diff TEisotools-1.1.a/TEiso/Tophat.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/TEiso/Tophat.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,161 +0,0 @@
-#!/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.
-
-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()
-