view commons/launcher/LaunchTRF.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
# liability. 
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# 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
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from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.checker.ConfigChecker import ConfigRules
from commons.core.checker.ConfigChecker import ConfigChecker
import subprocess
import glob
import os

LOG_DEPTH = "repet.launchers"

class LaunchTRF(object):
    
    def __init__(self, inFileName = "", outFileName = "", maxPeriod=15, doClean = False, verbosity = 0):
        self.inFileName = inFileName
        self.setOutFileName(outFileName)
        self.maxPeriod=maxPeriod
        self._doClean = doClean
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "Launch TRF to detect micro-satellites in sequences."
        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
        epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0"
        epilog += "\n\t"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-i", "--in",      dest = "inFileName", action = "store",       type = "string", help = "input file name [compulsory] [format: fasta]", default = "")
        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.TRF.set]", default = "")
        parser.add_option("-m", "--maxPeriod",  dest = "maxPeriod",     action = "store",       type = "int",    help = " maximum period size to report  [default: 15]", default = 15)
        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.setInFileName(options.inFileName)
        self.setOutFileName(options.outFileName)
        self.maxPeriod = options.maxPeriod
        self.setDoClean(options.doClean)
        self.setVerbosity(options.verbosity)
                
    def setInFileName(self, inFileName):
        self.inFileName = inFileName
        
    def setOutFileName(self, outFileName):
        if outFileName == "":
            self._outFileName = "%s.TRF.set" % self.inFileName
        else:
            self._outFileName = outFileName
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def _checkOptions(self):
        if self.inFileName == "":
            self._logAndRaise("ERROR: Missing input file name")
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
    
    
    def _launchTRF(self):
        cmd = "trf %s 2 3 5 80 10 20 %d -h -d" % (self.inFileName, self.maxPeriod)
        self._log.debug("Running : %s" % cmd)
        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        output = process.communicate()
        self._log.debug("Output:\n%s" % output[0])
        
    def _parseTRF(self):
        self._log.debug("Parsing TRF output")
        with open( "%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod),'r') as inFile:
            with open(self._outFileName,'w') as outFile:
                nbPatterns = 0
                nbInSeq = 0
                for line in inFile.readlines():
                    if line == "":
                        break
                    data = line.split(" ")
                    if len(data) > 1 and "Sequence:" in data[0]:
                        nbInSeq += 1
                        seqName = data[1][:-1]
                    if len(data) < 14:
                        continue
                    nbPatterns += 1
                    consensus = data[13]
                    copyNb = int( float(data[3]) + 0.5 )
                    start = data[0]
                    end = data[1]
                    outFile.write( "%i\t(%s)%i\t%s\t%s\t%s\n" % ( nbPatterns, consensus, copyNb, seqName, start, end ) )
        self._log.debug("Finished Parsing TRF output")
    
    def _clean(self):
        try:
            os.remove("%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod))
        except:pass
        

    def run(self):
        """
        Launch TRF to detect micro-satellites in sequences.
        """
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkOptions()
        self._log.info("START Launch")
        self._log.debug("Input file name: %s" % self.inFileName)
        
        self._launchTRF()
        self._parseTRF()
        
        if self._doClean:
            self._log.warning("Files will be cleaned")
            self._clean()
        self._log.info("END Launch")
  
if __name__ == "__main__":
    iLaunchTRF = LaunchTRF()
    iLaunchTRF.setAttributesFromCmdLine()
    iLaunchTRF.run()