diff TEisotools-1.0/TEiso/Cufflinks.py @ 6:20ec0d14798e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/TEiso/Cufflinks.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,124 @@
+#!/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()
+