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comparison smart_toolShed/SMART/Java/Python/modifyFasta.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 """Modify the content of a FASTA file"""
32
33 from optparse import OptionParser
34 from commons.core.parsing.FastaParser import FastaParser
35 from commons.core.writer.FastaWriter import FastaWriter
36 from SMART.Java.Python.misc.Progress import Progress
37
38
39 if __name__ == "__main__":
40
41 # parse command line
42 description = "Modify Sequence List v1.0.1: Extend or shring a list of sequences. [Category: Data Modification]"
43
44 parser = OptionParser(description = description)
45 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTA format]")
46 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in FASTA format]")
47 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="keep first nucleotides [format: int]")
48 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="keep last nucleotides [format: int]")
49 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
50 (options, args) = parser.parse_args()
51
52 parser = FastaParser(options.inputFileName, options.verbosity)
53 writer = FastaWriter(options.outputFileName, options.verbosity)
54 progress = Progress(parser.getNbSequences(), "Reading file %s" % (options.inputFileName), options.verbosity)
55 for sequence in parser.getIterator():
56 if options.start != None:
57 sequence.shrinkToFirstNucleotides(options.start)
58 if options.end != None:
59 sequence.shrinkToLastNucleotides(options.end)
60 writer.addSequence(sequence)
61 progress.inc()
62 progress.done()