Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/selectByNbOccurrences.py @ 9:1eb55963fe39
Updated CompareOverlappingSmall*.py
author | m-zytnicki |
---|---|
date | Thu, 14 Mar 2013 05:23:05 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
#! /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. # """Select the transcript that have not more that a given number of occurrences""" import os from optparse import OptionParser from SMART.Java.Python.structure.TranscriptContainer import * from commons.core.writer.Gff3Writer import * from SMART.Java.Python.misc.Progress import * from SMART.Java.Python.misc.RPlotter import * if __name__ == "__main__": # parse command line description = "Select by # of Occurrences v1.0.1: Keep the reads which have mapped less than a given number of times. [Category: Personnal]" 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("-n", "--occurrences", dest="occurrences", action="store", default=1, type="int", help="maximum number of occurrences allowed [format: int] [default: 1]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]") parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]") (options, args) = parser.parse_args() parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity) # get occurrences of the transcripts names = dict() progress = Progress(parser.getNbTranscripts(), "Reading names of %s" % (options.inputFileName), options.verbosity) for transcript in parser.getIterator(): name = transcript.name if name not in names: names[name] = 1 else: names[name] += 1 progress.inc() progress.done() # write output file nbWritten = 0 writer = Gff3Writer(options.outputFileName, options.verbosity) if options.mysql: mysqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity) progress = Progress(parser.getNbTranscripts(), "Writing transcripts", options.verbosity) for transcript in parser.getIterator(): name = transcript.name if names[name] <= options.occurrences: nbWritten += 1 writer.addTranscript(transcript) if options.mysql: mysqlWriter.addTranscript(transcript) progress.inc() progress.done() if options.mysql: mysqlWriter.write() print "%d input" % (parser.getNbTranscripts()) print "%d output (%.2f%%)" % (nbWritten, float(nbWritten) / parser.getNbTranscripts() * 100)