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comparison smart_toolShed/SMART/Java/Python/convertTranscriptFile.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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 Read a transcript file and convert it to another format
33 """
34
35 import os, re
36 from optparse import OptionParser
37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
38 from commons.core.writer.TranscriptWriter import TranscriptWriter
39 from SMART.Java.Python.misc.Progress import Progress
40
41
42 class ConvertTranscriptFile(object):
43 def __init__(self,inputFileName="", inputFormat ="", outputFileName="", outputFormat="", name="", sequenceFileName=None, strands=False, galaxy=False, feature=None, featurePart=None, verbosity=1):
44 self.inputFileName = inputFileName
45 self.inputFormat = inputFormat
46 self.outputFileName = outputFileName
47 self.outputFormat = outputFormat
48 self.name = name
49 self.sequenceFileName = sequenceFileName
50 self.strands = strands
51 self.galaxy = galaxy
52
53 self.feature=feature
54 self.featurePart=featurePart
55
56 self.verbosity = verbosity
57
58 def setAttributesFromCmdLine(self):
59 description = "Convert Transcript File v1.0.3: Convert a file from a format to another. [Category: Conversion]"
60 parser = OptionParser(description = description)
61 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in format given by -f]")
62 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript or mapping file format]")
63 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in format given by -g]")
64 parser.add_option("-g", "--outputFormat", dest="outputFormat", action="store", type="string", help="format of the output file [compulsory] [format: transcript file format]")
65 parser.add_option("-n", "--name", dest="name", action="store", default="SMART", type="string", help="name for the transcripts [format: string] [default: SMART]")
66 parser.add_option("-s", "--sequences", dest="sequenceFileName", action="store", default=None, type="string", help="give the corresponding Multi-Fasta file (useful for EMBL format) [format: string]")
67 parser.add_option("-t", "--strands", dest="strands", action="store_true", default=False, help="consider the 2 strands as different (only useful for writing WIG files) [format: bool] [default: False]")
68 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
69 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
70 (options, args) = parser.parse_args()
71 self._setAttributesFromOptions(options)
72
73 def _setAttributesFromOptions(self, options):
74 self.inputFileName = options.inputFileName
75 self.inputFormat = options.inputFormat
76 self.outputFileName = options.outputFileName
77 self.outputFormat = options.outputFormat
78 self.name = options.name
79 self.sequenceFileName = options.sequenceFileName
80 self.strands = options.strands
81 self.galaxy = options.galaxy
82 self.verbosity = options.verbosity
83
84 def run(self):
85 # create parser
86 parser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
87 # create writer
88 writer = TranscriptWriter(self.outputFileName, self.outputFormat, self.verbosity)
89 # connect parser and writer
90 writer.setContainer(parser)
91
92 if self.name != None:
93 writer.setTitle(self.name)
94 if self.feature != None:
95 writer.setFeature(self.feature)
96 if self.featurePart != None:
97 writer.setFeaturePart(self.featurePart)
98 if self.sequenceFileName != None:
99 writer.addSequenceFile(self.sequenceFileName)
100
101 nbItems = 0
102 if self.verbosity > 0:
103 nbItems = parser.getNbItems()
104 print "%i items found" % (nbItems)
105
106 if self.strands:
107 writer.setStrands(True)
108 # convert
109 writer.write()
110 writer.close()
111
112 if __name__ == "__main__":
113 iConvertTranscriptFile = ConvertTranscriptFile()
114 iConvertTranscriptFile.setAttributesFromCmdLine()
115 iConvertTranscriptFile.run()