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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Trim the sequences from a 5' adaptor"""
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32
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33 import sys
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34 from optparse import OptionParser
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35 from commons.core.parsing.FastaParser import FastaParser
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36 from commons.core.parsing.FastqParser import FastqParser
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37 from commons.core.writer.FastaWriter import FastaWriter
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38 from commons.core.writer.FastqWriter import FastqWriter
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39 from SMART.Java.Python.misc.Progress import Progress
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40 from SMART.Java.Python.misc import Utils
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41
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42
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43 if __name__ == "__main__":
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44
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45 # parse command line
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46 description = "Trim Adaptor v1.0.1: Remove the 3' adaptor of a list of reads. [Category: Data Modification]"
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47
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48 parser = OptionParser(description = description)
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49 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
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50 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: sequence file format]")
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51 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in sequence format given by -f]")
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52 parser.add_option("-a", "--adaptor", dest="adaptor", action="store", type="string", help="adaptor [compulsory] [format: string]")
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53 parser.add_option("-e", "--errors", dest="errors", action="store", default=0, type="int" , help="number of errors in percent [format: int] [default: 0]")
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54 parser.add_option("-n", "--noAdaptor", dest="noAdaptor", action="store", default=None, type="string", help="file name where to print sequences with no adaptor [format: output file in sequence format given by -f]")
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55 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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56 (options, args) = parser.parse_args()
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57
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58 minSize = 2
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59
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60 if options.format == "fasta":
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61 parser = FastaParser(options.inputFileName, options.verbosity)
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62 elif options.format == "fastq":
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63 parser = FastqParser(options.inputFileName, options.verbosity)
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64 else:
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65 sys.exit("Cannot handle files with '%s' format." % (options.format))
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66
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67 if options.format == "fasta":
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68 writer = FastaWriter(options.outputFileName, options.verbosity)
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69 elif options.format == "fastq":
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70 writer = FastqWriter(options.outputFileName, options.verbosity)
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71 else:
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72 sys.exit("Cannot handle files with '%s' format." % (options.format))
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73
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74 writerNoAdaptor = None
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75 if options.noAdaptor != None:
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76 if options.format == "fasta":
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77 writerNoAdaptor = FastaWriter(options.noAdaptor, options.verbosity)
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78 elif options.format == "fastq":
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79 writerNoAdaptor = FastqWriter(options.noAdaptor, options.verbosity)
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80 else:
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81 sys.exit("Cannot handle files with '%s' format." % (options.format))
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82
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83 nbFound = 0
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84
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85 progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
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86 for sequence in parser.getIterator():
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87 progress.inc()
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88 nucleotides = sequence.getSequence()
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89 found = False
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90 for i in range(len(nucleotides) - minSize):
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91 nucleotidesPart = nucleotides[i:]
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92 adaptorPart = options.adaptor if len(nucleotidesPart) >= len(options.adaptor) else options.adaptor[:len(nucleotidesPart)]
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93 nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)]
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94 if Utils.getHammingDistance(adaptorPart, nucleotidesPart) <= int(options.errors / 100.0 * len(adaptorPart)):
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95 nbFound += 1
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96 sequence.shrinkToFirstNucleotides(i)
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97 writer.addSequence(sequence)
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98 found = True
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99 break
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100 if not found:
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101 writer.addSequence(sequence)
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102 if writerNoAdaptor != None:
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103 writerNoAdaptor.addSequence(sequence)
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104 progress.done()
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105
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106 print "%d sequences with adaptors on %d (%.2f%%)" % (nbFound, parser.getNbSequences(), float(nbFound) / parser.getNbSequences() * 100)
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107
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