Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/splitByTag.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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 """Read a file and split it into several, depending on a tag""" | |
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 import Utils | |
39 | |
40 | |
41 if __name__ == "__main__": | |
42 | |
43 # parse command line | |
44 description = "Split By Tag v1.0.1: Read a file and split it into several, depending on a tag. [Category: Personnal]" | |
45 | |
46 parser = OptionParser(description = description) | |
47 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]") | |
48 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]") | |
49 parser.add_option("-t", "--tag", dest="tag", action="store", type="string", help="tag on which the split is made [compulsory] [format: string]") | |
50 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in CSV format]") | |
51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") | |
52 (options, args) = parser.parse_args() | |
53 | |
54 transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity) | |
55 writers = dict() | |
56 | |
57 progress = Progress(transcriptContainer.getNbTranscripts(), "Reading file %s" % (options.inputFileName), options.verbosity) | |
58 for transcript in transcriptContainer.getIterator(): | |
59 value = transcript.getTagValue(options.tag) | |
60 if value == None: | |
61 value = "noTag" | |
62 value = str(value).replace(" ", "_").title() | |
63 if value not in writers: | |
64 writers[value] = Gff3Writer("%s.gff3" % (os.path.join(options.outputFileName, value))) | |
65 writers[value].addTranscript(transcript) | |
66 | |
67 progress.inc() | |
68 progress.done() |