|
6
|
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
|
