Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/mappingToCoordinates.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
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
33 """Convert files with some mapping format to coordinates format"""
34
35 import os
36 from optparse import OptionParser
37 from commons.core.parsing.PslParser import PslParser
38 from commons.core.parsing.AxtParser import AxtParser
39 from commons.core.writer.Gff3Writer import Gff3Writer
40 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
42 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
43 from SMART.Java.Python.misc.Progress import Progress
44
45
46 class MappingToCoordinates(object):
47 def __init__(self,verbosity=1, inputFileName=None, format = None, output=None,galaxy = False, title="S-MART"):
48 self.verbosity = verbosity
49 self.inputFileName = inputFileName
50 self.format = format
51 self.output = output
52 self.galaxy = galaxy
53 self.title = title
54
55 def setAttributesFromCmdLine(self):
56 description = "Mapping To Coordinates v1.0.1: Convert a set of mappings (given by a mapping tool) to a set of transcripts. [Category: Conversion]"
57 parser = OptionParser(description = description)
58 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: mapping file format]")
60 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
62 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
63 (options, args) = parser.parse_args()
64
65 self.verbosity = options.verbosity
66 self.inputFileName = options.inputFileName
67 self.format = options.format
68 self.output = options.output
69 self.galaxy = options.galaxy
70
71 def run(self):
72 if self.verbosity > 0:
73 print "Reading input file..."
74 parser = TranscriptContainer(self.inputFileName, self.format, self.verbosity)
75 if self.verbosity > 0:
76 print "... done"
77 writer = Gff3Writer(self.output, self.verbosity, self.title)
78
79 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (self.inputFileName), self.verbosity)
80 for transcript in parser.getIterator():
81 writer.addTranscript(transcript)
82 progress.inc()
83 progress.done()
84
85 if self.galaxy:
86 os.rename("%s.gff3" % (self.output), self.output)
87
88 if __name__ == '__main__':
89 launcher = MappingToCoordinates()
90 launcher.setAttributesFromCmdLine()
91 launcher.run()