annotate SMART/Java/Python/mappingToCoordinates.py @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 #! /usr/bin/env python
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 # Copyright INRA-URGI 2009-2010
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 # This software is governed by the CeCILL license under French law and
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 # abiding by the rules of distribution of free software. You can use,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 # modify and/ or redistribute the software under the terms of the CeCILL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 # license as circulated by CEA, CNRS and INRIA at the following URL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 # "http://www.cecill.info".
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 # As a counterpart to the access to the source code and rights to copy,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 # modify and redistribute granted by the license, users are provided only
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 # with a limited warranty and the software's author, the holder of the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 # economic rights, and the successive licensors have only limited
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 # liability.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 # In this respect, the user's attention is drawn to the risks associated
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 # with loading, using, modifying and/or developing or reproducing the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 # software by the user in light of its specific status of free software,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 # that may mean that it is complicated to manipulate, and that also
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 # therefore means that it is reserved for developers and experienced
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 # professionals having in-depth computer knowledge. Users are therefore
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 # encouraged to load and test the software's suitability as regards their
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 # requirements in conditions enabling the security of their systems and/or
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 # data to be ensured and, more generally, to use and operate it in the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 # same conditions as regards security.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 # The fact that you are presently reading this means that you have had
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 # knowledge of the CeCILL license and that you accept its terms.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 """Convert files with some mapping format to coordinates format"""
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 import os
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 from optparse import OptionParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 from commons.core.parsing.PslParser import PslParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 from commons.core.parsing.AxtParser import AxtParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 from commons.core.writer.Gff3Writer import Gff3Writer
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 from SMART.Java.Python.misc.Progress import Progress
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 class MappingToCoordinates(object):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 def __init__(self,verbosity=1, inputFileName=None, format = None, output=None,galaxy = False, title="S-MART"):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 self.verbosity = verbosity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 self.inputFileName = inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 self.format = format
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 self.output = output
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 self.galaxy = galaxy
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 self.title = title
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 def setAttributesFromCmdLine(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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]"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 parser = OptionParser(description = description)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: mapping file format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 (options, args) = parser.parse_args()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 self.verbosity = options.verbosity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 self.inputFileName = options.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 self.format = options.format
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 self.output = options.output
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 self.galaxy = options.galaxy
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 def run(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72 if self.verbosity > 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73 print "Reading input file..."
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 parser = TranscriptContainer(self.inputFileName, self.format, self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 if self.verbosity > 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 print "... done"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 writer = Gff3Writer(self.output, self.verbosity, self.title)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (self.inputFileName), self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 for transcript in parser.getIterator():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81 writer.addTranscript(transcript)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82 progress.inc()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 progress.done()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85 if self.galaxy:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86 os.rename("%s.gff3" % (self.output), self.output)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 if __name__ == '__main__':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
89 launcher = MappingToCoordinates()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 launcher.setAttributesFromCmdLine()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91 launcher.run()