Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/changeTagName.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children | 783e6ed4eb66 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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 """ | |
32 Change the name of a tag | |
33 """ | |
34 | |
35 import os | |
36 import random | |
37 from optparse import OptionParser | |
38 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer | |
39 from SMART.Java.Python.misc.Progress import Progress | |
40 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter | |
41 from commons.core.writer.Gff3Writer import Gff3Writer | |
42 | |
43 | |
44 if __name__ == "__main__": | |
45 | |
46 # parse command line | |
47 description = "Change Tag Name v1.0.1: Change the name of tag of a list of transcripts. [Category: Data Modification]" | |
48 | |
49 parser = OptionParser(description = description) | |
50 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]") | |
51 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]") | |
52 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]") | |
53 parser.add_option("-t", "--tag", dest="tag", action="store", type="string", help="name of the tag to change [compulsory] [format: string]") | |
54 parser.add_option("-n", "--name", dest="name", action="store", type="string", help="new name for the tag [compulsory] [format: string]") | |
55 parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]") | |
56 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") | |
57 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]") | |
58 (options, args) = parser.parse_args() | |
59 | |
60 if options.log: | |
61 logHandle = open("%s.log" % options.outputFileName, "w") | |
62 | |
63 # create parser and writer(s) | |
64 parser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity) | |
65 tmpFileName = "tmpTranscriptFile%d.gff3" % (random.randint(0, 100000)) | |
66 writer = Gff3Writer(tmpFileName, options.verbosity) | |
67 if options.mysql: | |
68 mysqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity) | |
69 outputData = {} | |
70 | |
71 # process transcripts | |
72 progress = Progress(parser.getNbTranscripts(), "Printing transcripts %s" % (options.inputFileName), options.verbosity) | |
73 for transcript in parser.getIterator(): | |
74 if options.tag in transcript.tags: | |
75 value = transcript.tags[options.tag] | |
76 del transcript.tags[options.tag] | |
77 transcript.tags[options.name] = value | |
78 writer.addTranscript(transcript) | |
79 if options.mysql: | |
80 mysqlWriter.addTranscript(transcript) | |
81 progress.inc() | |
82 progress.done() | |
83 parser.transcriptListParser.close() | |
84 | |
85 writer.write() | |
86 | |
87 if options.mysql: | |
88 mysqlWriter.write() | |
89 | |
90 os.rename(tmpFileName, options.outputFileName) |