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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 from optparse import OptionParser
+ − 32 from commons.core.parsing.FastaParser import FastaParser
+ − 33 from commons.core.parsing.FastqParser import FastqParser
+ − 34 from commons.core.writer.FastaWriter import FastaWriter
+ − 35 from commons.core.writer.FastqWriter import FastqWriter
+ − 36 from SMART.Java.Python.misc.Progress import Progress
+ − 37 from SMART.Java.Python.misc import Utils
+ − 38
+ − 39
+ − 40 if __name__ == "__main__":
+ − 41
+ − 42 # parse command line
+ − 43 description = "Trim Sequences v1.0.3: Remove the 5' and/or 3' adaptors of a list of reads. [Category: Data Modification]"
+ − 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 sequence format given by -f]")
+ − 47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: sequence file format]")
+ − 48 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in sequence format given by -f]")
+ − 49 parser.add_option("-3", "--threePAdaptor", dest="threePAdaptor", action="store", default=None, type="string", help="3' adaptor [format: string] [default: None]")
+ − 50 parser.add_option("-5", "--fivePAdaptor", dest="fivePAdaptor", action="store", default=None, type="string", help="5' adaptor [format: string] [default: None]")
+ − 51 parser.add_option("-e", "--errors", dest="errors", action="store", default=0, type="int", help="number of errors in percent [format: int] [default: 0]")
+ − 52 parser.add_option("-d", "--indels", dest="indels", action="store_true", default=False, help="also accept indels [format: bool] [default: False]")
+ − 53 parser.add_option("-n", "--noAdaptor5p", dest="noAdaptor5p", action="store", default=None, type="string", help="print sequences with no 5' adaptor [format: output file in sequence format given by -f]")
+ − 54 parser.add_option("-m", "--noAdaptor3p", dest="noAdaptor3p", action="store", default=None, type="string", help="print sequences with no 3' adaptor [format: output file in sequence format given by -f]")
+ − 55 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 56 (options, args) = parser.parse_args()
+ − 57
+ − 58 minSize = 3
+ − 59
+ − 60 if options.format == "fasta":
+ − 61 parser = FastaParser(options.inputFileName, options.verbosity)
+ − 62 elif options.format == "fastq":
+ − 63 parser = FastqParser(options.inputFileName, options.verbosity)
+ − 64 else:
+ − 65 raise Exception("Cannot handle files with '%s' format." % (options.format))
+ − 66
+ − 67 if options.format == "fasta":
+ − 68 writer = FastaWriter(options.outputFileName, options.verbosity)
+ − 69 elif options.format == "fastq":
+ − 70 writer = FastqWriter(options.outputFileName, options.verbosity)
+ − 71 else:
+ − 72 raise Exception("Cannot handle files with '%s' format." % (options.format))
+ − 73
+ − 74
+ − 75 if options.noAdaptor5p != None:
+ − 76 if options.format == "fasta":
+ − 77 writer5pNoAdaptor = FastaWriter(options.noAdaptor5p, options.verbosity)
+ − 78 elif options.format == "fastq":
+ − 79 writer5pNoAdaptor = FastqWriter(options.noAdaptor5p, options.verbosity)
+ − 80 else:
+ − 81 raise Exception("Cannot handle files with '%s' format." % (options.format))
+ − 82 nbFound5p = 0
+ − 83
+ − 84 if options.noAdaptor3p != None:
+ − 85 if options.format == "fasta":
+ − 86 writer3pNoAdaptor = FastaWriter(options.noAdaptor3p, options.verbosity)
+ − 87 elif options.format == "fastq":
+ − 88 writer3pNoAdaptor = FastqWriter(options.noAdaptor3p, options.verbosity)
+ − 89 else:
+ − 90 raise Exception("Cannot handle files with '%s' format." % (options.format))
+ − 91 nbFound3p = 0
+ − 92
+ − 93 progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
+ − 94 for sequence in parser.getIterator():
+ − 95 progress.inc()
+ − 96 if options.threePAdaptor != None:
+ − 97 nucleotides = sequence.sequence
+ − 98 found = False
+ − 99 bestScore = 10000
+ − 100 bestRegion = 0
+ − 101 for i in range(len(nucleotides) - minSize):
+ − 102 nucleotidesPart = nucleotides[i:]
+ − 103 adaptorPart = options.threePAdaptor if len(nucleotidesPart) >= len(options.threePAdaptor) else options.threePAdaptor[:len(nucleotidesPart)]
+ − 104 nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)]
+ − 105 if options.indels:
+ − 106 score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart)
+ − 107 else:
+ − 108 score = Utils.getHammingDistance(adaptorPart, nucleotidesPart)
+ − 109 if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore:
+ − 110 bestScore = score
+ − 111 bestRegion = i
+ − 112 found = True
+ − 113 if found:
+ − 114 nbFound3p += 1
+ − 115 sequence.shrinkToFirstNucleotides(bestRegion)
+ − 116 elif options.noAdaptor3p:
+ − 117 writer3pNoAdaptor.addSequence(sequence)
+ − 118 if options.fivePAdaptor != None:
+ − 119 nucleotides = sequence.sequence
+ − 120 found = False
+ − 121 bestScore = 10000
+ − 122 bestRegion = 0
+ − 123 for i in reversed(range(minSize, len(nucleotides))):
+ − 124 nucleotidesPart = nucleotides[:i]
+ − 125 adaptorPart = options.fivePAdaptor if len(nucleotidesPart) >= len(options.fivePAdaptor) else options.fivePAdaptor[-len(nucleotidesPart):]
+ − 126 nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[-len(adaptorPart):]
+ − 127 if options.indels:
+ − 128 score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart)
+ − 129 else:
+ − 130 score = Utils.getHammingDistance(adaptorPart, nucleotidesPart)
+ − 131 if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore:
+ − 132 bestScore = score
+ − 133 bestRegion = i
+ − 134 found = True
+ − 135 if found:
+ − 136 nbFound5p += 1
+ − 137 sequence.shrinkToLastNucleotides(len(nucleotides) - bestRegion)
+ − 138 elif options.noAdaptor5p:
+ − 139 writer5pNoAdaptor.addSequence(sequence)
+ − 140 writer.addSequence(sequence)
+ − 141 progress.done()
+ − 142 writer.close()
+ − 143
+ − 144 print "%d sequences" % (parser.getNbSequences())
+ − 145 if options.fivePAdaptor != None:
+ − 146 print "%d sequences with 5' adaptors (%.2f%%)" % (nbFound5p, float(nbFound5p) / parser.getNbSequences() * 100)
+ − 147 if options.threePAdaptor != None:
+ − 148 print "%d sequences with 3' adaptors (%.2f%%)" % (nbFound3p, float(nbFound3p) / parser.getNbSequences() * 100)
+ − 149
