view commons/core/parsing/ @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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# Copyright INRA (Institut National de la Recherche Agronomique)
# 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
# "". 
# 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 optparse
import os
from commons.core.parsing.BlatParser import BlatParser

class BlatToGff(object):

    def __init__(self):
    def setAttributesFromCmdLine(self):
        help = '\
        \nThis Script Launch BlatToGff.\n\n\
        Example 1: python -i -o outputFile.gff3\n\n'
        parser = optparse.OptionParser(usage= help, version=" 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 !")
            self._inputFileBlat = self._options.inputBLAT
        if self._options.output == '':
            raise Exception("ERROR: No Output file specified for -o !")
            self._outputFileGFF = self._options.output
        self._methodName = self._options.methodName
    def run(self):
        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)
            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'
            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")
    def _printGFFLinesToOutputFile(self, line):
        GFFfile = open(self._outputFileGFF, 'a')

if __name__ == '__main__':
    iBlatToGff = BlatToGff()