view commons/tools/LaunchMatcherInParallel.py @ 18:94ab73e8a190

Uploaded

#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software.  You can  use, 
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
# As a counterpart to the access to the source code and  rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty  and the software's author,  the holder of the
# economic rights,  and the successive licensors  have only  limited
# liability. 
#
# In this respect, the user's attention is drawn to the risks associated
# with loading,  using,  modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean  that it is complicated to manipulate,  and  that  also
# therefore means  that it is reserved for developers  and  experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or 
# data to be ensured and,  more generally, to use and operate it in the 
# same conditions as regards security. 
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.

from commons.core.LoggerFactory import LoggerFactory
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
from commons.core.launcher.Launcher import Launcher
from commons.core.launcher.LauncherUtils import LauncherUtils
from commons.core.utils.FileUtils import FileUtils
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
from commons.core.coord.AlignUtils import AlignUtils
import shutil
import os

LOG_DEPTH = "repet.tools"


class LaunchMatcherInParallel(object):
    def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", alignPattern = ".*\.align", \
                 config = "", groupId = "", maxFileSize = 1000000, mergeResults=True, workingDir="tmpMatcher", doClean = False, verbosity = 0):
        self._alignFileName = align
        self._queryFileName = queryFileName
        self.setSubjectFileName(subjectFileName)
        self.setOutPrefix(prefix)
        self._alignPattern = alignPattern
        self._doJoin = doJoin
        self._eValue = evalue
        self._keepConflict = keepConflict
        self._configFileName = config
        self.setGroupId(groupId)
        self._maxFileSize = maxFileSize
        self._mergeResults = mergeResults
        self._doClean = doClean
        self._workingDir = workingDir
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        self._jobSectionName = "jobs"
        
    def setAttributesFromCmdLine(self):
        description = "Launch Matcher in parallel."
        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
        epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -v 0"
        epilog += "\n\t"
        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
        epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -q query.fa -s subject.fa -o query -c -v 2"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-a", "--align",      dest = "align",         action = "store",       type = "string", help = "input align file name [compulsory] [format: align]",       default = "")
        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta file name [optional] [format: fasta]",         default = "")
        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta file name [optional] [format: fasta]",       default = "")
        parser.add_option("-e", "--evalue",     dest = "evalue",        action = "store",       type = "string", help = "E-value filter [default: 1e10]",                           default = "1e-10")
        parser.add_option("-j", "--join",       dest = "doJoin",        action = "store_true",                   help = "join matches [default: False]",                            default = False)
        parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true",                   help = "keep conflicting subjects [default: False]",               default = False)
        parser.add_option("-o", "--outPrefix",  dest = "outPrefix",     action = "store",       type = "string", help = "output file prefix [default: align file name]",            default = "")
        parser.add_option("-p", "--alignPattern",dest = "alignPattern", action = "store",       type = "string", help = "align file pattern [default: .*\.align]",                  default = ".*\.align")
        parser.add_option("-n", "--maxFileSize",dest = "maxFileSize",   action = "store",       type = "int",    help = "max file size (1 file for 1 job) [default: 100000]",       default = 10000)
        parser.add_option("-m", "--notMergeResults",dest = "notMergeResults", action = "store_false",            help = "don't merge results files [default: True]",                default = True)
        parser.add_option("-w", "--workingDir",dest = "workingDir",     action = "store",       type = "string", help = "working directory [default: tmpMatcher]",                  default = "tmpMatcher")
        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [default: False]",                   default = False)
        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setAlignFileName(options.align)
        self.setQueryFileName(options.query)
        self.setSubjectFileName(options.subject)
        self.setEvalue(options.evalue)
        self.setDoJoin(options.doJoin)
        self.setKeepConflicts(options.keepConflict)
        self.setOutPrefix(options.outPrefix)
        self.setAlignPattern(options.alignPattern)
        self.setMaxFileSize(options.maxFileSize)
        self.setMergeResults(options.notMergeResults)
        self.setWorkingDir(options.workingDir)
        self.setDoClean(options.doClean)
        self.setVerbosity(options.verbosity)
        
    def setAlignFileName(self, alignFileName):
        self._alignFileName = alignFileName
        
    def setQueryFileName(self, queryFileName):
        self._queryFileName = queryFileName
        
    def setSubjectFileName(self, subjectFileName):
        self._subjectFileName = subjectFileName
        
    def setEvalue(self, evalue):
        self._eValue = evalue
        
    def setDoJoin(self, doJoin):
        self._doJoin = doJoin
        
    def setKeepConflicts(self, keepConflict):
        self._keepConflict = keepConflict
        
    def setOutPrefix(self, outPrefix):
        if outPrefix == "":
            self._outPrefix = self._alignFileName
        else:
            self._outPrefix = outPrefix
        
    def setAlignPattern(self, alignPattern):
        self._alignPattern = alignPattern
        
    def setGroupId(self, groupId):
        if groupId == "":
            self._groupId = "Matcher_%s" % os.getpid()
        else:
            self._groupId = groupId
            
    def setMaxFileSize(self, maxFileSize):
        self._maxFileSize = maxFileSize
        
    def setMergeResults(self, mergeResults):
        self._mergeResults = mergeResults
    
    def setWorkingDir(self, workingDir):
        self._workingDir = workingDir
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def _checkOptions(self):
        if self._alignFileName == "":
            self._logAndRaise("ERROR: Missing input align file name")
        
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
    
    def _checkConfig(self):       
        iConfigRules = ConfigRules()
        iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True)
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string")
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string")
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool")
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool")

        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
        self._iConfig = iConfigChecker.getConfig()
        self._setAttributesFromConfig()
        
    def _setAttributesFromConfig(self):
        self._resources = self._iConfig.get(self._jobSectionName, "resources")
        self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir")
        self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy")
        self._doClean = self._iConfig.get(self._jobSectionName, "clean")
        
        if self._isCopyOnNode and not self._tmpDir:
            self._isCopyOnNode = False
        self._log.debug("The copy option is: %s." % self._isCopyOnNode)

    def _getLaunchMatcherCmd(self, iLauncher, file):
        lArgs = []
        lArgs.append("-a %s" % file)
        if self._queryFileName:
            lArgs.append("-q %s" % self._queryFileName)
        if self._subjectFileName:
            lArgs.append("-s %s" % self._subjectFileName)
        lArgs.append("-e %s" % self._eValue)
        lArgs.append("-o %s" % file)
        if self._doJoin:
            lArgs.append("-j")
        if self._keepConflict:
            lArgs.append("-k")
        lArgs.append("-v %i" % (self._verbosity - 1))
        return iLauncher.getSystemCommand("LaunchMatcher.py", lArgs)
    
    def _splitAlignFilePerSeq(self):
        lAlign = AlignUtils.getAlignListFromFile(self._alignFileName)
        lAlignList = AlignUtils.splitAlignListByQueryName(lAlign)
        inputFileNameWithoutExtension = os.path.splitext(os.path.basename(self._alignFileName))[0]
        AlignUtils.createAlignFiles(lAlignList, inputFileNameWithoutExtension, self._workingDir)
        
    def _writeTabHeader(self, outTabFileName):
        with open(outTabFileName, 'w') as f:
            f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")

    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkConfig()
        self._checkOptions()
        
        self._log.info("START LaunchMatcherInParallel")
        self._log.debug("Align file name: %s" % self._alignFileName)
        self._log.debug("Query file name: %s" % self._queryFileName)
        self._log.debug("Subject file name: %s" % self._subjectFileName)
        if not os.path.exists(self._workingDir):
            os.makedirs(self._workingDir)
        else:
            self._doClean = False
        self._splitAlignFilePerSeq()
        os.chdir(self._workingDir)
        os.symlink("../%s" % self._queryFileName, self._queryFileName)
        if self._queryFileName != self._subjectFileName:
            os.symlink("../%s" % self._subjectFileName, self._subjectFileName)
            
        cDir = os.getcwd()
        if not self._tmpDir:
            self._tmpDir = cDir
        
        acronym = "Matcher"
        iDb = DbFactory.createInstance()
        jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
        iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode)

        lCmdsTuples = []
        lCmdSize = []
        lCmdCopy = []

        lFiles = FileUtils.getFileNamesList(".", self._alignPattern)
        lFileSizeTuples = []
        for fileName in lFiles:
            fileSize = os.path.getsize(fileName)
            lFileSizeTuples.append((fileName, fileSize))
        lFileSizeList = LauncherUtils.createHomogeneousSizeList(lFileSizeTuples, self._maxFileSize)
        
        for lFiles in lFileSizeList:
            lCmds = []
            lCmdStart = []
            lCmdFinish = []
            if self._queryFileName:
                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._queryFileName, self._queryFileName))
            if self._subjectFileName and self._subjectFileName != self._queryFileName:
                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._subjectFileName, self._subjectFileName))
            for file in lFiles:
                lCmds.append(self._getLaunchMatcherCmd(iLauncher, file))
                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, file, file))
                lCmdFinish.append("if os.path.exists(\"%s.match.path\"):" % file)
                lCmdFinish.append("\tshutil.move(\"%s.match.path\", \"%s/.\" )" % (file, cDir))
                lCmdFinish.append("if os.path.exists(\"%s.match.tab\"):" % file)
                lCmdFinish.append("\tshutil.move(\"%s.match.tab\", \"%s/.\" )" % (file, cDir))
            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy))
        
        iLauncher.runLauncherForMultipleJobs("Matcher", lCmdsTuples, self._doClean, self._isCopyOnNode)

        if self._mergeResults:
            FileUtils.catFilesByPattern("*.match.path", "../%s.match.path" % self._outPrefix)
            if self._queryFileName or self._subjectFileName:
                outTabFileName = "../%s.match.tab" % self._outPrefix
                self._writeTabHeader(outTabFileName)
                FileUtils.catFilesByPattern("*.match.tab", outTabFileName, skipHeaders = True)
        os.chdir("..")
        if self._doClean and self._mergeResults:
            self._log.warning("Working directory will be cleaned")
            shutil.rmtree(self._workingDir)
        self._log.info("END LaunchMatchInParallel")

if __name__ == "__main__":
    iLaunch = LaunchMatcherInParallel()
    iLaunch.setAttributesFromCmdLine()
    iLaunch.run()