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+ − 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