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

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#!/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.
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# 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,
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# therefore means  that it is reserved for developers  and  experienced
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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()