annotate TEisotools-1.0/TEiso/Tophat.py @ 9:a662930cfb16 draft

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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".
#
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# 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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import os, glob
import subprocess
import time
from commons.core.checker.CheckerUtils import CheckerUtils
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.FileUtils import FileUtils

LOG_DEPTH = "repet.RNAseq_pipe"


class Tophat(object):
    
    def __init__(self, workingDir = "", index_genome = "", single_paired = "", single_read = "", left_read ="", right_read = "", verbosity = 3):
        #self._transcripts = input_transcripts
        self._outputDir = workingDir
        self._bowtie_index = index_genome
        self._type = single_paired
        self._single_read = single_read
        self._left_read = left_read
        self._right_read = right_read
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
    def setAttributesFromCmdLine(self):
        description = "TopHat maps short sequences from spliced transcripts to whole genomes..\n" 
        usage = "if reads are single:/n Tophat.py -G <GTF/GFF with known transcripts> -b <bowtie_index> -t single -r <single_read> \n"
        usage +="if reads are paired:/n Tophat.py -G <GTF/GFF with known transcripts> -b <bowtie_index> -t paired -r1 <reads_left> -r2 <reads_right>\n"
        parser = RepetOptionParser(description = description, usage = usage)
       # parser.add_option( '-G', '--input_transcripts', dest='input_transcripts', help='GTF/GFF with known transcripts', default = "")
        parser.add_option( '-o', '--outputDir', dest='outputDir', help='write all output files to this directory', default = "")
        parser.add_option( '-b', '--index_genome', dest='index_genome', help='Indexing reference genome', default = "")
        parser.add_option( '-e', '--single_paired', dest='single_paired', help='types of input reads', default = "paired")
        parser.add_option( '-s', '--single_read', dest = 'single_read', help='a single input read', default = "" )
        parser.add_option( '-l', '--left_read', dest='left_read', help='left reads', default = "" )
        parser.add_option( '-r', '--right_read', dest='right_read', help='right reads', default = "" )
        options, args = parser.parse_args()
        self.setAttributesFromOptions(options)
        
    def setAttributesFromOptions(self, options):
##        self._transcripts = options.input_transcripts
        self._outputDir = options.outputDir
        self._bowtie_index = options.index_genome
        self._type = options.single_paired
        self._single_read = options.single_read
        self._left_read = options.left_read
        self._right_read = options.right_read
        
        
    def checkExecutables(self):
   
        if not CheckerUtils.isExecutableInUserPath("tophat2"):
            raise Exception("ERROR: tophat must be in your path")
    
    def checkOptions(self):   
        if self._bowtie_index == "":
            raise Exception("ERROR: No specified -b option!")
        
  ##      if self._transcripts != "":
  ##          if not FileUtils.isRessourceExists(self._transcripts):
  ##              raise Exception("ERROR: %s does not exist!" % self._transcripts)
    
        if self._type == "paired":
            for f in self._left_read:
                if not FileUtils.isRessourceExists(f):
                    raise Exception("ERROR: %s does not exist!" % f)
            for f in self._right_read:
                if not FileUtils.isRessourceExists(f):
                    raise Exception("ERROR: %s does not exist!" % f)   
        elif self._type == "single":
            for f in self._single_read: 
                if not FileUtils.isRessourceExists(f):
                    raise Exception("ERROR: %s does not exist!" % f)
        else:
            raise Exception("ERROR: No specified -t option!")
        
    def getTophatCmd_single(self, out_tophat, BowtiePrefix, single_read):
        cmd = "tophat2 -p 8 -o %s %s %s" % (out_tophat, BowtiePrefix, ",".join(single_read))
        return cmd
    
    def getTophatCmd_paired(self, out_tophat, BowtiePrefix, left_read, right_read):
	####sur SGE comme saruman
        #cmd = "echo " + "'tophat -p 8 -o %s ../%s %s %s'" % (out_tophat, prefix, ",".join(left_Read), ",".join(right_Read))+ "|qsub -V -cwd -pe multithread 8"
        cmd = "tophat2 -p 8 -o %s %s %s %s" % (out_tophat, BowtiePrefix, ",".join(left_read), ",".join(right_read))
	#print cmd
        return cmd
    
    def run(self):
        self.checkExecutables()
        self.checkOptions()
        try:
            if os.path.exists(self._outputDir):
                raise Exception("ERROR: %s already exists." % self._outputDir)
            if self._type == "single":
                cmd_tophat = self.getTophatCmd_single(self._outputDir, self._bowtie_index, self._single_read)
            if self._type == "paired":
                cmd_tophat = self.getTophatCmd_paired(self._outputDir, self._bowtie_index, self._left_read, self._right_read)
            #print cmd_tophat
            ## hide output of subprocess: stdout = index_dir_stderr
            fstdout = open( "tophat.log" , 'w' )
            process = subprocess.Popen(cmd_tophat, shell = True, stdout = fstdout, stderr=subprocess.STDOUT)
            returncode = process.wait()
            fstdout.close()
            # get stderr, allowing for case where it's very large
            fstdout = open("tophat.log", 'rb' )
            stderr = ''
            buffsize = 1048576
            try:
                while True:
                    stderr += fstdout.read( buffsize )
                    if not stderr or len( stderr ) % buffsize != 0:
                        break
            except OverflowError:
                    pass
            fstdout.close()
            if returncode != 0:
                    raise Exception, stderr
        
            os.system("mv tophat.log  %s/tophat.log " % self._outputDir) 
        except Exception:
            raise Exception("ERROR in %s " % cmd_tophat)
        
        
          
                  
if __name__ == "__main__":
    iLaunch = Tophat()
    iLaunch.setAttributesFromCmdLine()
    iLaunch.run()