Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/RemoveExons.py @ 57:36eaa579fdb6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Fri, 07 Feb 2014 08:29:48 -0500
parents
children
comparison
equal deleted inserted replaced
56:97aa2e42bfdf 57:36eaa579fdb6
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 from optparse import OptionParser
32 from commons.core.parsing.ParserChooser import ParserChooser
33 from commons.core.writer.TranscriptWriter import TranscriptWriter
34 from SMART.Java.Python.structure.Transcript import Transcript
35 from SMART.Java.Python.misc.Progress import Progress
36
37 class RemoveExons(object):
38
39 def __init__(self, verbosity):
40 self.verbosity = verbosity
41 self.selection = False
42
43 def setInputFile(self, fileName, format):
44 chooser = ParserChooser(self.verbosity)
45 chooser.findFormat(format)
46 self.parser = chooser.getParser(fileName)
47
48 def setOutputFile(self, fileName):
49 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
50
51 def run(self):
52 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
53 for transcript in self.parser.getIterator():
54 transcript.removeExons()
55 self.writer.addTranscript(transcript)
56 progress.inc()
57 self.writer.write()
58 self.writer.close()
59 progress.done()
60
61 if __name__ == "__main__":
62
63 description = "Remove Exons v1.0.1: Excluse the exons of a set of transcripts. [Category: Data Modification]"
64
65 parser = OptionParser(description = description)
66 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
67 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
68 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
69 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
70 (options, args) = parser.parse_args()
71
72 re = RemoveExons(options.verbosity)
73 re.setInputFile(options.inputFileName, options.format)
74 re.setOutputFile(options.outputFileName)
75 re.run()