Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/modifyGenomicCoordinates.py @ 38:2c0c0a89fad7
Uploaded
author | m-zytnicki |
---|---|
date | Thu, 02 May 2013 09:56:47 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/modifyGenomicCoordinates.py Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,80 @@ +#! /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 +# 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. +# +"""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()