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comparison SMART/Java/Python/adaptorStripper.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 """Remove adaptors"""
32
33 import os
34 from optparse import OptionParser
35 from SMART.Java.Python.structure.Sequence import Sequence
36 from SMART.Java.Python.structure.SequenceList import SequenceList
37 from commons.core.parsing.FastaParser import FastaParser
38 from commons.core.writer.FastaWriter import FastaWriter
39 from SMART.Java.Python.misc.Progress import Progress
40
41
42 def distance (string1, string2):
43 if len(string1) != len(string2):
44 return None
45 distance = 0
46 for i in range(0, len(string1)):
47 if string1[i] != string2[i]:
48 distance += 1
49 return distance
50
51
52
53 if __name__ == "__main__":
54 nbRemaining = 0
55
56 # parse command line
57 description = "Adaptor Stripper v1.0.1: Remove the adaptor of a list of reads. [Category: Personnal]"
58
59 parser = OptionParser(description = description)
60 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTA format]")
61 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
62 parser.add_option("-5", "--5primeAdaptor", dest="fivePrimeAdaptor", action="store", type="string", help="five prime adaptor [format: string]")
63 parser.add_option("-3", "--3primeAdaptor", dest="threePrimeAdaptor", action="store", type="string", help="three prime adaptor [format: string]")
64 parser.add_option("-d", "--5primeDist", dest="fivePrimeDistance", action="store", default=3, type="int", help="five prime distance [format: int] [default: 3]")
65 parser.add_option("-e", "--3primeDist", dest="threePrimeDistance", action="store", default=3, type="int", help="three prime distance [format: int [default: 3]]")
66 parser.add_option("-m", "--3primeSize", dest="threePrimeSize", action="store", default=10, type="int", help="three prime size [format: int] [default: 10]")
67 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
68 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
69 (options, args) = parser.parse_args()
70
71 if options.log:
72 logHandle = open(options.outputFileName + ".log", "w")
73
74
75 writer = FastaWriter(options.outputFileName + ".fas", options.verbosity)
76 sequenceParser = FastaParser(options.inputFileName, options.verbosity)
77 nbSequences = sequenceParser.getNbSequences()
78
79 # treat sequences
80 progress = Progress(sequenceParser.getNbSequences(), "Analyzing " + options.inputFileName, options.verbosity)
81 for sequence in sequenceParser.getIterator():
82 fivePrimeAdaptor = sequence.getSequence()[0:len(options.fivePrimeAdaptor)]
83 threePrimeAdaptor = sequence.getSequence()[len(sequence.sequence)-len(options.threePrimeAdaptor):]
84
85 # check 5' adaptor
86 fivePrimeDistance = distance(fivePrimeAdaptor, options.fivePrimeAdaptor)
87 # check 3' adaptor
88 threePrimeDistance = len(threePrimeAdaptor)
89 for i in range(options.threePrimeSize, len(threePrimeAdaptor)+1):
90 threePrimeDistance = min(threePrimeDistance, distance(threePrimeAdaptor[-i:], options.threePrimeAdaptor[:i]))
91
92 # sort candidates
93 if fivePrimeDistance > options.fivePrimeDistance:
94 if options.log:
95 logHandle.write("Sequence %s does not start with the right adaptor (%s != %s)\n" % (sequence.getSequence(), fivePrimeAdaptor, options.fivePrimeAdaptor))
96 elif threePrimeDistance > options.threePrimeDistance:
97 if options.log:
98 logHandle.write("Sequence %s does not end with the right adaptor (%s != %s)\n" % (sequence.getSequence(), threePrimeAdaptor, options.threePrimeAdaptor))
99 else:
100 nbRemaining += 1
101 sequence.setSequence(sequence.getSequence()[len(options.fivePrimeAdaptor):len(sequence.getSequence())-len(options.threePrimeAdaptor)])
102 writer.addSequence(sequence)
103
104 progress.inc()
105
106 progress.done()
107
108 if options.log:
109 logHandle.close()
110
111 writer.write()
112
113 print "kept %i over %i (%.f%%)" % (nbRemaining, nbSequences, float(nbRemaining) / nbSequences * 100)
114
115