annotate SMART/Java/Python/restrictSequenceList.py @ 62:8c42a6d7ffd4

Added simple test BED file.

#! /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".
# 
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# modify and redistribute granted by the license, users are provided only
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"""Restrict a sequence list with some names"""

from optparse import OptionParser
from commons.core.parsing.ParserChooser import ParserChooser
from commons.core.writer.WriterChooser import WriterChooser
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc import Utils

class RestrictSequenceList(object):

    def __init__(self, verbosity):
        self.verbosity = verbosity
        self.exclude   = False

    def setInputFileName(self, fileName, format):
        chooser = ParserChooser(self.verbosity)
        chooser.findFormat(format)
        self.parser = chooser.getParser(fileName)

    def setExclusion(self, boolean):
        self.exclude = boolean

    def setOutputFileName(self, fileName, format):
        chooser = WriterChooser(self.verbosity)
        chooser.findFormat(format)
        self.writer = chooser.getWriter(fileName)

    def setNamesFileName(self, fileName):
        self.namesFileName = fileName

    def _readNames(self):
        self.names = []
        handle = open(self.namesFileName)
        for name in handle:
            self.names.append(name.strip())
        handle.close()

    def _write(self):
        nbElements = self.parser.getNbItems()
        progress   = Progress(nbElements, "Parsing input file", self.verbosity)
        nbRead     = 0
        nbWritten  = 0
        for element in self.parser.getIterator():
            name    = element.getName()
            nbRead += 1
            if Utils.xor(name in self.names, self.exclude):
                self.writer.addElement(element)
                nbWritten += 1
            if name in self.names:
                self.names.remove(name)
            progress.inc()
        progress.done()
        if self.verbosity > 0:
            print "%d read" % (nbRead)
            print "%d written (%d%%)" % (nbWritten, 0 if nbRead == 0 else round(float(nbWritten) / nbRead * 100))
    
    def run(self):
        self._readNames()
        self._write()
        if self.names:
            print "Some names are not present in the file: %s" % ", ".join(self.names)
        


if __name__ == "__main__":
    
    description = "Restrict Sequence List v1.0.1: Keep the elements of a list of sequences whose name is mentionned in a given file. [Category: Data Selection]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",     dest="inputFile",  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",      default="fasta", type="string", help="format of the input and output files [compulsory] [format: sequence file format] [default: fasta]")
    parser.add_option("-n", "--name",      dest="names",      action="store",                       type="string", help="names of the transcripts [compulsory] [format: file in TXT format]")
    parser.add_option("-o", "--output",    dest="outputFile", action="store",                       type="string", help="output file [format: output file in sequence format given by -f]")
    parser.add_option("-x", "--exclude",   dest="exclude",    action="store_true", default=False,                  help="output all those whose name is NOT on the list [format: boolean]")
    parser.add_option("-v", "--verbosity", dest="verbosity",  action="store",      default=1,       type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    rsl = RestrictSequenceList(options.verbosity)
    rsl.setInputFileName(options.inputFile, options.format)
    rsl.setOutputFileName(options.outputFile, options.format)
    rsl.setNamesFileName(options.names)
    rsl.setExclusion(options.exclude)
    rsl.run()