annotate SMART/Java/Python/getIntrons.py @ 62:8c42a6d7ffd4

Added simple test BED file.

#! /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.
#
from optparse import OptionParser
from commons.core.parsing.ParserChooser import ParserChooser
from commons.core.writer.TranscriptWriter import TranscriptWriter
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.misc.Progress import Progress

class GetIntrons(object):

    def __init__(self, verbosity):
        self.verbosity = verbosity

    def setInputFile(self, fileName, format):
        chooser = ParserChooser(self.verbosity)
        chooser.findFormat(format)
        self.parser = chooser.getParser(fileName)

    def setOutputFile(self, fileName):
        self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
        
    def run(self):
        progress  = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
        nbIntrons = 0
        for cpt1, transcript in enumerate(self.parser.getIterator()):
            for cpt2, intron in enumerate(transcript.getIntrons()):
                intronTranscript = Transcript()
                intronTranscript.copy(intron)
                if "Parent" in intronTranscript.tags:
                    del intronTranscript.tags["Parent"]
                intronTranscript.tags["feature"] = "transcript"
                if "ID" not in intronTranscript.tags or intronTranscript.tags["ID"] == "unnamed transcript":
                    intronTranscript.tags["ID"] = "intron_%d-%d" % (cpt1+1, cpt2+1)
                if intronTranscript.getName() == "unnamed transcript":
                    intronTranscript.setName("intron_%d-%d" % (cpt1+1, cpt2+1))
                self.writer.addTranscript(intronTranscript)
                nbIntrons += 1
            progress.inc()
        self.writer.write()
        self.writer.close()
        progress.done()
        if self.verbosity > 1:
            print "%d transcripts read" % (self.parser.getNbTranscripts())
            print "%d introns written" % (nbIntrons)


if __name__ == "__main__":
    
    description = "Get Introns v1.0.1: Get the introns of a set of transcripts. [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 file [compulsory] [format: transcript file format]")
    parser.add_option("-o", "--output",    dest="outputFileName", action="store",             type="string", help="output file [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()

    gi = GetIntrons(options.verbosity)
    gi.setInputFile(options.inputFileName, options.format)
    gi.setOutputFile(options.outputFileName)
    gi.run()