Mercurial > repos > yufei-luo > s_mart

--- a/commons/launcher/BlatClusterLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/BlatProgramLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/LaunchBlastclust.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/LaunchLastZ.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/LaunchMCL.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/LaunchMap.py	Tue Apr 30 14:33:21 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: <input>.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
--- a/commons/launcher/LaunchMatcher.py	Tue Apr 30 14:33:21 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
--- a/commons/launcher/LaunchMummerPlot.py	Tue Apr 30 14:33:21 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
--- a/commons/launcher/LaunchNucmer.py	Tue Apr 30 14:33:21 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
--- a/commons/launcher/LaunchPhyML.py	Tue Apr 30 14:33:21 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: <input>.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")
-
-
--- a/commons/launcher/LaunchPromer.py	Tue Apr 30 14:33:21 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
--- a/commons/launcher/LaunchRefAlign.py	Tue Apr 30 14:33:21 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: <input>.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()
--- a/commons/launcher/LaunchRefalign_old.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/LaunchRepeatMasker.py	Tue Apr 30 14:33:21 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
--- a/commons/launcher/LaunchTRF.py	Tue Apr 30 14:33:21 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: <input>.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()
-
--- a/commons/launcher/LaunchTallymer.py	Tue Apr 30 14:33:21 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
--- a/commons/launcher/MafftClusterLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/MafftProgramLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/MapClusterLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/MapProgramLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/NWalignProgramLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/RepeatMaskerClusterLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/RepeatMaskerProgramLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/YassClusterLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/YassProgramLauncher.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchBlasterMatcherPerQuery.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchMafft.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchMreps.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchPhyML.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchPrank.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchTCoffee.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/launchTEclass.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/tests/MockDataBankForBlat.py	Tue Apr 30 14:33:21 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()
--- a/commons/launcher/tests/MockESTBankForBlat.py	Tue Apr 30 14:33:21 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(&qu