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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/TEiso/Cuffcompare.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,125 @@
+#!/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
+from commons.core.checker.CheckerUtils import CheckerUtils
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+from commons.core.utils.FileUtils import FileUtils
+import subprocess
+
+class Cuffcompare(object):
+         
+    def __init__(self, reference = "", transcripts = "", outprefix ="" , workingDir = "", verbosity = 3):
+        self._reference = reference
+        self._transcripts = transcripts
+        self._outprefix = outprefix
+        self._output_Dir = workingDir
+        self._verbosity = verbosity
+        
+    def setAttributesFromCmdLine(self):
+        description = "Cuffcompare provides classification, reference annotation mapping and various statistics for Cufflinks transfrags.\n" 
+        usage = " Cuffcompare -r <reference> -i <transcripts> -o <outprefix>\n"
+        parser = RepetOptionParser(description = description, usage = usage)
+        parser.add_option( '-r', '--reference', dest='reference', help='a set of known mRNAs to use as a reference for assessing the accuracy of mRNAs or gene models given in <input.gtf>' )
+        parser.add_option( '-i', '--transcripts', dest='transcripts', help='input transfrags' )
+        parser.add_option( '-o', '--outprefix', dest='outprefix', help='write all output files with out prefix', default = "cuffcompare")
+        options, args = parser.parse_args()
+        self.setAttributesFromOptions(options)
+    
+    def setAttributesFromOptions(self, options):
+        self._reference = options.reference
+        self._transcripts = options.transcripts
+        self._outprefix = options.outprefix
+        
+    def checkExecutables(self):
+        if not CheckerUtils.isExecutableInUserPath("cuffcompare"):
+            raise Exception("ERROR: cuffcompare must be in your path")
+    
+    def checkOptions(self):   
+        if self._transcripts != "":
+            if not FileUtils.isRessourceExists(self._transcripts):
+                raise Exception("ERROR: input file %s does not exist!" % self._transcripts)
+        else:
+            raise Exception("ERROR: No specified -i option!")
+        
+        if self._reference != "":
+            if not FileUtils.isRessourceExists(self._reference):
+                raise Exception("ERROR: reference file %s does not exist!" % self._reference)
+        else:
+            raise Exception("ERROR: No specified -r option!")
+   
+    def getCuffcompareCmd(self, reference, transcripts, outprefix):
+        cmd = 'cuffcompare -R -C -r %s %s -o %s' % (reference, transcripts, outprefix)
+        ##print cmd
+        return cmd
+    
+    def run(self):
+        self.checkExecutables()
+        self.checkOptions()
+        try:
+            workingDir =  self._output_Dir
+            if os.path.exists(workingDir):
+                raise Exception("ERROR: %s already exists." % workingDir)
+            cmd_cuffcompare = self.getCuffcompareCmd(self._reference, self._transcripts, self._outprefix)
+            ## hide output of subprocess: stdout = index_dir_stderr
+            fstdout = open( "cuffcompare.log" , 'w' )
+            process = subprocess.Popen(cmd_cuffcompare, shell = True, stdout = fstdout, stderr=subprocess.STDOUT)
+            returncode = process.wait()
+            fstdout.close()
+            # get stderr, allowing for case where it's very large
+            fstdout = open("cuffcompare.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
+            
+            if not os.path.exists(workingDir):
+                os.mkdir(workingDir)
+                ##os.system("mv cuffcompare.log  %s/cuffcompare.log " % workingDir)
+                os.system("mv cuffcompare.*  %s" % workingDir) 
+        except Exception:
+            raise Exception("ERROR in %s " % cmd_cuffcompare)
+        
+                
+if __name__ == "__main__":
+    iLaunch = Cuffcompare()
+    iLaunch.setAttributesFromCmdLine()
+    iLaunch.run()
+