467e-44\t85\t79.2079\n") - f.write("65\tA_contig00033\t6800\t6825\tRXX-LARD-chim_3b_Itr1_v2-L-B1790-Map1_reversed\t3426\t3399\t0\t21\t79.1667\n") - f.write("66\tA_contig00033\t10193\t10228\tRLX-comp-chim_3b_Itr1_v2-L-B1760-Map1_reversed\t1470\t1504\t8.7e-23\t29\t80.5195\n") - f.write("67\tA_contig00033\t6542\t6603\tRXX-LARD-chim_3b_Itr1_v2-L-B1741-Map1_reversed\t5509\t5567\t0\t48\t77.9412\n") - f.write("69\tA_contig00033\t12769\t12816\tRLX-comp-chim_3b_Itr1_v2-L-B1518-Map1\t2026\t1979\t0\t39\t81.25\n") - f.write("70\tA_contig00033\t28383\t29146\tRLX-comp-chim_3b_Itr1_v2-L-B1494-Map1_reversed\t999\t1761\t0\t672\t88.0282\n") - f.write("71\tA_contig00033\t21712\t28382\tRLX-incomp-chim_3b_Itr1_v2-L-B1485-Map1\t1132\t7813\t0\t6011\t90.1124\n") - f.write("71\tA_contig00033\t20784\t21728\tRLX-incomp-chim_3b_Itr1_v2-L-B1485-Map1\t159\t1113\t0\t833\t88.172 \n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_F_TEclassifierPE.py --- a/commons/tools/tests/Test_F_TEclassifierPE.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -import os -import unittest -from commons.tools.TEclassifierPE import TEclassifierPE -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbFactory import DbFactory - -class Test_F_TEclassifierPE(unittest.TestCase): - - def test_run(self): - projectName = "dummy" - configFileName = "dummy.cfg" - self.writeConfigFile(configFileName, projectName) - inputFileName = "dummy.fa" - with open(inputFileName, "w") as f: - f.write(">dummySSR\n") - f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n") - f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n") - expFileName = "exp.classif" - with open(expFileName, "w") as f: - f.write("dummySSR\t120\t.\tok\tNA\tSSR\tNA\tCI=100; struct=(TElength: <150bps; SSRCoverage=0.00)\n") - obsFileName = "%s.classif" % projectName - statsFileName = "%s.classif_stats.txt" % projectName - analysisFileName = "%s.SSR.set" % inputFileName - - iTEclassifierPE = TEclassifierPE(inputFileName, configFileName, doClean = True) - iTEclassifierPE.run() - - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - - iDb = DbFactory.createInstance() - iDb.dropTable("%s_TR_set" % projectName) - iDb.dropTable("%s_polyA_set" % projectName) - iDb.dropTable("%s_ORF_map" % projectName) - iDb.dropTable("%s_SSR_set" % projectName) - iDb.close() - os.remove(configFileName) - os.remove(inputFileName) - os.remove(expFileName) - os.remove(obsFileName) - os.remove(statsFileName) - os.remove(analysisFileName) - - def writeConfigFile(self, fileName, projectName): - with open(fileName, "w") as f: - f.write("[repet_env]\n") - f.write("repet_host: %s\n" % os.environ["REPET_HOST"]) - f.write("repet_user: %s\n" % os.environ["REPET_USER"]) - f.write("repet_pw: %s\n" % os.environ["REPET_PW"]) - f.write("repet_db: %s\n" % os.environ["REPET_DB"]) - f.write("repet_port: %s\n" % os.environ["REPET_PORT"]) - f.write("\n") - f.write("[project]\n") - f.write("project_name: %s\n" % projectName) - f.write("project_dir: %s\n" % os.getcwd()) - f.write("\n") - f.write("[detect_features]\n") - f.write("clean: yes\n") - f.write("blast: ncbi\n") - f.write("term_rep: no\n") - f.write("polyA: no\n") - f.write("tand_rep: yes\n") - f.write("orf: no\n") - f.write("TE_HMMER: no\n") - f.write("TE_BLRtx: no\n") - f.write("TE_BLRn: no\n") - f.write("TE_BLRx: no\n") - f.write("HG_BLRn: no\n") - f.write("rDNA_BLRn: no\n") - f.write("tRNA_scan: no\n") - f.write("TRFmaxPeriod: 15\n") - f.write("\n") - f.write("[classif_consensus]\n") - f.write("max_profiles_evalue: 1e-3\n") - f.write("min_TE_profiles_coverage: 20\n") - f.write("min_HG_profiles_coverage: 75\n") - f.write("max_helitron_extremities_evalue: 1e-3\n") - f.write("min_TE_bank_coverage: 5\n") - f.write("min_HG_bank_coverage: 95\n") - f.write("min_rDNA_bank_coverage: 95\n") - f.write("min_HG_bank_identity: 90\n") - f.write("min_rDNA_bank_identity: 90\n") - f.write("min_SSR_coverage: 0.75\n") - f.write("max_SSR_size: 150\n") - f.write("clean: yes\n") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.py --- a/commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -import unittest -import os -import time -from commons.core.sql.DbMySql import DbMySql -from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq -from commons.core.utils.FileUtils import FileUtils - - -class Test_GetMultAlignAndPhylogenyPerTErefSeq( unittest.TestCase ): - - def setUp( self ): - self.fileUtils = FileUtils() - self._inputTEFile = "dummyTE" - self._iGMAP = GetMultAlignAndPhylogenyPerTErefSeq() - self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() ) - self._configFileName = "dummyConfig_%s" % self._uniqId - configFile = open( self._configFileName, "w" ) - configFile.write("[repet_env]\n") - configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) - configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) - configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) - configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) - configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) - configFile.close() - - def tearDown( self ): - os.remove( self._configFileName ) - os.remove( self._inputTEFile ) - - - def test_getNamesOfTErefSeq_fromFile_ok(self): - expTEList =["DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed", - "DT-comp_DmelChr4-B-P0.0-Map3", "RLX-incomp_Blc3_DmelChr4-L-B3-Map1"] - self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile) - self.writeInputTEFile() - obsTEList = self._iGMAP.getNamesOfTErefSeq() - self.assertEqual(obsTEList, expTEList) - - def test_getNamesOfTErefSeq_from_empty_file(self): - expTEList =[] - self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile) - with open(self._inputTEFile,"w") as TEFile: - TEFile.write("") - obsTEList = self._iGMAP.getNamesOfTErefSeq() - self.assertEqual(obsTEList, expTEList) - - def writeInputTEFile(self): - with open(self._inputTEFile,"w") as TEFile: - TEFile.write("""DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed -RLX-incomp_Blc3_DmelChr4-L-B3-Map1\t reverse -DT-comp_DmelChr4-B-P0.0-Map3\t""") - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_GetSpecificTELibAccordingToAnnotation.py --- a/commons/tools/tests/Test_GetSpecificTELibAccordingToAnnotation.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -import os -import unittest -from commons.core.utils.FileUtils import FileUtils -from commons.core.sql.DbMySql import DbMySql -from commons.tools.GetSpecificTELibAccordingToAnnotation import GetSpecificTELibAccordingToAnnotation - -class Test_GetSpecificTELibAccordingToAnnotation(unittest.TestCase): - - def test_writeFastaFileFromGiveInfoTEAnnot(self): - self._iDb = DbMySql() - fileName = "GiveInfoTEannot.txt" - self._writeGiveInfoTEannotOutput(fileName) - tableName = "projectName_refTEs_chr_seq" - self._createConsensusTable(tableName) - expFileName = "consensusExp.fa" - self._writeExpConsensusFile(expFileName) - obsFileName = "%s.fa" % os.path.splitext(fileName)[0] - iGetTElib = GetSpecificTELibAccordingToAnnotation() - iGetTElib.setTableName(tableName) - iGetTElib.writeFastaFileFromGiveInfoTEAnnot(fileName) - self._iDb.dropTable(tableName) - self._iDb.close() - self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) - os.remove(fileName) - os.remove(expFileName) - os.remove(obsFileName) - - def _writeGiveInfoTEannotOutput(self, fileName): - f = open(fileName, "w") - f.write("TE\tmaxLength\tmeanLength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tsdId\tminId\tq25Id\tmedId\tq75Id\tmaxId\tmeanLgth\tsdLgth\tminLgth\tq25Lgth\tmedLgth\tq75Lgth\tmaxLgth\tmeanLgthPerc\tsdLgthPerc\tminLgthPerc\tq25LgthPerc\tmedLgthPerc\tq75LgthPerc\tmaxLgthPerc\n") - f.write("Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\t2150\t2150\t195657\t158\t49\t152\t52\t84.88\t8.75\t74.29\t77.16\t80.08\t96.40\t97.83\t1287.32\t776.47\t21\t570.00\t1320.50\t2077.00\t2272\t59.88\t36.11\t0.98\t26.51\t61.42\t96.60\t105.67\n") - f.write("Atha_benchs-B-R1047-Map6_classI-LINE-comp\t1653\t1653\t25423\t57\t4\t56\t4\t79.09\t8.21\t64.32\t73.63\t79.21\t83.65\t96.65\t453.98\t488.66\t29\t98.00\t244.00\t634.00\t1650\t27.46\t29.56\t1.75\t5.93\t14.76\t38.35\t99.82\n") - f.write("Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\t1293\t1293\t24416\t48\t4\t47\t4\t80.31\t5.74\t75.14\t77.00\t78.25\t80.89\t99.46\t519.60\t419.01\t37\t171.00\t334.00\t838.00\t1296\t40.19\t32.41\t2.86\t13.23\t25.83\t64.81\t100.23\n") - f.close() - - def _createConsensusTable(self, tableName): - fileName = "consensus.fa" - f = open(fileName, "w") - f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n") - f.write("ATGCTAGCTAGCT\n") - f.write(">Atha_benchs-B-R12-Map5_classII-Helitron-comp\n") - f.write("ATGCTAGCTAGCTATGCTAGCTAGCATGCTAGCTAGCTT\n") - f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n") - f.write("ATGCTAGCTAGCT\n") - f.write(">Atha_benchs-B-G56-Map5_classII-Helitron-comp\n") - f.write("ATGCTAGCTAGCTATGCTAGCTAGCT\n") - f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n") - f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n") - f.close() - self._iDb.createTable(tableName, "seq", fileName, True) - os.remove(fileName) - - def _writeExpConsensusFile(self, fileName): - f = open(fileName, "w") - f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n") - f.write("ATGCTAGCTAGCT\n") - f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n") - f.write("ATGCTAGCTAGCT\n") - f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n") - f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_OrientSequences.py --- a/commons/tools/tests/Test_OrientSequences.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -import unittest -import time -import os -from commons.core.utils.FileUtils import FileUtils -from commons.tools.OrientSequences import OrientSequences - - -class Test_OrientSequences( unittest.TestCase ): - - def setUp( self ): - self._i = OrientSequences () - self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() ) - - - def tearDown( self ): - self._i = None - self._uniqId = None - - - def test_parseMummerOutput( self ): - inFileName = "dummyInFile_%s" % ( self._uniqId ) - inF = open( inFileName, "w" ) - inF.write( "> seq1\n" ) - inF.write( " seq2 20 1 20\n" ) - inF.write( "> seq1 Reverse\n" ) - inF.write( " seq2 100 1 100\n" ) - inF.write( " seq2 450 400 50\n" ) - inF.close() - dExp = { "direct": 1, "reverse": 2 } - self._i._verbose = 0 - dObs = self._i.parseMummerOutput( inFileName, "seq1", "seq2" ) - self.assertEqual( dObs, dExp ) - os.remove( inFileName ) - - - def test_getSequencesToReverseFromMatrix_2seq( self ): - lNewHeaders = [ "seq1", "seq2" ] - dMatrix = { "1_vs_2": { "direct": 1, "reverse": 2 } } - lExp = [ "seq2" ] - self._i._verbose = 0 - lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) - lExp.sort() - lObs.sort() - self.assertEqual( lObs, lExp ) - - - def test_getSequencesToReverseFromMatrix_3seq( self ): - lNewHeaders = [ "seq1", "seq2", "seq3" ] - dMatrix = { "1_vs_2": { "direct": 1, "reverse": 10 }, - "1_vs_3": { "direct": 10, "reverse": 1 }, - "2_vs_3": { "direct": 1, "reverse": 10 } } - lExp = [ "seq2" ] - self._i._verbose = 0 - lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_getSequencesToReverseFromMatrix_4seq( self ): - lNewHeaders = [ "seq1", "seq2", "seq3", "seq4" ] - dMatrix = { "1_vs_2": { "direct": 10, "reverse": 1 }, - "1_vs_3": { "direct": 1, "reverse": 10 }, - "1_vs_4": { "direct": 1, "reverse": 10 }, - "2_vs_3": { "direct": 1, "reverse": 10 }, - "2_vs_4": { "direct": 1, "reverse": 10 }, - "3_vs_4": { "direct": 1, "reverse": 2 } } - lExp = [ "seq3", "seq4" ] - self._i._verbose = 0 - lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) - lExp.sort() - lObs.sort() - self.assertEqual( lExp, lObs ) - - - def test_orientInputSequences( self ): - lSeqToOrient = [ "seq1" ] - tmpFileName = "dummyInFile_%s" % ( self._uniqId ) - tmpF = open( tmpFileName, "w" ) - tmpF.write( ">seq1\n" ) - tmpF.write( "ATGCGGTGCATG\n" ) - tmpF.write( ">seq2\n" ) - tmpF.write( "GGCGAAGTGAAA\n" ) - tmpF.close() - expFileName = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFileName, "w" ) - expF.write( ">seq1 re-oriented\n" ) - expF.write( "CATGCACCGCAT\n" ) - expF.write( ">seq2\n" ) - expF.write( "GGCGAAGTGAAA\n" ) - expF.close() - obsFileName = "dummyObsFile_%s" % ( self._uniqId ) - self._i._verbose = 0 - self._i._outFileName = obsFileName - self._i.orientInputSequences( lSeqToOrient, tmpFileName ) - self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [ tmpFileName, expFileName, obsFileName ]: - os.remove( f ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_RmvPairAlignInChunkOverlaps.py --- a/commons/tools/tests/Test_RmvPairAlignInChunkOverlaps.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,161 +0,0 @@ -import unittest -import os -import time -from commons.core.coord.Align import Align -from commons.core.utils.FileUtils import FileUtils -from commons.tools.RmvPairAlignInChunkOverlaps import RmvPairAlignInChunkOverlaps - - -class Test_RmvPairAlignInChunkOverlaps( unittest.TestCase ): - - def setUp( self ): - self._i = RmvPairAlignInChunkOverlaps() - self._uniqId = "%s" % ( time.strftime("%Y%m%d%H%M%S") ) - - - def tearDown( self ): - self._i = None - self._uniqId = None - - - def test_isPairAlignAChunkOverlap( self ): - a = Align() - a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "100", "0.0", "125", "97.6" ) ) - self._i.setChunkLength( 500 ) - self._i.setChunkOverlap( 100 ) - obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 ) - self.assertTrue( obs ) - a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "100", "0.0", "125", "97.6" ) ) # reverse subject - obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 ) - self.assertTrue( obs ) - a.setFromTuple( ( "chunk1", "401", "500", "chunk3", "1", "100", "0.0", "125", "97.6" ) ) # chunk subject not contiguous - obs = self._i.isPairAlignAChunkOverlap( a, 1, 3 ) - self.assertFalse( obs ) - a.setFromTuple( ( "chunk1", "390", "500", "chunk2", "1", "110", "0.0", "125", "97.6" ) ) # hit longer than chunk overlap - obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 ) - self.assertFalse( obs ) - a.setFromTuple( ( "chunk2", "1", "101", "chunk1", "401", "500", "0.0", "500", "100.0" ) ) # chunk overlap returned by PALS (+1), query > subject - obs = self._i.isPairAlignAChunkOverlap( a, 2, 1 ) - self.assertTrue( obs ) - a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "101", "0.0", "500", "100.0" ) ) # chunk overlap returned by PALS (+1), query < subject - obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 ) - self.assertTrue( obs ) - - - def test_isPairAlignWithinAndDueToAChunkOverlap( self ): - a = Align() - a.setFromTuple( ( "chunk1", "411", "450", "chunk2", "11", "50", "0.0", "73", "97.6" ) ) # included, due to overlap - self._i.setChunkLength( 500 ) - self._i.setChunkOverlap( 100 ) - self._i._verbose = 0 - obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 ) - self.assertTrue( obs ) - a.setFromTuple( ( "chunk1", "411", "450", "chunk2", "50", "11", "0.0", "73", "97.6" ) ) # reverse subject - obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 ) - self.assertFalse( obs ) - a.setFromTuple( ( "chunk1", "401", "500", "chunk3", "1", "100", "0.0", "125", "97.6" ) ) # chunk subject not contiguous - obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 3 ) - self.assertFalse( obs ) - a.setFromTuple( ( "chunk1", "390", "500", "chunk2", "1", "110", "0.0", "125", "97.6" ) ) # hit longer than chunk overlap - obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 ) - self.assertFalse( obs ) - a.setFromTuple( ( "chunk1", "411", "430", "chunk2", "16", "35", "0.0", "73", "97.6" ) ) # repeat within overlap... - self._i._margin = 2 # ... but not due to it - obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 ) - self.assertFalse( obs ) - self._i._margin = 10 # ... and due to it - obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 ) - self.assertTrue( obs ) - - - def test_removeChunkOverlaps( self ): - inFileName = "dummyInFile_%s" % ( self._uniqId ) - inF = open( inFileName, "w" ) - a = Align() - a.setFromTuple( ( "chunk1", "411", "490", "chunk2", "11", "90", "0.0", "73", "97.6" ) ) - a.write( inF ) - a.setFromTuple( ( "chunk1", "1", "500", "chunk1", "1", "500", "0.0", "500", "100.0" ) ) - a.write( inF ) - inF.close() - self._i.setInputFileName( inFileName ) - self._i.setChunkLength( 500 ) - self._i.setChunkOverlap( 100 ) - obsFileName = "dummyObsFile_%s" %( self._uniqId ) - self._i.setOutputFileName( obsFileName ) - d = self._i.removeChunkOverlaps() - expFileName = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFileName, "w" ) - expF.write( "" ) - expF.close() - self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [ inFileName, obsFileName, expFileName ]: os.remove( f ) - - - def test_zRunAsScript( self ): - cDir = os.getcwd() - - alignFileName = "dummyInFile_%s" % ( self._uniqId ) - aF = open( alignFileName, "w" ) - aF.write( "chunk1\t401\t500\tchunk2\t1\t100\t0.0\t131\t100.0\n" ) # remove - aF.write( "chunk2\t1\t100\tchunk1\t401\t500\t0.0\t132\t100.0\n" ) # remove - aF.write( "chunk1\t401\t500\tchunk3\t1\t100\t0.0\t132\t100.0\n" ) # keep because non-contiguous chunks - aF.write( "chunk3\t401\t500\tchunk1\t1\t100\t0.0\t132\t100.0\n" ) # keep because non-contiguous chunks - aF.write( "chunk1\t401\t500\tchunk2\t100\t1\t0.0\t132\t100.0\n" ) # keep because within overlap but reverse - aF.write( "chunk1\t431\t490\tchunk2\t31\t90\t0.0\t132\t100.0\n" ) # remove because within and due to overlap - aF.write( "chunk1\t411\t430\tchunk2\t61\t90\t0.0\t132\t100.0\n" ) # keep because within but not due to overlap - aF.write( "chunk1\t390\t500\tchunk2\t1\t100\t0.0\t132\t100.0\n" ) # keep because longer HSP on query - aF.close() - - expFileName = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFileName, "w" ) - expF.write( "chunk1\t401\t500\tchunk3\t1\t100\t0\t132\t100.000000\n" ) - expF.write( "chunk3\t401\t500\tchunk1\t1\t100\t0\t132\t100.000000\n" ) - expF.write( "chunk1\t401\t500\tchunk2\t100\t1\t0\t132\t100.000000\n" ) - expF.write( "chunk1\t411\t430\tchunk2\t61\t90\t0\t132\t100.000000\n" ) - expF.write( "chunk1\t390\t500\tchunk2\t1\t100\t0\t132\t100.000000\n" ) - expF.close() - - obsFileName = "dummyObsFile_%s" % ( self._uniqId ) - cmd = "RmvPairAlignInChunkOverlaps.py" - cmd += " -i %s" % ( alignFileName ) - cmd += " -l 500" - cmd += " -o 100" - cmd += " -O %s" % ( obsFileName ) - cmd += " -v 0" - os.system( cmd ) - - self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [ alignFileName, expFileName, obsFileName ]: os.remove( f ) - os.chdir( cDir ) - - def test_zRunAsScript_bug_to_fix(self): - cDir = os.getcwd() - - alignFileName = "dummyInFile_%s" % ( self._uniqId ) - aF = open( alignFileName, "w" ) - aF.write("chunk4\t63217\t63680\tchunk5\t195316\t194837\t0\t676\t92.71\n") - aF.write("chunk4\t63217\t63680\tchunk6\t2618\t3101\t0\t714\t93.6\n") - aF.write("chunk4\t63217\t63680\tchunk6\t5316\t4837\t0\t676\t92.71\n") - aF.close() - - expFileName = "dummyExpFile_%s" % ( self._uniqId ) - expF = open( expFileName, "w" ) - expF.write("chunk4\t63217\t63680\tchunk5\t195316\t194837\t0\t676\t92.71\n") - expF.write("chunk4\t63217\t63680\tchunk6\t2618\t3101\t0\t714\t93.6\n") - expF.close() - - obsFileName = "dummyObsFile_%s" % ( self._uniqId ) - cmd = "RmvPairAlignInChunkOverlaps.py" - cmd += " -i %s" % ( alignFileName ) - cmd += " -l 200000" - cmd += " -o 10000" - cmd += " -O %s" % ( obsFileName ) - cmd += " -v 0" - os.system( cmd ) - - self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [ alignFileName, expFileName, obsFileName ]: os.remove( f ) - os.chdir( cDir ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_SpliceTEsFromGenome.py --- a/commons/tools/tests/Test_SpliceTEsFromGenome.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from commons.tools.SpliceTEsFromGenome import SpliceTEsFromGenome - - -class Test_SpliceTEsFromGenome( unittest.TestCase ): - - def setUp( self ): - self._i = SpliceTEsFromGenome() - - - def test_zLaunchAsScript( self ): - cDir = os.getcwd() - - coordFile = "dummyCoordFile" - coordFileHandler = open( coordFile, "w" ) - coordFileHandler.write( "TE1\tchr1\t2\t5\n" ) - coordFileHandler.write( "TE2\tchr1\t11\t15\n" ) - coordFileHandler.write( "TE3\tchr1\t12\t14\n" ) - coordFileHandler.close() - - genomeFile = "dummyGenomeFile" - genomeFileHandler = open( genomeFile, "w" ) - genomeFileHandler.write( ">chr1\n" ) - genomeFileHandler.write( "AGGGGAAAAACCCCCAAAAA\n" ) - genomeFileHandler.write( ">chr2\n" ) - genomeFileHandler.write( "TTTTTTTTTT\n" ) - genomeFileHandler.close() - - expFile = "dummyExpFile" - expFileHandler = open( expFile, "w" ) - expFileHandler.write( ">chr1\n" ) - expFileHandler.write( "AAAAAAAAAAA\n" ) - expFileHandler.write( ">chr2\n" ) - expFileHandler.write( "TTTTTTTTTT\n" ) - expFileHandler.close() - - obsFile = "dummyObsFile" - - cmd = "SpliceTEsFromGenome.py" - cmd += " -i %s" % ( coordFile ) - cmd += " -f %s" % ( "map" ) - cmd += " -g %s" % ( genomeFile ) - cmd += " -o %s" % ( obsFile ) - cmd += " -v %i" % ( 0 ) - returnStatus = os.system( cmd ) - - self.assertTrue( returnStatus == 0 ) - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ coordFile, genomeFile, expFile, obsFile ]: - os.remove( f ) - os.chdir( cDir ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_getCumulLengthFromTEannot.py --- a/commons/tools/tests/Test_getCumulLengthFromTEannot.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -import unittest -import os -import time -from commons.core.sql.DbMySql import DbMySql -from commons.tools.getCumulLengthFromTEannot import getCumulLengthFromTEannot -from commons.core.utils.FileUtils import FileUtils - - -class Test_getCumulLengthFromTEannot( unittest.TestCase ): - - def setUp( self ): - self.fileUtils = FileUtils() - self._getCumulLengthFromTEannot = None - self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() ) - self._configFileName = "dummyConfig_%s" % self._uniqId - configFile = open( self._configFileName, "w" ) - configFile.write("[repet_env]\n") - configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) - configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) - configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) - configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) - configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) - configFile.close() - - - def tearDown( self ): - os.remove( self._configFileName ) - - - def test_getAllSubjectsAsMapOfQueries( self ): - inFileName = "dummyInFile_%s" % self._uniqId - expFileName = "dummyExp_%s" % self._uniqId - for f in [inFileName,expFileName]: - if os.path.exists(f): os.remove(f) - inFile = open( inFileName, "w" ) - inFile.write( "1\tchr1\t1501\t2500\tTE1\t1\t500\t0.0\t880\t95.7\n" ) - inFile.write( "2\tchr1\t3401\t4000\tTE3\t101\t700\t0.0\t950\t97.2\n" ) - inFile.close() - inTable = "dummyPathTable_%s" % self._uniqId - db = DbMySql(cfgFileName=self._configFileName) - db.createTable(inTable, "path", inFileName) - expFile = open( expFileName, "w" ) - expFile.write( "TE1\tchr1\t1501\t2500\n" ) - expFile.write( "TE3\tchr1\t3401\t4000\n" ) - expFile.close() - self._getCumulLengthFromTEannot = getCumulLengthFromTEannot() - self._getCumulLengthFromTEannot._tableName = inTable - self._getCumulLengthFromTEannot._configFileName = self._configFileName - self._getCumulLengthFromTEannot.setAdaptatorToTable() - obsFileName = self._getCumulLengthFromTEannot.getAllSubjectsAsMapOfQueries() - self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [inFileName,inTable+".map",expFileName]: - if os.path.exists(f): os.remove(f) - db.dropTable(inTable) - db.close() - - - def test_getCumulLength( self ): - mergeFileName = "dummyInFile_%s" % self._uniqId - mergeFile = open( mergeFileName, "w" ) - mergeFile.write( "TE1\tchr1\t1501\t2500\n" ) - mergeFile.write( "TE3\tchr1\t4000\t3401\n" ) - mergeFile.close() - exp = 1000+600 - self._getCumulLengthFromTEannot = getCumulLengthFromTEannot() - obs = self._getCumulLengthFromTEannot.getCumulLength( mergeFileName ) - self.assertEqual( obs, exp ) - os.remove( mergeFileName ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_pathnum2id.py --- a/commons/tools/tests/Test_pathnum2id.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils - - -class Test_pathnum2id( unittest.TestCase ): - - def setUp( self ): - self._inputFileName = "dummyInputPathFile" - self._outputFileName = "dummyOutputPathFile" - self._expectedFileName = "dummyExpectedPathFile" - self._prg = "pathnum2id.py" - - - def test_runWhithoutReturnAtEndOfFile( self ): - cDir = os.getcwd() - - self._createAndFillInputFileWhithoutReturnAtTheEnd() - self._createExpectedFile() - cmd = self._prg - cmd += " -i %s" % ( self._inputFileName ) - cmd += " -o %s" % ( self._outputFileName ) - os.system( cmd ) - self.assertTrue( FileUtils.are2FilesIdentical( self._outputFileName, self._expectedFileName ) ) - - os.remove( self._inputFileName ) - os.remove( self._expectedFileName ) - if os.path.exists( self._outputFileName ): - os.remove( self._outputFileName ) - os.chdir( cDir ) - - - def test_runWhithReturnAtEndOfFile( self ): - cDir = os.getcwd() - - self._createAndFillInputFileWhithReturnAtTheEnd() - self._createExpectedFile() - cmd = self._prg - cmd += " -i %s" % ( self._inputFileName ) - cmd += " -o %s" % ( self._outputFileName ) - os.system( cmd ) - self.assertTrue( FileUtils.are2FilesIdentical( self._outputFileName, self._expectedFileName ) ) - - os.remove( self._inputFileName ) - os.remove( self._expectedFileName ) - if os.path.exists( self._outputFileName ): - os.remove( self._outputFileName ) - os.chdir( cDir ) - - - def _createExpectedFile( self ): - f = open(self._expectedFileName, "w") - f.write("1\tblumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("2\tblumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("3\tblumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("4\tblumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2e-06\t0.0\t0\n") - f.write("5\tblumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("6\tblumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n") - f.close() - - - def _createAndFillInputFileWhithoutReturnAtTheEnd( self ): - f = open(self._inputFileName, "w") - f.write("1\tblumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("2\tblumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("3\tblumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("1\tblumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2e-06\t0.0\t0\n") - f.write("2\tblumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("3\tblumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0") - f.close() - - - def _createAndFillInputFileWhithReturnAtTheEnd( self ): - f = open(self._inputFileName, "w") - f.write("1\tblumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t1.5\t3.2\t0\n") - f.write("2\tblumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t2.9\t0\n") - f.write("3\tblumeria_Grouper_590_20:NoCat_3\t30\t37\tCPW_WPC\t1\t9\t7.7\t1.5\t0\n") - f.write("1\tblumeria_Grouper_590_20:NoCat_3\t55\t69\tHECT\t341\t355\t9.2e-06\t0.0\t0\n") - f.write("2\tblumeria_Grouper_590_20:NoCat_4\t82\t91\tDUF46\t173\t182\t0.11\t6.4\t0\n") - f.write("3\tblumeria_Grouper_590_20:NoCat_5\t121\t125\tPOC4\t276\t280\t6.3\t-1.7\t0\n") - f.close() - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_refalign2fasta.py --- a/commons/tools/tests/Test_refalign2fasta.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,135 +0,0 @@ -import unittest -import time -from commons.tools.refalign2fasta import * -from commons.core.utils.FileUtils import FileUtils - - -class Test_refalign2fasta( unittest.TestCase ): - - - def setUp( self ): - self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) - - - def tearDown( self ): - self._uniqId = None - - - def test_getAlignments( self ): - inFile = "dummyInFile_%s" % ( self._uniqId ) - inFileHandler = open( inFile, "w" ) - inFileHandler.write( "AAAACTTTT-T\tAAAA-TTTGGT\trefseq::1 chr3 1..10\n" ) # 1 insertion and 1 deletion in the copy + 1 mismatch - inFileHandler.close() - lExp = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ] - lObs = getAlignments( inFile ) - self.assertEqual( lExp, lObs ) - os.remove( inFile ) - - - def test_getGaps_OneGap( self ): - sequence = "AAAACTTTT-T" - lExp = [ ( 9, 1 ) ] - lObs = getGaps( sequence ) - self.assertEqual( lExp, lObs ) - - - def test_getGaps_TwoGaps( self ): - sequence = "AAAA--CTTT-TT" - lExp = [ ( 4, 2 ), ( 8, 1 ) ] - lObs = getGaps( sequence ) - self.assertEqual( lExp, lObs ) - - - def test_getGapsOnRefSeq_OneSeq( self ): - lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ] - lExp = [ [ ( 9, 1 ) ] ] - lObs = getGapsOnRefSeq( lAlign ) - self.assertEqual( lExp, lObs ) - - - def test_getGapsOnRefSeq_TwoSeq( self ): - lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ] - lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) ) - lExp = [ [ ( 9, 1 ) ] ] - lExp.append( [ ( 4, 2 ), ( 8, 1 ) ] ) - lObs = getGapsOnRefSeq( lAlign ) - self.assertEqual( lExp, lObs ) - - - def test_insertGap( self ): - sequence = "GGGGAAAGTTG" - start = 5 - length = 3 - exp = "GGGGA---AAGTTG" - obs = insertGap( sequence, start, length ) - self.assertEqual( exp, obs ) - - - def test_insertListGaps( self ): - sequence = "GGGGAAAGTTG" - lGaps =[ ( 5, 3 ), ( 9, 1 ) ] - exp = "GGGGA---AAGT-TG" - obs = insertListGaps( sequence, lGaps ) - self.assertEqual( exp, obs ) - - - def test_insertGapsInRefSeq( self ): - lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ] - lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) ) - lGapsOnRefSeqPerAlign = [ [ ( 9, 1 ) ] ] - lGapsOnRefSeqPerAlign.append( [ ( 4, 2 ), ( 8, 1 ) ] ) - refseqName = "reference_sequence" - lExp = ( refseqName, "AAAA--CTTT-T-T" ) - lObs = insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName ) - self.assertEqual( lExp, lObs ) - - - def test_insertgap_seq( self ): - # AAAACTTTT-T (refseq) - # AAAA-TTTGGT ( copy 1) - # - # AAAA--CTTT-TT (refseq) - # AAAAGGCTTTGTT (copy 2) - lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ] - lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) ) - lGapsOnRefSeqPerAlign = [ [ ( 9, 1 ) ] ] - lGapsOnRefSeqPerAlign.append( [ ( 4, 2 ), ( 8, 1 ) ] ) - lExp = [ ( "refseq::1 chr3 1..10", "AAAA---TTT-GGT" ) ] - lExp.append( ( "refseq::2 chr5 1..10", "AAAAGGCTTTGT-T" ) ) - lObs = insertgap_seq( lAlign, lGapsOnRefSeqPerAlign ) - self.assertEqual( lExp, lObs ) - - - def test_getSeqWithDeletions( self ): - lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ] - lExp = [ ( "refseq::1 chr3 1..10", "AAAA-TTTGT" ) ] - lObs = getSeqWithDeletions( lAlign ) - self.assertEqual( lExp, lObs ) - - - def test_saveOnlyWithDeletions( self ): - refseqName = "Dm-B-G54-Map3" - lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "Dm-B-G54-Map3::1 chr3 1..10" ) ] - lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "Dm-B-G54-Map3::2 chr5 1..10" ) ) - - expFile = "dummyExpFile_%s" %( self._uniqId ) - expFileHandler = open( expFile, "w" ) - expFileHandler.write( ">Dm-B-G54-Map3\n" ) - expFileHandler.write( "AAAACTTTTT\n" ) - expFileHandler.write( ">Dm-B-G54-Map3::1 chr3 1..10\n" ) - expFileHandler.write( "AAAA-TTTGT\n" ) - expFileHandler.write( ">Dm-B-G54-Map3::2 chr5 1..10\n" ) - expFileHandler.write( "AAAACTTTTT\n" ) - expFileHandler.close() - - obsFile = "dummyObsFile_%s" % ( self._uniqId ) - - saveOnlyWithDeletions( lAlign, refseqName, obsFile ) - - self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) - - for f in [ expFile, obsFile ]: - os.remove( f ) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/Test_srptTableOverlap.py --- a/commons/tools/tests/Test_srptTableOverlap.py Mon Apr 29 03:23:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ -import unittest -import os -import time -import pyRepet.sql.RepetDBMySQL -from commons.core.utils.FileUtils import FileUtils -from commons.tools import srptTableOverlap - - -class Test_srptTableOverlap( unittest.TestCase ): - - def setUp(self): - self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) - self._db = pyRepet.sql.RepetDBMySQL.RepetDB( os.environ["REPET_USER"], - os.environ["REPET_HOST"], - os.environ["REPET_PW"], - os.environ["REPET_DB"] ) - - - def test_getOverlapAllPaths(self): - qryFileName = "dummyQryFile_%s" % ( self._uniqId ) - qryF = open( qryFileName, "w" ) - qryF.write("1\tchr1\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n") - qryF.close() - qryTable = "dummyQryTable_%s" % ( self._uniqId ) - self._db.create_table( self._db, qryTable, qryFileName, "path" ) - sbjFileName = "dummySbjFile_%s" % ( self._uniqId ) - sbjF = open( sbjFileName, "w" ) - sbjF.write("1\tchr1\t1001\t1500\tTE1\t11\t17\t1e-20\t30\t90.2\n") # 200-bp overlap: 1301-1500 - sbjF.write("2\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n") # 300-bp overlap: 1501-1800 - sbjF.write("3\tchr1\t2001\t2100\tTE2\t11\t17\t1e-20\t30\t90.2\n") - sbjF.write("4\tchr2\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n") # different query - sbjF.close() - sbjTable = "dummySbjTable_%s" % ( self._uniqId ) - self._db.create_table( self._db, sbjTable, sbjFileName, "path" ) - exp_sum_osize, exp_sum_non_osize, exp_sum_qsize = 500, 200, 700 - obs_sum_osize, obs_sum_non_osize, obs_sum_qsize = srptTableOverlap.getOverlapAllPaths( qryTable, "path", sbjTable, "path", self._db ) - self.assertEqual( obs_sum_osize, exp_sum_osize ) - self.assertEqual( obs_sum_non_osize, exp_sum_non_osize ) - self.assertEqual( obs_sum_qsize, exp_sum_qsize ) - os.remove( qryFileName ) - os.remove( sbjFileName ) - self._db.remove_if_exist( qryTable ) - self._db.remove_if_exist( sbjTable ) - - - def test_pathOverlapByPath(self): - qryFileName = "dummyQryFile_%s" % ( self._uniqId ) - qryF = open( qryFileName, "w" ) - qryF.write("1\tchr1\t1301\t2000\tTE2\t1\t700\t1e-80\t850\t90.2\n") - qryF.write("1\tchr1\t2301\t3000\tTE2\t801\t1500\t1e-90\t930\t90.2\n") - qryF.close() - qryTable = "dummyQryTable_%s" % ( self._uniqId ) - self._db.create_table( self._db, qryTable, qryFileName, "path" ) - sbjFileName = "dummySbjFile_%s" % ( self._uniqId ) - sbjF = open( sbjFileName, "w" ) - sbjF.write("1\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n") - sbjF.write("1\tchr1\t2101\t250000\tTE2\t11\t17\t1e-20\t30\t90.2\n") - sbjF.write("2\tchr1\t3501\t4000\tTE3\t11\t17\t1e-20\t30\t90.2\n") - sbjF.close() - sbjTable = "dummySbjTable_%s" % ( self._uniqId ) - self._db.create_table( self._db, sbjTable, sbjFileName, "path" ) - expFileName = "dummyOutFileExp_%s" % ( self._uniqId ) - expF = open( expFileName, "w" ) - expF.write("1\tTE2\t1400\t1:TE2\t1\t248300\t1100\t0.785714\t0.004430\n") - expF.close() - obsFileName = "dummyOutFileObs_%s" % ( self._uniqId ) - obsF = open( obsFileName, "w" ) - srptTableOverlap.pathOverlapByPath( qryTable, "path", sbjTable, "path", self._db, obsF ) - obsF.close() - self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) - for f in [ qryFileName, sbjFileName, expFileName, obsFileName ]: - os.remove( f ) - self._db.remove_if_exist( qryTable ) - self._db.remove_if_exist( sbjTable ) - self._db.remove_if_exist( sbjTable+"_bin" ) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff -r 9bcfa7936eec -r c265f13066d8 commons/tools/tests/__init__.py