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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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#! /usr/bin/env python
# Copyright INRA-URGI 2009-2010
# 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.
"""Convert a GFF with REPET format to BED format"""

import os
from optparse import OptionParser
from commons.core.parsing.GffParser import *
from commons.core.writer.BedWriter import *
from SMART.Java.Python.misc.Progress import *

if __name__ == "__main__":
    # parse command line
    description = "Repet GFF Convert v1.0.1: Convert REPET-flavored GFF to normal GFF. [Category: Personnal]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",                        dest="inputFileName",    action="store",                                         type="string", help="input file [compulsory] [format: file in GFF3 format]")
    parser.add_option("-o", "--output",                     dest="outputFileName", action="store",                                         type="string", help="output file [compulsory] [format: output file in GFF3 format]")
    parser.add_option("-v", "--verbosity",                dest="verbosity",            action="store",            default=1,         type="int",        help="trace level [format: int]")
    (options, args) = parser.parse_args()

    parser            = GffParser(options.inputFileName, options.verbosity)
    transcripts = dict()
    progress        = Progress(parser.getNbTranscripts(), "Analyzing file %s" % (options.inputFileName), options.verbosity)
    for transcript in parser.getIterator():
        if transcript.feature.endswith("range"):
            transcripts[] = transcript
        elif transcript.feature.endswith("hsp"):
            if in transcripts:
                sys.exit("Transcript %s is not defined\n" % (
            sys.exit("Do not understand feature %s" % (transcript.feature))
    writer = BedWriter(options.outputFileName, options.verbosity)
    for name in transcripts:
    print "%d transcripts out of %d written (%.2f%%)" % (len(transcripts.keys()), parser.getNbTranscripts(), float(len(transcripts.keys())) / parser.getNbTranscripts() * 100)