annotate smart_toolShed/SMART/Java/Python/adaptorStripper.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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# "http://www.cecill.info".
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"""Remove adaptors"""

import os
from optparse import OptionParser
from SMART.Java.Python.structure.Sequence import Sequence
from SMART.Java.Python.structure.SequenceList import SequenceList
from commons.core.parsing.FastaParser import FastaParser
from commons.core.writer.FastaWriter import FastaWriter
from SMART.Java.Python.misc.Progress import Progress


def distance (string1, string2):
    if len(string1) != len(string2):
        return None
    distance = 0
    for i in range(0, len(string1)):
        if string1[i] != string2[i]:
            distance += 1
    return distance



if __name__ == "__main__":
    nbRemaining = 0
    
    # parse command line
    description = "Adaptor Stripper v1.0.1: Remove the adaptor of a list of reads. [Category: Personnal]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",         dest="inputFileName",      action="store",                     type="string", help="input file [compulsory] [format: file in FASTA format]")
    parser.add_option("-o", "--output",        dest="outputFileName",     action="store",                     type="string", help="output file [compulsory] [format: output file in FASTA format]")
    parser.add_option("-5", "--5primeAdaptor", dest="fivePrimeAdaptor",   action="store",                     type="string", help="five prime adaptor [format: string]")
    parser.add_option("-3", "--3primeAdaptor", dest="threePrimeAdaptor",  action="store",                     type="string", help="three prime adaptor [format: string]")
    parser.add_option("-d", "--5primeDist",    dest="fivePrimeDistance",  action="store",      default=3,     type="int",    help="five prime distance [format: int] [default: 3]")
    parser.add_option("-e", "--3primeDist",    dest="threePrimeDistance", action="store",      default=3,     type="int",    help="three prime distance [format: int [default: 3]]")
    parser.add_option("-m", "--3primeSize",    dest="threePrimeSize",     action="store",      default=10,    type="int",    help="three prime size [format: int] [default: 10]")
    parser.add_option("-v", "--verbosity",     dest="verbosity",          action="store",      default=1,     type="int",    help="trace level [format: int] [default: 1]")
    parser.add_option("-l", "--log",           dest="log",                action="store_true", default=False,                help="write a log file [format: bool] [default: false]")
    (options, args) = parser.parse_args()

    if options.log:
        logHandle = open(options.outputFileName + ".log", "w")


    writer         = FastaWriter(options.outputFileName + ".fas", options.verbosity)
    sequenceParser = FastaParser(options.inputFileName, options.verbosity)
    nbSequences    = sequenceParser.getNbSequences()

    # treat sequences
    progress = Progress(sequenceParser.getNbSequences(), "Analyzing " + options.inputFileName, options.verbosity)
    for sequence in sequenceParser.getIterator():
        fivePrimeAdaptor  = sequence.getSequence()[0:len(options.fivePrimeAdaptor)]
        threePrimeAdaptor = sequence.getSequence()[len(sequence.sequence)-len(options.threePrimeAdaptor):]

        # check 5' adaptor
        fivePrimeDistance = distance(fivePrimeAdaptor, options.fivePrimeAdaptor)
        # check 3' adaptor
        threePrimeDistance = len(threePrimeAdaptor)
        for i in range(options.threePrimeSize, len(threePrimeAdaptor)+1):
            threePrimeDistance = min(threePrimeDistance, distance(threePrimeAdaptor[-i:], options.threePrimeAdaptor[:i]))

        # sort candidates
        if fivePrimeDistance > options.fivePrimeDistance:
            if options.log:
                logHandle.write("Sequence %s does not start with the right adaptor (%s != %s)\n" % (sequence.getSequence(), fivePrimeAdaptor, options.fivePrimeAdaptor))
        elif threePrimeDistance > options.threePrimeDistance:
            if options.log:
                logHandle.write("Sequence %s does not end with the right adaptor (%s != %s)\n" % (sequence.getSequence(), threePrimeAdaptor, options.threePrimeAdaptor))
        else:
            nbRemaining += 1
            sequence.setSequence(sequence.getSequence()[len(options.fivePrimeAdaptor):len(sequence.getSequence())-len(options.threePrimeAdaptor)])
            writer.addSequence(sequence)

        progress.inc()

    progress.done()

    if options.log:
        logHandle.close()

    writer.write()

    print "kept %i over %i (%.f%%)" % (nbRemaining, nbSequences, float(nbRemaining) / nbSequences * 100)