|
6
|
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()
|
