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comparison SMART/Java/Python/coordinatesToSequence.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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 """Convert a list of coordinates to sequences"""
32
33 from optparse import OptionParser
34 from commons.core.parsing.FastaParser import FastaParser
35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
36 from commons.core.writer.FastaWriter import FastaWriter
37 from SMART.Java.Python.misc.Progress import Progress
38
39
40 if __name__ == "__main__":
41
42 # parse command line
43 description = "Coordinates to Sequences v1.0.2: Extract the sequences from a list of coordinates. [Category: Conversion]"
44
45 parser = OptionParser(description = description)
46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
48 parser.add_option("-s", "--sequences", dest="sequences", action="store", type="string", help="file that contains the sequences [compulsory] [format: file in FASTA format]")
49 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file (FASTA format) [format: output file in FASTA format]")
50 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
51 (options, args) = parser.parse_args()
52
53 # create parser
54 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
55
56 sequenceParser = FastaParser(options.sequences, options.verbosity)
57
58 writer = FastaWriter(options.outputFileName, options.verbosity)
59 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (options.inputFileName), options.verbosity)
60 for transcript in parser.getIterator():
61 sequence = transcript.extractSequence(sequenceParser)
62 writer.addSequence(sequence)
63 progress.inc()
64 progress.done()