38
+ − 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 """
+ − 32 Remove empty sequences from a FASTA or FASTQ file
+ − 33 """
+ − 34
+ − 35 import os, random
+ − 36 from optparse import OptionParser
+ − 37 from commons.core.parsing.FastaParser import *
+ − 38 from commons.core.parsing.FastqParser import *
+ − 39 from commons.core.writer.FastaWriter import *
+ − 40 from commons.core.writer.FastqWriter import *
+ − 41 from SMART.Java.Python.misc.Progress import *
+ − 42
+ − 43
+ − 44 class EmptySequenceRemover(object):
+ − 45
+ − 46 def __init__(self, verbosity = 1):
+ − 47 self.verbosity = verbosity
+ − 48 self.inputFileName = None
+ − 49 self.parser = None
+ − 50 self.format = None
+ − 51 self.writer = None
+ − 52 self.forbiddenNames = {}
+ − 53 self.removedNames = {}
+ − 54
+ − 55
+ − 56 def setInputFileName(self, fileName, format):
+ − 57 self.inputFileName = fileName
+ − 58 self.format = format
+ − 59 if options.format == "fasta":
+ − 60 self.parser = FastaParser(self.inputFileName, self.verbosity)
+ − 61 elif options.format == "fastq":
+ − 62 self.parser = FastqParser(self.inputFileName, self.verbosity)
+ − 63 else:
+ − 64 sys.exit("Do not understand '%s' file format." % (self.format))
+ − 65
+ − 66
+ − 67 def setOutputFileName(self, fileName):
+ − 68 if options.format == "fasta":
+ − 69 self.writer = FastaWriter(fileName, self.verbosity)
+ − 70 elif options.format == "fastq":
+ − 71 self.writer = FastqWriter(fileName, self.verbosity)
+ − 72
+ − 73
+ − 74 def parse(self):
+ − 75 progress = Progress(self.parser.getNbSequences(), "Reading sequences in %s" % (options.inputFileName), options.verbosity)
+ − 76 for sequence in self.parser.getIterator():
+ − 77 name = sequence.name.split("/")[0]
+ − 78 if name not in self.forbiddenNames:
+ − 79 if sequence.sequence == "":
+ − 80 self.removedNames[name] = 1
+ − 81 else:
+ − 82 self.writer.addSequence(sequence)
+ − 83 progress.inc()
+ − 84 progress.done()
+ − 85 self.writer.write()
+ − 86
+ − 87
+ − 88 if __name__ == "__main__":
+ − 89
+ − 90 # parse command line
+ − 91 description = "Remove Empty Sequences v1.0.2: Remove all the empty sequences in a list. [Category: Personal]"
+ − 92
+ − 93 parser = OptionParser(description = description)
+ − 94 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
+ − 95 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: sequence file format]")
+ − 96 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 (in case of pair end reads) [format: file in sequence format given by -f] [default: None]")
+ − 97 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in format given by -f]")
+ − 98 parser.add_option("-p", "--output2", dest="outputFileName2", action="store", default=None, type="string", help="output file 2 (in case of pair end reads) [format: output file in sequence format given by -f] [default: None]")
+ − 99 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
+ − 100 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
+ − 101 (options, args) = parser.parse_args()
+ − 102
+ − 103 if options.log:
+ − 104 logHandle = open("%s.log" % options.outputFileName, "w")
+ − 105
+ − 106 remover = EmptySequenceRemover(options.verbosity)
+ − 107 remover.setInputFileName(options.inputFileName, options.format)
+ − 108 remover.setOutputFileName(options.outputFileName)
+ − 109 remover.parse()
+ − 110 removedNames = remover.removedNames
+ − 111 if options.log:
+ − 112 for name in removedNames:
+ − 113 logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName))
+ − 114 nbSequences = remover.parser.getNbSequences()
+ − 115
+ − 116 newRemovedNames = {}
+ − 117 if options.inputFileName2 != None:
+ − 118 remover = EmptySequenceRemover(options.verbosity)
+ − 119 remover.setInputFileName(options.inputFileName2, options.format)
+ − 120 remover.setOutputFileName(options.outputFileName2)
+ − 121 remover.forbiddenNames = removedNames
+ − 122 remover.parse()
+ − 123 newRemovedNames = remover.removedNames
+ − 124 if options.log:
+ − 125 for name in newRemovedNames:
+ − 126 logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName2))
+ − 127
+ − 128 remover = EmptySequenceRemover(options.verbosity)
+ − 129 remover.setInputFileName(options.inputFileName, options.format)
+ − 130 remover.setOutputFileName(options.outputFileName)
+ − 131 remover.forbiddenNames = newRemovedNames
+ − 132 remover.parse()
+ − 133
+ − 134 nbRemoved = len(removedNames.keys()) + len(newRemovedNames.keys())
+ − 135 print "%d over %d sequences are empty (%.2f%%)." % (nbRemoved, nbSequences, float(nbRemoved) / nbSequences * 100)
