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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/TEiso/CufflinksGTFToBed.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,107 @@
+#!/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.
+
+from commons.core.LoggerFactory             import LoggerFactory
+from commons.core.utils.RepetOptionParser   import RepetOptionParser
+from commons.core.checker.RepetException    import RepetException
+from commons.core.utils.FileUtils           import FileUtils
+from commons.core.parsing.GtfParser import GtfParser
+import os
+LOG_NAME = "TEiso"
+
+class CufflinksGTFToBed(object):
+    
+    def __init__(self, inputFile = "", outputFile = "", verbosity = 3):
+        self._inputFile = inputFile
+        self._outputFile = outputFile
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_NAME, self.__class__.__name__), self._verbosity)
+            
+    def setAttributesFromCmdLine(self):
+        self._toolVersion = "1.0"
+        description = "CufflinksGTFToBed version %s" % self._toolVersion
+        epilog = "\n parses a GTF file of Cufflinks and create a bed file. \n"
+        epilog += "example: CufflinksGTFToBed.py -i <inputFile> -o  <outputFile>\n"
+        parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "Input GTF File name (transcript.gtf of Cufflinks).",  default = "")
+        parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "")
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "Verbosity [optional] [default: 3]",default = 3)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._inputFile  = options.inputFile
+        self._outputFile = options.outputFile
+        self._verbosity  = options.verbosity
+                    
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise RepetException(errorMsg)
+
+    def checkoption(self):
+        if self._outputFile == "":
+            #self._log.info("Missing output file destination")
+            self._outputFile = "%s.bed" % os.path.splitext(self._inputFile)[0]
+        else:
+            if FileUtils.isRessourceExists(self._outputFile):
+                self._log.info("Output file '%s' already exists!" % self._outputFile)
+            
+        if self._inputFile == "":
+            self._log.info("Missing input file")
+        
+    def getTranscriptToBed (self, inputFile ,outputFile):
+        try:
+            filewrite=open(outputFile, "w")
+            gtfParser = GtfParser(self._inputFile, assemblyTools=True)
+            for transcript in gtfParser.getIterator():
+                if(transcript.getDirection()==1):
+                    strand="+"
+                else:
+                    strand="-"
+                filewrite.write("%s\t%s\t%s\t%s\t%s\t%s\t%.3f\n"  % (transcript.getChromosome(),transcript.getStart(),
+                transcript.getEnd(), transcript.getTagValue("ID"), transcript.getTagValue("gene_id"),
+                strand,float(transcript.getTagValue("FPKM")) ))
+            filewrite.close()
+        except:
+                raise Exception("Couldn't open %s for writing" % outputFile)
+                
+    def run(self):
+        self.checkoption()
+        self.getTranscriptToBed(self._inputFile, self._outputFile)
+        
+
+if __name__== "__main__":
+    iTranscriptToBed = CufflinksGTFToBed()
+    iTranscriptToBed.setAttributesFromCmdLine()
+    iTranscriptToBed.run()
+
+