annotate commons/tools/TEclassifierPE_parallelized.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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# same conditions as regards security. 
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# 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 shutil

if not "REPET_PATH" in os.environ.keys():
    print "ERROR: no environment variable REPET_PATH"
    sys.exit(1)
sys.path.append(os.environ["REPET_PATH"])
if not "PYTHONPATH" in os.environ.keys():
    os.environ["PYTHONPATH"] = os.environ["REPET_PATH"]
else:
    os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"])
    
from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.utils.FileUtils import FileUtils
from commons.core.checker.ConfigChecker import ConfigRules
from commons.core.checker.ConfigChecker import ConfigChecker
from commons.core.seq.FastaUtils import FastaUtils
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
from commons.core.launcher.Launcher import Launcher
from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif
from denovo_pipe.DetectTEFeatures_parallelized import DetectTEFeatures_parallelized
from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif
from denovo_pipe.LaunchPASTEC import LaunchPASTEC
from PASTEC.StatPastec import StatPastec

LOG_DEPTH = "repet.tools"
#LOG_FORMAT = "%(message)s"

####TEclassifier PASTEC Edition - parallelized
#
class TEclassifierPE_parallelized(object):
    
    def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0):
        self._fastaFileName = fastaFileName
        self._addWickerCode = addWickerCode
        self._reverseComp = reverseComp
        self._configFileName = configFileName
        self._doClean = doClean
        self._verbosity = verbosity
        self._projectName = ""
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "TE classifier PASTEC Edition.\n"
        description += "Detect TE features on consensus and classify them. Give some classification statistics.\n"
        description += "Can rename headers with classification info and Wicker's code at the beginning.\n"
        description += "Can reverse-complement consensus if they are detected in reverse strand.\n"
        epilog = "\n"
        epilog += "Example 1: launch and clean temporary files\n"
        epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n"
        epilog += "\n"
        epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n"
        epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\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("-C", "--config",     dest = "configFileName",action = "store",       type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "")
        parser.add_option("-w", "--wicker",     dest = "addWickerCode", action = "store_true",                   help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False)
        parser.add_option("-r", "--reverse",    dest = "reverseComp",   action = "store_true",                   help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", 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: 3, from 1 to 4]", default = 3)
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setFastaFileName(options.fastaFileName)
        self.setAddWickerCode(options.addWickerCode)
        self.setReverseComp(options.reverseComp)
        self.setConfigFileName(options.configFileName)
        self.setDoClean(options.doClean)
        self.setVerbosity(options.verbosity)

    def _checkConfig(self):       
        iConfigRules = ConfigRules()
        iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string")
        sectionName = "classif_consensus"
        iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool")
        iConfigRules.addRuleOption(section=sectionName, option ="limit_job_nb", type="int")
        iConfigRules.addRuleOption(section=sectionName, option ="resources", type="string")
        iConfigRules.addRuleOption(section=sectionName, option ="tmpDir", type="string")
        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
        iConfig = iConfigChecker.getConfig()
        self._setAttributesFromConfig(iConfig)
        
    def _setAttributesFromConfig(self, iConfig):
        self.setProjectName(iConfig.get("project", "project_name"))
        sectionName = "classif_consensus"
        self.setDoClean(iConfig.get(sectionName, "clean"))
        self._maxJobNb = iConfig.get(sectionName, "limit_job_nb")
        self._resources = iConfig.get(sectionName, "resources")
        self._tmpDir = iConfig.get(sectionName, "tmpDir")
        
    def setFastaFileName(self, fastaFileName):
        self._fastaFileName = fastaFileName
        
    def setConfigFileName(self, configFileName):
        self._configFileName = configFileName
        
    def setAddWickerCode(self, addWickerCode):
        self._addWickerCode = addWickerCode
        
    def setReverseComp(self, reverseComp):
        self._reverseComp = reverseComp
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def setProjectName(self, projectName):
        self._projectName = projectName
        
    def _checkOptions(self):
        if self._fastaFileName == "":
            self._logAndRaise("ERROR: Missing input fasta file name")
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
    
#    def setup_env(config):
#        os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
#        os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
#        os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
#        os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
#        os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
#        os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")
#        os.environ["REPET_QUEUE"] = config.get("repet_env", "repet_job_manager")
#        os.environ["REPET_JOBS"] = "MySQL"
    
    def getPASTECcommand(self, iLauncher, fileName):
        lArgs = []
        lArgs.append("-C %s" % self._configFileName)
        lArgs.append("-P %s" % self._projectName)
        lArgs.append("-S 2")
        lArgs.append("-i %s" % fileName)
        lArgs.append("-v %s" % self._verbosity)
        return iLauncher.getSystemCommand("LaunchPASTEC.py", lArgs)
                    
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        if self._configFileName:
            self._checkConfig()
        self._checkOptions()
        self._log.info("START TEclassifier PASTEC Edition")
        self._log.debug("Fasta file name: %s" % self._fastaFileName)
        nbSeq = FastaUtils.dbSize(self._fastaFileName)
        self._log.debug("Total number of sequences: %i)" % nbSeq)

        self._log.debug("Launch DetectTEFeatures on each batch")
        iDF = DetectTEFeatures_parallelized(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity)
        iDF.run()
        
        self._log.debug("Insert banks in database")
        iLP = LaunchPASTEC(self._configFileName, "1", projectName = self._projectName, verbose = self._verbosity)
        iLP.run()
        
        self._log.info("Split fasta file")
        if self._maxJobNb == 0 or nbSeq / self._maxJobNb <= 1.0:
            nbSeqPerBatch = nbSeq
        else:
            nbSeqPerBatch = nbSeq / self._maxJobNb + 1
        FastaUtils.dbSplit(self._fastaFileName, nbSeqPerBatch, True, verbose = self._verbosity - 2)
        
        self._log.info("Launch PASTEC on each batch")
        queue = self._resources
        cDir = os.getcwd()
        if self._tmpDir != "":
            tmpDir = self._tmpDir
        else:
            tmpDir = cDir
            
        #TODO: allow not to parallelize
        groupid = "%s_PASTEC" % self._projectName
        acronym = "PASTEC"
        iDb = DbFactory.createInstance()
        iTJA = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
        iLauncher = Launcher(iTJA, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid)
        lCmdsTuples = []
        lFiles = FileUtils.getFileNamesList("%s/batches" % cDir, "batch_")
        if len(lFiles) == 0:
            self._logAndRaise("ERROR: directory 'batches' is empty")
        classifFileName = "%s.classif" % self._projectName
        count = 0
        for file in lFiles:
            count += 1
            lCmds = [self.getPASTECcommand(iLauncher, file)]    
            lCmdStart = []
            lCmdStart.append("shutil.copy(\"%s/batches/%s\", \".\")" % (cDir, file))
            lCmdStart.append("shutil.copy(\"%s/%s\", \".\")" % (cDir, self._configFileName))
            lCmdFinish = []
            lCmdFinish.append("shutil.move(\"%s\", \"%s/%s_%i\")" % (classifFileName, cDir, classifFileName, count))
            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
        iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, self._doClean)  
        
        FileUtils.catFilesByPattern("%s_*" % classifFileName, classifFileName)
        if self._doClean:
            FileUtils.removeFilesByPattern("%s_*" % classifFileName)
            shutil.rmtree("batches")

        self._log.debug("Compute stats about classification")
        iSP = StatPastec(classifFileName)
        iSP.run()
        
        if self._reverseComp:
            self._log.debug("Reverse complement")
            iRevComplAccording2Classif = ReverseComplementAccordingToClassif()
            iRevComplAccording2Classif.setFastaFile(self._fastaFileName)
            iRevComplAccording2Classif.setClassifFile(classifFileName)
            iRevComplAccording2Classif.run()
            newFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0]
        else:
            newFastaFileName = self._fastaFileName

        if self._addWickerCode:
            self._log.debug("Rename headers according to Wicker's code")
            iRHC = RenameHeaderClassif(classifFileName, newFastaFileName, self._projectName)
            iRHC.setOutputFileName("")
            iRHC.run()
        
        self._log.info("END TEclassifier PASTEC Edition")

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