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comparison smart_toolShed/SMART/Java/Python/selectByNbOccurrences.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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 """Select the transcript that have not more that a given number of occurrences"""
32
33 import os
34 from optparse import OptionParser
35 from SMART.Java.Python.structure.TranscriptContainer import *
36 from commons.core.writer.Gff3Writer import *
37 from SMART.Java.Python.misc.Progress import *
38 from SMART.Java.Python.misc.RPlotter import *
39
40
41 if __name__ == "__main__":
42
43 # parse command line
44 description = "Select by # of Occurrences v1.0.1: Keep the reads which have mapped less than a given number of times. [Category: Personnal]"
45
46 parser = OptionParser(description = description)
47 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
48 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: transcript file format]")
49 parser.add_option("-n", "--occurrences", dest="occurrences", action="store", default=1, type="int", help="maximum number of occurrences allowed [format: int] [default: 1]")
50 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
51 parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]")
52 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
53 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
54 (options, args) = parser.parse_args()
55
56 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
57
58 # get occurrences of the transcripts
59 names = dict()
60 progress = Progress(parser.getNbTranscripts(), "Reading names of %s" % (options.inputFileName), options.verbosity)
61 for transcript in parser.getIterator():
62 name = transcript.name
63 if name not in names:
64 names[name] = 1
65 else:
66 names[name] += 1
67 progress.inc()
68 progress.done()
69
70 # write output file
71 nbWritten = 0
72 writer = Gff3Writer(options.outputFileName, options.verbosity)
73 if options.mysql:
74 mysqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
75 progress = Progress(parser.getNbTranscripts(), "Writing transcripts", options.verbosity)
76 for transcript in parser.getIterator():
77 name = transcript.name
78 if names[name] <= options.occurrences:
79 nbWritten += 1
80 writer.addTranscript(transcript)
81 if options.mysql:
82 mysqlWriter.addTranscript(transcript)
83 progress.inc()
84 progress.done()
85
86 if options.mysql:
87 mysqlWriter.write()
88 print "%d input" % (parser.getNbTranscripts())
89 print "%d output (%.2f%%)" % (nbWritten, float(nbWritten) / parser.getNbTranscripts() * 100)