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comparison SMART/Java/Python/qualToFastq.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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 import sys
32 from optparse import OptionParser
33 from commons.core.parsing.SequenceListParser import SequenceListParser
34 from SMART.Java.Python.misc.Progress import Progress
35
36 """
37 Transform qual and fasta files to a single fastq file
38 """
39
40 if __name__ == "__main__":
41
42 # parse command line
43 description = "Qual To FastQ v1.0.2: Convert a file in FASTA/Qual format to FastQ format. [Category: Conversion]"
44
45 parser = OptionParser(description = description)
46 parser.add_option("-f", "--fasta", dest="fastaFileName", action="store", type="string", help="input fasta file [compulsory] [format: file in FASTA format]")
47 parser.add_option("-q", "--qual", dest="qualFileName", action="store", type="string", help="input qual file [compulsory] [format: file in TXT format]")
48 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in FASTQ format]")
49 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
50 (options, args) = parser.parse_args()
51
52 fastaFile = open(options.fastaFileName)
53 qualFile = open(options.qualFileName)
54 fastqFile = open(options.outputFileName, "w")
55
56 fastaLine = fastaFile.readline().strip()
57 qualLine = qualFile.readline().strip()
58 header = None
59 cpt = 0
60 while fastaLine:
61 if not qualLine:
62 raise Exception("Qual file is shorter!")
63 if fastaLine[0] == ">":
64 header = fastaLine[1:]
65 if qualLine[0] != ">":
66 raise Exception("Discrepencies around %s!" % (header))
67 fastqFile.write("@%s\n" % (header))
68 else:
69 if qualLine[0] == ">":
70 raise Exception("Discrepencies around %s!" % (qualLine[1:]))
71 intQualities = qualLine.split()
72 if len(intQualities) != len(fastaLine):
73 raise Exception("Sizes of read and quality diverge in %s!" % (header))
74 chrQualities = [chr(min(int(quality), 93) + 33) for quality in intQualities]
75 fastqFile.write("%s\n+\n%s\n" % (fastaLine, "".join(chrQualities)))
76 fastaLine = fastaFile.readline().strip()
77 qualLine = qualFile.readline().strip()
78 if cpt % 1000 == 0 and options.verbosity > 1:
79 sys.stdout.write("%d lines read\r" % (cpt))
80 sys.stdout.flush()
81 cpt += 1
82 if options.verbosity > 0:
83 print "%d lines read" % (cpt)
84
85 if qualLine:
86 raise Exception("Qual file is longer!")
87