diff TEisotools-1.1.a/TEiso/Tophat.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/TEiso/Tophat.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,161 @@
+#!/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()
+