annotate smart_toolShed/SMART/Java/Python/trimAdaptor.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /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
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"""Trim the sequences from a 5' adaptor"""

import sys
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 Adaptor v1.0.1: Remove the 3' adaptor 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("-a", "--adaptor",   dest="adaptor",        action="store",               type="string", help="adaptor [compulsory] [format: string]")
    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("-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]")
    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    minSize = 2

    if options.format == "fasta":
        parser = FastaParser(options.inputFileName, options.verbosity)
    elif options.format == "fastq":
        parser = FastqParser(options.inputFileName, options.verbosity)
    else:
        sys.exit("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:
        sys.exit("Cannot handle files with '%s' format." % (options.format))

    writerNoAdaptor = None
    if options.noAdaptor != None:
        if options.format == "fasta":
            writerNoAdaptor = FastaWriter(options.noAdaptor, options.verbosity)
        elif options.format == "fastq":
            writerNoAdaptor = FastqWriter(options.noAdaptor, options.verbosity)
        else:
            sys.exit("Cannot handle files with '%s' format." % (options.format))

    nbFound = 0
        
    progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
    for sequence in parser.getIterator():
        progress.inc()
        nucleotides = sequence.getSequence()
        found       = False
        for i in range(len(nucleotides) - minSize):
            nucleotidesPart = nucleotides[i:]
            adaptorPart     = options.adaptor if len(nucleotidesPart) >= len(options.adaptor) else options.adaptor[:len(nucleotidesPart)]
            nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)]
            if Utils.getHammingDistance(adaptorPart, nucleotidesPart) <= int(options.errors / 100.0 * len(adaptorPart)):
                nbFound += 1
                sequence.shrinkToFirstNucleotides(i)
                writer.addSequence(sequence)
                found = True
                break
        if not found:
            writer.addSequence(sequence)
            if writerNoAdaptor != None:
                writerNoAdaptor.addSequence(sequence)
    progress.done()

    print "%d sequences with adaptors on %d (%.2f%%)" % (nbFound, parser.getNbSequences(), float(nbFound) / parser.getNbSequences() * 100)