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comparison SMART/Java/Python/modifySequenceList.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 """Modify the content of a FASTA file"""
32 import sys
33 from optparse import OptionParser
34 from commons.core.parsing.FastaParser import FastaParser
35 from commons.core.parsing.FastqParser import FastqParser
36 from commons.core.writer.FastaWriter import FastaWriter
37 from commons.core.writer.FastqWriter import FastqWriter
38 from SMART.Java.Python.misc.Progress import Progress
39
40
41 if __name__ == "__main__":
42
43 # parse command line
44 description = "Modify Sequence List v1.0.1: Extend or shring a list of sequences. [Category: Data Modification]"
45
46 parser = OptionParser(description = description)
47 parser.add_option("-i", "--input", dest="inputFileName",action="store", type="string", help="input file [compulsory] [format: file in format given by -f]")
48 parser.add_option("-o", "--output", dest="outputFileName", action="store",default=None, type="string", help="output file [compulsory] [format: output file in format given by -f]")
49 parser.add_option("-f", "--format", dest="format",action="store",type="string", help="format of the file [compulsory] [format: sequence file format]")
50 parser.add_option("-s", "--start", dest="start", action="store", default=None,type="int",help="keep first nucleotides [format: int]")
51 parser.add_option("-e", "--end", dest="end", action="store",default=None,type="int",help="keep last nucleotides [format: int]")
52 parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]")
53 (options, args) = parser.parse_args()
54
55 if options.format == "fasta":
56 parser = FastaParser(options.inputFileName, options.verbosity)
57 writer = FastaWriter(options.outputFileName, options.verbosity)
58 elif options.format == "fastq":
59 parser = FastqParser(options.inputFileName, options.verbosity)
60 writer = FastqWriter(options.outputFileName, options.verbosity)
61 else:
62 sys.exit("Do not understand '%s' file format." % (options.format))
63
64 progress = Progress(parser.getNbSequences(), "Reading file %s" % (options.inputFileName), options.verbosity)
65 for sequence in parser.getIterator():
66 if options.start != None:
67 sequence.shrinkToFirstNucleotides(options.start)
68 if options.end != None:
69 sequence.shrinkToLastNucleotides(options.end)
70 writer.addSequence(sequence)
71 progress.inc()
72 progress.done()