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comparison smart_toolShed/SMART/Java/Python/wrongFastqToQual.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 """Convert a pseudo-FASTQ file to QUAL files"""
32
33 import os
34 from optparse import OptionParser
35 from SMART.Java.Python.misc.Progress import *
36 from math import *
37
38 if __name__ == "__main__":
39
40 # parse command line
41 description = "Wrong FastQ to Qual v1.0.1: Convert a pseudo-FastQ (i.e. a FastQ file with a wrong format) into a Qual file. [Category: Personnal]"
42
43 parser = OptionParser(description = description)
44 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTQ format]")
45 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in QUAL format]")
46 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
47 (options, args) = parser.parse_args()
48
49 inputFile = open(options.inputFileName)
50 outputFastaFile = open("%s.fasta" % (options.outputFileName), "w")
51 outputQualFile = open("%s.qual" % (options.outputFileName), "w")
52
53 inSequence = False
54 inQuality = True
55 sequenceName = None
56 for line in inputFile:
57 line = line.strip()
58 if line[0] == "@":
59 if inQuality == False:
60 sys.exit("Quality of %s is missing" % (sequenceName))
61 inSequence = True
62 inQuality = False
63 sequenceName = line[1:]
64 outputFastaFile.write(">%s\n" % (sequenceName))
65 elif line[0] == "+":
66 if inSequence == False:
67 sys.exit("Sequence of %s is missing" % (line[1:]))
68 inSequence = False
69 inQuality = True
70 if sequenceName != line[1:]:
71 sys.exit("Names in sequence and qual are different (%s, %s)" % (sequenceName, line[1:]))
72 outputQualFile.write(">%s\n" % (sequenceName))
73 else:
74 if inSequence:
75 outputFastaFile.write("%s\n" % (line))
76 elif inQuality:
77 outputQualFile.write("%s\n" % (line))
78
79 inputFile.close()
80 outputFastaFile.close()
81 outputQualFile.close()