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

Uploaded

--- a/TEisotools-1.1.a/TEiso/GFFToBed.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +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.
-
-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
-import os
-from commons.core.parsing.GffParser import GffParser
-LOG_NAME = "TEiso"
-
-class GFFToBed(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 = "1.1.a"
-        description = "GFFToBed version %s" % self._toolVersion
-        epilog = "\n parses a GFF3 file and create a bed file. \n"
-        epilog += "example: GFFToBed.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 GFF3 File name.",  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 getGFFToBed (self, inputFile ,outputFile):
-        try:
-            filewrite=open(outputFile, "w")
-            gffParser = GffParser(inputFile)
-            for transcript in gffParser.getIterator():
-                if(transcript.getDirection()==1):
-                    strand="+"
-                else:
-                    strand="-"
-                filewrite.write("%s\t%s\t%s\t%s\t%s\t%s\n"  % (transcript.getChromosome(),transcript.getStart(),
-                transcript.getEnd(), transcript.getTagValue("ID"), transcript.getTagValue("Target"), strand) )
-            filewrite.close()
-        except:
-            raise Exception("Couldn't open %s for writing" % outputFile)
-
-                
-    def run(self):
-        self.checkoption()
-        self.getGFFToBed(self._inputFile, self._outputFile)
-        
-
-if __name__== "__main__":
-    iGFFToBed = GFFToBed()
-    iGFFToBed.setAttributesFromCmdLine()
-    iGFFToBed.run()
-
-