view commons/launcher/LaunchMap.py @ 18:94ab73e8a190

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#!/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
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# 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
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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()