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

Uploaded

--- a/TEisotools-1.1.a/TEiso/Cufflinks.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +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, sys
-from commons.core.checker.CheckerUtils import CheckerUtils
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-from commons.core.utils.FileUtils import FileUtils
-import subprocess
-
-class Cufflinks(object):
-         
-    def __init__(self, input_mapped = "", input_transcripts = "", workingDir = "", verbosity = 3):
-        self._input_mapped = input_mapped
-	self._transcripts = input_transcripts
-        self._output_dir = workingDir
-        self._verbosity = verbosity
-        
-    def setAttributesFromCmdLine(self):
-        description = "It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts." 
-        usage = "Cufflinks.py -i  <hits.bam> -g <transcripts.gtf> -o <output-dir>\n"
-        parser = RepetOptionParser(description = description, usage = usage)
-        parser.add_option( '-i', '--input_mapped', dest='input_mapped', help='aligned RNA-Seq reads' )
-	parser.add_option( '-g' , '--input_transcripts', dest='input_transcripts', help='GTF/GFF with known transcripts'    , default="" )
-        parser.add_option( '-o', '--output_dir', dest='output_dir', help='write all output files to this directory', default = "")
-        options, args = parser.parse_args()
-        self.setAttributesFromOptions(options)
-    
-    def setAttributesFromOptions(self, options):
-        self._input_mapped = options.input_mapped
-	self._transcripts = options.input_transcripts
-        self._output_dir = options.output_dir
-        
-    def checkExecutables(self):
-        if not CheckerUtils.isExecutableInUserPath("cufflinks"):
-            raise Exception("ERROR: cufflinks must be in your path")
-    
-    def checkOptions(self):   
-        if self._input_mapped != "":
-            if not FileUtils.isRessourceExists(self._input_mapped):
-                raise Exception("ERROR: reference file %s does not exist!" % self._input_mapped)
-        else:
-            raise Exception("ERROR: No specified -i option!")
-
-	if self._transcripts != "" :
-	    if not FileUtils.isRessourceExists(self._input_mapped):
-                raise Exception("ERROR: reference file %s does not exist!" % self._transcripts)
-
-   
-    def getCufflinksCmd(self, mapped, transcripts, output_dir ): 
-	if self._transcripts != "" :
-	        cmd = 'cufflinks %s -g %s -o %s' % (mapped, transcripts , output_dir)
-	else:
-		cmd = 'cufflinks %s -o %s' % (mapped , output_dir)
-#        print cmd
-        return cmd
-    
-    def run(self):
-        self.checkExecutables()
-        self.checkOptions()
-        try:
-            workingDir =  self._output_dir
-            if os.path.exists(workingDir):
-		print "ERROR: %s already exists." % workingDir
-		sys.exit(1)
-                raise Exception("ERROR: %s already exists." % workingDir)
-            cmd_cufflinks = self.getCufflinksCmd(self._input_mapped, self._transcripts,  self._output_dir)
-            ## hide output of subprocess: stdout = index_dir_stderr
-            fstdout = open( "cufflinks.log" , 'w' )
-            process = subprocess.Popen(cmd_cufflinks, shell = True, stdout = fstdout, stderr=subprocess.STDOUT)
-            returncode = process.wait()
-            fstdout.close()
-            # get stderr, allowing for case where it's very large
-            fstdout = open("cufflinks.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 cufflinks.log  %s/cufflinks.log " % workingDir) 
-        except Exception:
-            raise Exception("ERROR in %s " % cmd_cufflinks)
-        
-                
-if __name__ == "__main__":
-    iLaunch = Cufflinks()
-    iLaunch.setAttributesFromCmdLine()
-    iLaunch.run()
-