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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 """Restrict a transcript list with some parameters (regions)"""
+ − 32
+ − 33 from optparse import OptionParser
+ − 34 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 35 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 36 from SMART.Java.Python.misc.Progress import Progress
+ − 37
+ − 38 STRAND2DIRECTION = {"+": 1, "-": -1, None: None}
+ − 39
+ − 40 if __name__ == "__main__":
+ − 41
+ − 42 # parse command line
+ − 43 description = "Restrict Transcript List v1.0.2: Keep the coordinates which are located in a given position. [Category: Data Selection]"
+ − 44
+ − 45 parser = OptionParser(description = description)
+ − 46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format [compulsory] [format: transcript file format]")
+ − 48 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="chromosome [format: string]")
+ − 49 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="start [format: int]")
+ − 50 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="end [format: int]")
+ − 51 parser.add_option("-t", "--strand", dest="strand", action="store", default=None, type="string", help="strand (+ or -) [format: string]")
+ − 52 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 53 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 54 (options, args) = parser.parse_args()
+ − 55
+ − 56 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+ − 57 writer = TranscriptWriter(options.outputFileName, options.format, options.verbosity)
+ − 58
+ − 59 direction = STRAND2DIRECTION[options.strand]
+ − 60
+ − 61 nbTranscripts = parser.getNbTranscripts()
+ − 62 progress = Progress(nbTranscripts, "Parsing file %s" % (options.inputFileName), options.verbosity)
+ − 63
+ − 64 nbTotal = 0
+ − 65 nbKept = 0
+ − 66 for transcript in parser.getIterator():
+ − 67 progress.inc()
+ − 68 nbTotal += 1
+ − 69 if options.chromosome != None and options.chromosome != transcript.getChromosome():
+ − 70 continue
+ − 71 if options.start != None and options.start > transcript.getEnd():
+ − 72 continue
+ − 73 if options.end != None and options.end < transcript.getStart():
+ − 74 continue
+ − 75 if options.end != None and options.end < transcript.getStart():
+ − 76 continue
+ − 77 if direction != None and direction != transcript.getDirection():
+ − 78 continue
+ − 79 nbKept += 1
+ − 80 writer.addTranscript(transcript)
+ − 81 progress.done()
+ − 82
+ − 83 writer.write()
+ − 84
+ − 85 print "%d out of %d are kept (%f%%)" % (nbKept, nbTotal, (float(nbKept) / nbTotal * 100))
