Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/trimSequences.py @ 58:5f5c9b74c2dd
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author | m-zytnicki |
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date | Fri, 07 Feb 2014 11:53:36 -0500 |
parents | 769e306b7933 |
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#! /usr/bin/env python # # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # from optparse import OptionParser from commons.core.parsing.FastaParser import FastaParser from commons.core.parsing.FastqParser import FastqParser from commons.core.writer.FastaWriter import FastaWriter from commons.core.writer.FastqWriter import FastqWriter from SMART.Java.Python.misc.Progress import Progress from SMART.Java.Python.misc import Utils if __name__ == "__main__": # parse command line description = "Trim Sequences v1.0.3: Remove the 5' and/or 3' adaptors of a list of reads. [Category: Data Modification]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]") parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: sequence file format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in sequence format given by -f]") parser.add_option("-3", "--threePAdaptor", dest="threePAdaptor", action="store", default=None, type="string", help="3' adaptor [format: string] [default: None]") parser.add_option("-5", "--fivePAdaptor", dest="fivePAdaptor", action="store", default=None, type="string", help="5' adaptor [format: string] [default: None]") parser.add_option("-e", "--errors", dest="errors", action="store", default=0, type="int", help="number of errors in percent [format: int] [default: 0]") parser.add_option("-d", "--indels", dest="indels", action="store_true", default=False, help="also accept indels [format: bool] [default: False]") 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]") 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]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") (options, args) = parser.parse_args() minSize = 3 if options.format == "fasta": parser = FastaParser(options.inputFileName, options.verbosity) elif options.format == "fastq": parser = FastqParser(options.inputFileName, options.verbosity) else: raise Exception("Cannot handle files with '%s' format." % (options.format)) if options.format == "fasta": writer = FastaWriter(options.outputFileName, options.verbosity) elif options.format == "fastq": writer = FastqWriter(options.outputFileName, options.verbosity) else: raise Exception("Cannot handle files with '%s' format." % (options.format)) if options.noAdaptor5p != None: if options.format == "fasta": writer5pNoAdaptor = FastaWriter(options.noAdaptor5p, options.verbosity) elif options.format == "fastq": writer5pNoAdaptor = FastqWriter(options.noAdaptor5p, options.verbosity) else: raise Exception("Cannot handle files with '%s' format." % (options.format)) nbFound5p = 0 if options.noAdaptor3p != None: if options.format == "fasta": writer3pNoAdaptor = FastaWriter(options.noAdaptor3p, options.verbosity) elif options.format == "fastq": writer3pNoAdaptor = FastqWriter(options.noAdaptor3p, options.verbosity) else: raise Exception("Cannot handle files with '%s' format." % (options.format)) nbFound3p = 0 progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity) for sequence in parser.getIterator(): progress.inc() if options.threePAdaptor != None: nucleotides = sequence.sequence found = False bestScore = 10000 bestRegion = 0 for i in range(len(nucleotides) - minSize): nucleotidesPart = nucleotides[i:] adaptorPart = options.threePAdaptor if len(nucleotidesPart) >= len(options.threePAdaptor) else options.threePAdaptor[:len(nucleotidesPart)] nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)] if options.indels: score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart) else: score = Utils.getHammingDistance(adaptorPart, nucleotidesPart) if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore: bestScore = score bestRegion = i found = True if found: nbFound3p += 1 sequence.shrinkToFirstNucleotides(bestRegion) elif options.noAdaptor3p: writer3pNoAdaptor.addSequence(sequence) if options.fivePAdaptor != None: nucleotides = sequence.sequence found = False bestScore = 10000 bestRegion = 0 for i in reversed(range(minSize, len(nucleotides))): nucleotidesPart = nucleotides[:i] adaptorPart = options.fivePAdaptor if len(nucleotidesPart) >= len(options.fivePAdaptor) else options.fivePAdaptor[-len(nucleotidesPart):] nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[-len(adaptorPart):] if options.indels: score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart) else: score = Utils.getHammingDistance(adaptorPart, nucleotidesPart) if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore: bestScore = score bestRegion = i found = True if found: nbFound5p += 1 sequence.shrinkToLastNucleotides(len(nucleotides) - bestRegion) elif options.noAdaptor5p: writer5pNoAdaptor.addSequence(sequence) writer.addSequence(sequence) progress.done() writer.close() print "%d sequences" % (parser.getNbSequences()) if options.fivePAdaptor != None: print "%d sequences with 5' adaptors (%.2f%%)" % (nbFound5p, float(nbFound5p) / parser.getNbSequences() * 100) if options.threePAdaptor != None: print "%d sequences with 3' adaptors (%.2f%%)" % (nbFound3p, float(nbFound3p) / parser.getNbSequences() * 100)