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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
# "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
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"""Modify the genomic coordinates of a file"""

from optparse import OptionParser
from commons.core.writer.TranscriptWriter import TranscriptWriter
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.misc.Progress import Progress


if __name__ == "__main__":
    
    # parse command line
    description = "Modify Genomic Coordinates v1.0.1: Extend or shrink a list of genomic coordinates. [Category: Data Modification]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",      dest="inputFileName",  action="store",               type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format",     dest="format",         action="store",               type="string", help="format of the input [compulsory] [format: transcript file 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("-s", "--start",      dest="start",          action="store", default=None, type="int",    help="restrict to the start of the transcript [format: int]")
    parser.add_option("-e", "--end",        dest="end",            action="store", default=None, type="int",    help="restrict to the end of the transcript [format: int]")
    parser.add_option("-5", "--fivePrime",  dest="fivePrime",      action="store", default=None, type="int",    help="extend to the 5' direction [format: int]")
    parser.add_option("-3", "--threePrime", dest="threePrime",     action="store", default=None, type="int",    help="extend to the 3' direction [format: int]")
    parser.add_option("-v", "--verbosity",  dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")

    (options, args) = parser.parse_args()

    parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
        
    writer = TranscriptWriter(options.outputFileName, "gff3", options.verbosity)

    nbItems = 0
    nbItems = parser.getNbItems()
    print "%i items found" % (nbItems)

    progress = Progress(nbItems, "Analyzing sequences of " + options.inputFileName, options.verbosity)
    for transcript in parser.getIterator():
        if options.start != None:
            transcript.restrictStart(options.start)
        if options.end != None:
            transcript.restrictEnd(options.end)
        if options.fivePrime != None:
            transcript.extendStart(options.fivePrime)
        if options.threePrime != None:
            transcript.extendEnd(options.threePrime)

        writer.addTranscript(transcript)

        progress.inc()
    progress.done()

    writer.write()