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comparison smart_toolShed/SMART/Java/Python/trimSequence.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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-1:000000000000 0:e0f8dcca02ed
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 """Remove sequences with low reliability"""
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 = "Trim Sequences v1.0.1: Remove sequences with low reliability: low occurrences and highly repeted. [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="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
47 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
48 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
49 (options, args) = parser.parse_args()
50
51 parser = SequenceListParser(options.inputFileName, options.verbosity)
52 nbSequences = parser.getNbSequences()
53 progress = Progress(nbSequences, "Parsing file %s" % (options.inputFileName), options.verbosity)
54
55 writer = FastaWriter(options.outputFileName, options.verbosity)
56 if options.log:
57 logHandle = open("log.txt", "w")
58
59 letters = ("A", "C", "G", "T")
60 nbLowComplexity = 0
61 nbTooManyOccurrences = 0
62
63 for sequence in parser.getIteractor():
64 halfSize = len(sequence.sequence) / 2
65 occurrences = set()
66 nbOccurrences = dict(zip(letters, [0 for letter in letters]))
67 tooManyOccurrences = False
68 good = True
69
70 for char in sequence.sequence:
71 if char in letters:
72 occurrences.add(char)
73 nbOccurrences[char] += 1
74
75
76 if len(occurrences) < 4:
77 nbLowComplexity += 1
78 if options.log:
79 logHandle.write("Low complexity for %s\n" % (sequence.sequence))
80 good = False
81
82 if good:
83 for letter, nbOccurrence in nbOccurrences.iteritems():
84 if nbOccurrence > halfSize:
85 if not tooManyOccurrences:
86 nbTooManyOccurrences += 1
87 if options.log:
88 logHandle.write("Too many occurrences for %s\n" % (sequence.sequence))
89 tooManyOccurrences = True
90 good = False
91
92 if good:
93 writer.addSequence(sequence)
94
95 progress.inc()
96 progress.done()
97
98 if options.log:
99 logHandle.close()
100
101 print "%d out of %d have low complexity (%f%%)" % (nbLowComplexity, nbSequences, (float(nbLowComplexity) / nbSequences * 100))
102 print "%d out of %d have too many occurrences (%f%%)" % (nbTooManyOccurrences, nbSequences, (float(nbTooManyOccurrences) / nbSequences * 100))