comparison commons/launcher/LaunchMCL.py @ 18:94ab73e8a190

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18:94ab73e8a190

#!/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
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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()