Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/sequenceListSplitter.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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 """Split a FASTA file into several shorter ones"""
32
33 from optparse import OptionParser
34 from commons.core.parsing.SequenceListParser import *
35 from commons.core.writer.FastaWriter import *
36 from SMART.Java.Python.misc.Progress import *
37
38
39 if __name__ == "__main__":
40
41 # parse command line
42 description = "Sequence List Splitter v1.0.1: Split a list of big sequences into small chunks. [Category: Personnal]"
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="outputFileNames", action="store", type="string", help="output files [compulsory] [format: output file in FASTA format]")
47 parser.add_option("-n", "--number", dest="number", action="store", default=10, type="int", help="number of splits [compulsory] [format: int] [default: 10]")
48 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
49 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
50 (options, args) = parser.parse_args()
51
52 if options.log:
53 logHandle = open(options.outputFileNames + ".log", "w")
54
55 # split file
56 sequenceListParser = SequenceListParser(options.inputFileName, options.verbosity)
57 nbSequences = sequenceListParser.getNbSequences()
58 nbSequencesByFile = math.ceil(nbSequences / options.number)
59
60 # write into files
61 currentFileNumber = 1
62 writer = FastaWriter("%s%i.fasta" % (options.outputFileNames, currentFileNumber), options.verbosity)
63 nbSequencesHere = 0
64 progress = Progress(nbSequences, "Writing files", options.verbosity)
65 for sequence in sequenceListParser.getIterator():
66 writer.addSequence(sequence)
67 nbSequencesHere += 1
68 if nbSequencesHere == nbSequencesByFile:
69 currentFileNumber += 1
70 writer = FastaWriter("%s%i.fasta" % (options.outputFileNames, currentFileNumber), options.verbosity)
71 nbSequencesHere = 0
72 progress.inc()
73 progress.done()