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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 from optparse import OptionParser
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32 from commons.core.parsing.FastaParser import FastaParser
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33 from commons.core.parsing.FastqParser import FastqParser
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34 from commons.core.writer.FastaWriter import FastaWriter
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35 from commons.core.writer.FastqWriter import FastqWriter
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36 from SMART.Java.Python.misc.Progress import Progress
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37 from SMART.Java.Python.misc import Utils
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38
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39
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40 if __name__ == "__main__":
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41
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42 # parse command line
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43 description = "Trim Sequences v1.0.3: Remove the 5' and/or 3' adaptors of a list of reads. [Category: Data Modification]"
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44
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45 parser = OptionParser(description = description)
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46 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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47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: sequence file format]")
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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]")
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49 parser.add_option("-3", "--threePAdaptor", dest="threePAdaptor", action="store", default=None, type="string", help="3' adaptor [format: string] [default: None]")
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50 parser.add_option("-5", "--fivePAdaptor", dest="fivePAdaptor", action="store", default=None, type="string", help="5' adaptor [format: string] [default: None]")
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51 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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52 parser.add_option("-d", "--indels", dest="indels", action="store_true", default=False, help="also accept indels [format: bool] [default: False]")
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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]")
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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]")
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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 = 3
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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 raise Exception("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 raise Exception("Cannot handle files with '%s' format." % (options.format))
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73
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74
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75 if options.noAdaptor5p != None:
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76 if options.format == "fasta":
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77 writer5pNoAdaptor = FastaWriter(options.noAdaptor5p, options.verbosity)
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78 elif options.format == "fastq":
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79 writer5pNoAdaptor = FastqWriter(options.noAdaptor5p, options.verbosity)
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80 else:
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81 raise Exception("Cannot handle files with '%s' format." % (options.format))
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82 nbFound5p = 0
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83
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84 if options.noAdaptor3p != None:
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85 if options.format == "fasta":
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86 writer3pNoAdaptor = FastaWriter(options.noAdaptor3p, options.verbosity)
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87 elif options.format == "fastq":
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88 writer3pNoAdaptor = FastqWriter(options.noAdaptor3p, options.verbosity)
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89 else:
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90 raise Exception("Cannot handle files with '%s' format." % (options.format))
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91 nbFound3p = 0
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92
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93 progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
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94 for sequence in parser.getIterator():
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95 progress.inc()
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96 if options.threePAdaptor != None:
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97 nucleotides = sequence.sequence
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98 found = False
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99 bestScore = 10000
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100 bestRegion = 0
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101 for i in range(len(nucleotides) - minSize):
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102 nucleotidesPart = nucleotides[i:]
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103 adaptorPart = options.threePAdaptor if len(nucleotidesPart) >= len(options.threePAdaptor) else options.threePAdaptor[:len(nucleotidesPart)]
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104 nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)]
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105 if options.indels:
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106 score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart)
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107 else:
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108 score = Utils.getHammingDistance(adaptorPart, nucleotidesPart)
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109 if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore:
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110 bestScore = score
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111 bestRegion = i
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112 found = True
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113 if found:
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114 nbFound3p += 1
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115 sequence.shrinkToFirstNucleotides(bestRegion)
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116 elif options.noAdaptor3p:
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117 writer3pNoAdaptor.addSequence(sequence)
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118 if options.fivePAdaptor != None:
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119 nucleotides = sequence.sequence
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120 found = False
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121 bestScore = 10000
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122 bestRegion = 0
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123 for i in reversed(range(minSize, len(nucleotides))):
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124 nucleotidesPart = nucleotides[:i]
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125 adaptorPart = options.fivePAdaptor if len(nucleotidesPart) >= len(options.fivePAdaptor) else options.fivePAdaptor[-len(nucleotidesPart):]
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126 nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[-len(adaptorPart):]
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127 if options.indels:
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128 score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart)
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129 else:
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130 score = Utils.getHammingDistance(adaptorPart, nucleotidesPart)
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131 if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore:
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132 bestScore = score
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133 bestRegion = i
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134 found = True
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135 if found:
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136 nbFound5p += 1
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137 sequence.shrinkToLastNucleotides(len(nucleotides) - bestRegion)
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138 elif options.noAdaptor5p:
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139 writer5pNoAdaptor.addSequence(sequence)
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140 writer.addSequence(sequence)
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141 progress.done()
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142 writer.close()
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143
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144 print "%d sequences" % (parser.getNbSequences())
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145 if options.fivePAdaptor != None:
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146 print "%d sequences with 5' adaptors (%.2f%%)" % (nbFound5p, float(nbFound5p) / parser.getNbSequences() * 100)
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147 if options.threePAdaptor != None:
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148 print "%d sequences with 3' adaptors (%.2f%%)" % (nbFound3p, float(nbFound3p) / parser.getNbSequences() * 100)
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149
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