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comparison smart_toolShed/SMART/Java/Python/updateQual.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 """Update a .qual file given a .fasta file"""
32
33 from optparse import OptionParser
34 from commons.core.parsing.FastaParser import *
35 from SMART.Java.Python.misc.Progress import *
36
37
38 if __name__ == "__main__":
39
40 # parse command line
41 description = "Update Qual v1.0.1: Remove the sequence in a Qual file which are not in the corresponding Fasta file. [Category: Personnal]"
42
43 parser = OptionParser(description = description)
44 parser.add_option("-f", "--fasta", dest="fastaFile", action="store", type="string", help="fasta file [compulsory] [format: file in FASTA format]")
45 parser.add_option("-q", "--qual", dest="qualFile", action="store", type="string", help="qual file [compulsory] [format: file in QUAL format]")
46 parser.add_option("-o", "--output", dest="outputFile", action="store", type="string", help="output file [compulsory] [format: output file in QUAL format]")
47 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
48 (options, args) = parser.parse_args()
49
50 parser = SequenceListParser(options.fastaFile, options.verbosity)
51 nbSequences = parser.getNbSequences()
52 progress = Progress(nbSequences, "Parsing file %s" % (options.fastaFile), options.verbosity)
53 qualHandle = open(options.qualFile)
54 outputHandle = open(options.outputFile, "w")
55 nbRefused = 0
56 nbTotal = 0
57
58 names = []
59 while parser.getNextSequence():
60 sequence = parser.getCurrentSequence()
61 nbTotal += 1
62
63 found = False
64 name = None
65 for line in qualHandle:
66 line = line.strip()
67 if line[0] == ">":
68 name = line[1:]
69 if name == sequence.name:
70 found = True
71 else:
72 nbRefused += 1
73 else:
74 if found:
75 outputHandle.write(">%s\n%s\n" % (name, line))
76 found = False
77 name = None
78 break
79 progress.inc()
80 progress.done()
81
82
83 outputHandle.close()
84 qualHandle.close()
85
86 print "%d out of %d are refused (%f%%)" % (nbRefused, nbTotal, (float(nbRefused) / nbTotal * 100))