annotate SMART/Java/Python/adaptorStripper.py @ 71:d96f6c9a39e0 draft default tip

Removed pyc files.

#! /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
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
# 
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
# 
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
# 
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
#
"""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)