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comparison SMART/Java/Python/restrictTranscriptList.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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))