comparison SMART/Java/Python/selectByNbOccurrences.py @ 6:769e306b7933

Change the repository level.

6:769e306b7933

#! /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)