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comparison SMART/Java/Python/fastqToFasta.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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 FASTQ file to a FASTA file"""
32
33 import os
34 import sys
35 from optparse import OptionParser
36 from SMART.Java.Python.misc.RPlotter import RPlotter
37 from SMART.Java.Python.misc.Progress import Progress
38 from math import *
39
40 if __name__ == "__main__":
41
42 # parse command line
43 description = "FastQ to FastA v1.0.1: Convert a FastQ file into a FastA file. [Category: Personnal]"
44
45 parser = OptionParser(description = description)
46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTQ format]")
47 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
48 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
49 (options, args) = parser.parse_args()
50
51 inputFile = open(options.inputFileName)
52 outputFastaFile = open(options.outputFileName, "w")
53
54 inSequenceName = False
55 inQualityName = False
56 inSequence = False
57 inQuality = True
58 sequenceName = None
59 lineNumber = 1
60
61 for line in inputFile:
62
63 if inSequenceName:
64 inSequence = True
65 inSequenceName = False
66 elif inQualityName:
67 inQuality = True
68 inQualityName = False
69 elif inSequence:
70 inQualityName = True
71 inSequence = False
72 elif inQuality:
73 inSequenceName = True
74 inQuality = False
75 else:
76 sys.exit("Error! Do not in which section I am (line is %d)" % (lineNumber))
77
78 line = line.strip()
79 if inSequenceName:
80 if line[0] != "@":
81 sys.exit("Error! Sequence name '%s' does not start with '@' (line is %d)" % (line, lineNumber))
82 sequenceName = line[1:]
83 outputFastaFile.write(">%s\n" % (sequenceName))
84 elif inQualityName:
85 if line[0] != "+":
86 sys.exit("Error! Quality name '%s' does not start with '+' (line is %d)" % (line, lineNumber))
87 if len(line) > 1 and sequenceName != line[1:]:
88 sys.exit("Names in sequence and qual are different (%s, %s) (line is %d)" % (sequenceName, line[1:], lineNumber))
89 elif inSequence:
90 outputFastaFile.write("%s\n" % (line))
91 elif inQuality:
92 pass
93 lineNumber += 1
94
95 inputFile.close()
96 outputFastaFile.close()