annotate commons/tools/LaunchBlasterInParallel.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
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# 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". 
#
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import os
import shutil
from commons.core.LoggerFactory import LoggerFactory
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
from commons.core.launcher.Launcher import Launcher
from commons.core.utils.FileUtils import FileUtils
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
from commons.tools.MergeMatchsFiles import MergeMatchsFiles

LOG_DEPTH = "repet.tools"

##Launch BLASTER in parallel
#
class LaunchBlasterInParallel(object):
    
    def __init__(self, queryDirectory = "", subjectFilePath = "", outFileName = "", configFileName = "", groupId = "", queryPattern = ".*\.fa", \
                 doAllByall = False, nbCPU = 1, eValue="1e-300", type = "ncbi", program="blastn", extraParams="", verbosity = 0):
        self._queryDirectory = queryDirectory
        self._queryPattern = queryPattern
        self.setSubjectFilePath(subjectFilePath)
        self._outFileName = outFileName
        self._configFileName = configFileName
        self.setGroupId(groupId)
        self._doAllByall = doAllByall
        self._blastType = type
        self._program = program
        self._extraParams = extraParams
        self._nbCPU = nbCPU
        self._jobSectionName = "jobs"
        self._blasterSectionName = "alignment"
        self._prepareDataSectionName = "prepare_data"
        self._eValue = eValue
        
        self._doClean = None
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "Launch Blaster in parallel."
        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
        epilog += "\t$ python LaunchBlasterInParallel.py -q query -o query.align -v 0"
        epilog += "\n\t"
        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
        epilog += "\t$ python LaunchBlasterInParallel.py -q query -o query.align -s nr.fa -c -v 2"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta directory absolute path [compulsory]",         default = "")
        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta absolute path [compulsory] [format: fasta]", default = "")
        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output align file name [compulsory] [format: align]",      default = "")
        parser.add_option("-C", "--config",     dest = "configFileName",action = "store",       type = "string", help = "configuration file name [compulsory] [format: cfg]",       default = "")
        parser.add_option("-g", "--groupId",    dest = "groupId",       action = "store",       type = "string", help = "jobs groupId [default: Blaster_<pid>]",                    default = "")
        parser.add_option("-p", "--queryPattern",dest = "queryPattern", action = "store",       type = "string", help = "query file pattern [default: .*\.fa]",                     default = ".*\.fa")
        parser.add_option("-a", "--aba",        dest = "doAllByall",    action = "store_true",                   help = "all-by-all Blast [default: False]",                        default = False)
        parser.add_option("-e", "--eValue",     dest = "eValue",        action = "store",       type = "string", help = "Blast e-value [default: 1e300]",                           default = "1e-300")
        parser.add_option("-t", "--type",       dest = "type",          action = "store",       type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]",         default = "ncbi")
        parser.add_option("-u", "--program",    dest = "program",       action = "store",       type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]",         default = "blastn")
        parser.add_option("-x", "--extraParams",dest = "extraParams",   action = "store",       type = "string", help = "Additional blast program parameters[default: '']",         default = "")
        parser.add_option("-n", "--ncpu",       dest = "cpu",           action = "store",       type = "int",    help = "Number of CPUs to use [default: 1]",                       default = 1)
        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setQueryDirectory(options.query)
        self.setQueryPattern(options.queryPattern)
        self.setSubjectFilePath(options.subject)
        self.setOutFileName(options.outFileName)
        self.setConfigFileName(options.configFileName)
        self.setGroupId(options.groupId)
        self.setDoAllByall(options.doAllByall)
        self.setEValue(options.eValue)
        self.setType(options.type)
        self.setProgram(options.program)
        self.setExtraParams(options.extraParams)
        self.setCPU(options.cpu)
        self.setVerbosity(options.verbosity)
        
    def setQueryDirectory(self, queryDirectory):
        self._queryDirectory = queryDirectory
        
    def setQueryPattern(self, queryPattern):
        self._queryPattern = queryPattern
        
    def setSubjectFilePath(self, subjectFilePath):
        self._subjectFilePath = subjectFilePath
        self._subjectFileName = os.path.basename(subjectFilePath)
            
    def setOutFileName(self, outFileName):
        self._outFileName = outFileName
        
    def setConfigFileName(self, configFileName):
        self._configFileName = configFileName
        
    def setGroupId(self, groupId):
        if groupId == "":
            self._groupId = "Blaster_%s" % os.getpid()
        else:
            self._groupId = groupId
        
    def setDoAllByall(self, doAllByall):
        self._doAllByall = doAllByall
        
    def setType(self, blastType):
        self._blastType = blastType
        
    def setProgram(self, program):
        self._program = program
        
    def setExtraParams(self, extraParams):
        self._extraParams = extraParams
        
    def setEValue(self, eValue):
        self._eValue = eValue
        
    def setCPU(self, cpu):
        self._nbCPU = cpu
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def _checkOptions(self):
        if self._queryPattern == "":
            self._logAndRaise("ERROR: Missing input fasta file name")
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
    
    def _checkConfig(self):       
        iConfigRules = ConfigRules()
        iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True)
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string")
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string")
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool")
        iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool")
        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="blast", mandatory=True, type="string", set = ("ncbi", "blastplus", "wu"))
        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="Evalue", mandatory=True, type="string")
        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="length", mandatory=True, type="string")
        iConfigRules.addRuleOption(section=self._blasterSectionName, option ="identity", mandatory=True, type="string")

        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
        self._iConfig = iConfigChecker.getConfig()
        self._setAttributesFromConfig()
        
    def _setAttributesFromConfig(self):
        self._chunkLength = self._iConfig.get(self._prepareDataSectionName, "chunk_length")
        self._chunkOverlap = self._iConfig.get(self._prepareDataSectionName, "chunk_overlap")
        self._resources = self._iConfig.get(self._jobSectionName, "resources")
        self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir")
        self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy")
        self._doClean = self._iConfig.get(self._jobSectionName, "clean")
        self._blastType = self._iConfig.get(self._blasterSectionName, "blast")
        self._eValue = self._iConfig.get(self._blasterSectionName, "Evalue")
        self._length = self._iConfig.get(self._blasterSectionName, "length")
        self._identity = self._iConfig.get(self._blasterSectionName, "identity")
        
        if self._isCopyOnNode and not self._tmpDir:
            self._isCopyOnNode = False
        self._log.debug("The copy option is: %s." % self._isCopyOnNode)

    def _getLaunchBlasterCmd(self, iLauncher, file):
        lArgs = []
        lArgs.append("-u %s" % self._program)
        lArgs.append("-q %s" % file)
        lArgs.append("-s %s" % self._subjectFileName)
        if self._doAllByall:
            lArgs.append("-a")
        lArgs.append("-e %s" % self._eValue)
        lArgs.append("-l %s" % self._length)
        lArgs.append("-d %s" % self._identity)
        lArgs.append("-t %s" % self._blastType)
        lArgs.append("-x '%s'" % self._extraParams)
        if self._doClean:
            lArgs.append("-c")
        lArgs.append("-v %i" % (self._verbosity - 1))
        return iLauncher.getSystemCommand("LaunchBlaster.py", lArgs)
    
    def _getRmvPairAlignInChunkOverlapsCmd(self, iLauncher, inFileName, outFileName):
        lArgs = []
        lArgs.append("-i %s" % inFileName)
        lArgs.append("-l %s" % self._chunkLength)
        lArgs.append("-o %s" % self._chunkOverlap)
        lArgs.append("-m 10")
        lArgs.append("-O %s" % outFileName)
        lArgs.append("-v %d" % (self._verbosity - 1))
        return iLauncher.getSystemCommand("RmvPairAlignInChunkOverlaps.py", lArgs)

    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkConfig()
        self._checkOptions()
        self._log.info("START LaunchBlasterInParallel")
        self._log.debug("Query file name: %s" % self._queryPattern)
        self._log.debug("Subject file name: %s" % self._subjectFileName)
        
        cDir = os.getcwd()
        if not self._tmpDir:
            self._tmpDir = cDir
    
        acronym = "Blaster"
        iDb = DbFactory.createInstance()
        jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
        iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode)

        lCmdsTuples = []
        fileSize = float(os.path.getsize(self._subjectFilePath) + 5000000) / 1000000000
        
        lCmdSize = []
        lCmdCopy = []
        if self._isCopyOnNode:
            lCmdSize.append("fileSize = %f" % fileSize)       
            lCmdCopy.append("shutil.copy(\"%s\", \".\")" % self._subjectFilePath)
            
        lFiles = FileUtils.getFileNamesList(self._queryDirectory, self._queryPattern)
        for file in lFiles:
            lCmds = []
            lCmds.append(self._getLaunchBlasterCmd(iLauncher, file))
            lCmdStart = []
            if self._isCopyOnNode:
                lCmdStart.append("os.symlink(\"../%s\", \"%s\")" % (self._subjectFileName, self._subjectFileName))
                lCmdStart.append("shutil.copy(\"%s/%s\", \".\")" % (self._queryDirectory, file))
            else:
                lCmdStart.append("os.symlink(\"%s\", \"%s\")" % (self._subjectFilePath, self._subjectFileName))
                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (self._queryDirectory, file, file))
            lCmdFinish = []
            lCmdFinish.append("if os.path.exists(\"%s.align\"):" % file)
            lCmdFinish.append("\tshutil.move(\"%s.align\", \"%s/.\" )" % (file, cDir))
            lCmdFinish.append("shutil.move(\"%s.param\", \"%s/.\" )" % (file, cDir))
            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy))
        
        iLauncher.runLauncherForMultipleJobs("Blaster", lCmdsTuples, self._doClean, self._isCopyOnNode)

        tmpFileName = "tmp_%s.align" % os.getpid()
        iMMF = MergeMatchsFiles("align", "tmp_%s" % os.getpid(), allByAll = self._doAllByall, clean = self._doClean)
        iMMF.run()

        if self._doAllByall:
            iDb = DbFactory.createInstance()
            jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
            iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, "%s_RmvPairAlignInChunkOverlaps" % self._groupId)
        
            lCmdsTuples = []
            lCmds = []
            lCmds.append(self._getRmvPairAlignInChunkOverlapsCmd(iLauncher, tmpFileName, self._outFileName))
            lCmdStart = [] 
            lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, tmpFileName, tmpFileName))
            lCmdFinish = []
            lCmdFinish.append("shutil.move(\"%s\", \"%s/.\")" % (self._outFileName, cDir))
            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
        
            iLauncher.runLauncherForMultipleJobs("RmvPairAlignInChunkOverlaps", lCmdsTuples, self._doClean)
            if self._doClean:
                os.remove(tmpFileName)
        else:
            shutil.move(tmpFileName, self._outFileName)
            
        if self._doClean:
            FileUtils.removeFilesByPattern("*.param")
        
        self._log.info("END LaunchBlasterInParallel")

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