annotate smart_toolShed/commons/core/parsing/BlatToGff.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
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# This software is governed by the CeCILL license under French law and
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import optparse
import os
from commons.core.parsing.BlatParser import BlatParser

class BlatToGff(object):


    def __init__(self):
        pass
    
    def setAttributesFromCmdLine(self):
        help = '\
        \nThis Script Launch BlatToGff.\n\n\
        Example 1: python BlatToGff.py -i blatResultsFile.tab -o outputFile.gff3\n\n'
        parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
        parser.add_option( '-i', '--input', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None )
        parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
        parser.add_option( '-n', '--methodname', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
        ( options, args ) = parser.parse_args()
        self._options = options
    
    def checkOptions(self):
        if self._options.inputBLAT == '':
            raise Exception("ERROR: No Blat file specified for -i !")
        elif not os.path.exists(self._options.inputBLAT):
            raise Exception("ERROR: Blat Input File doesn't exist !")
        else:
            self._inputFileBlat = self._options.inputBLAT
            
        if self._options.output == '':
            raise Exception("ERROR: No Output file specified for -o !")
        else:
            self._outputFileGFF = self._options.output
            
        self._methodName = self._options.methodName
            
    def run(self):
        self.checkOptions()
        self._createGFFOutputFile()
        BLATFile = open(self._inputFileBlat, 'r')
        
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        blatLine = BLATFile.readline()
        numberLine = 6
        while blatLine != '':
            gffLine = self.convertBlatObjectToGffLine(blatLine, numberLine)
            self._printGFFLinesToOutputFile(gffLine)
            blatLine = BLATFile.readline()
            numberLine = numberLine + 1
            
    def convertBlatObjectToGffLine(self, blatLine, numberLine):
        iBlatHit = BlatParser()
        iBlatHit.setAttributesFromString(blatLine, numberLine)
        col1 = iBlatHit.getTName()
        col2 = 'BlatToGff'
        if self._methodName == '' or self._methodName == None:
            col3 = 'BES'
        else:
            col3 = '%s:BES' % self._methodName
        col4 = iBlatHit.getTStart()
        col5 = iBlatHit.getTEnd()
        col6 = '.'
        col7 = '+'
        col8 = '.'
        col9 = 'ID=%s;Name=%s;bes_start=%s;bes_end=%s;bes_size=%s' % (iBlatHit.getQName(), iBlatHit.getQName(), iBlatHit.getTStart(), iBlatHit.getTEnd(), iBlatHit.getTSize())
        gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
        return gffLine
    
    def _createGFFOutputFile(self):
        GFFfile = open(self._outputFileGFF, 'w')
        GFFfile.write("##gff-version 3\n")
        GFFfile.close()
        
    def _printGFFLinesToOutputFile(self, line):
        GFFfile = open(self._outputFileGFF, 'a')
        GFFfile.write(line)
        GFFfile.close()

if __name__ == '__main__':
    iBlatToGff = BlatToGff()
    iBlatToGff.setAttributesFromCmdLine()
    iBlatToGff.run()