Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/restrictFromSize.py @ 67:f4de72c80eac draft
Uploaded
author | m-zytnicki |
---|---|
date | Mon, 16 Nov 2015 11:59:35 -0500 |
parents | 769e306b7933 |
children |
line wrap: on
line source
#! /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. # """Get the size distribution of a Fasta / BED file""" import os from optparse import OptionParser from commons.core.parsing.FastaParser import * from commons.core.parsing.FastqParser import * from SMART.Java.Python.structure.TranscriptContainer import * from commons.core.writer.TranscriptWriter import * from commons.core.writer.FastaWriter import * from commons.core.writer.FastqWriter import * from SMART.Java.Python.misc.Progress import * from SMART.Java.Python.misc.RPlotter import * if __name__ == "__main__": # parse command line description = "Restrict from Size v1.0.1: Select the elements of a list of sequences or transcripts with a given size. [Category: Data Selection]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript or sequence format given by -f]") parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: sequence or transcript file format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in transcript or sequence format given by -f]") parser.add_option("-m", "--minSize", dest="minSize", action="store", default=None, type="int", help="minimum size [format: int]") parser.add_option("-M", "--maxSize", dest="maxSize", action="store", default=None, type="int", help="maximum size [format: int]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") 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.format == "fasta": parser = FastaParser(options.inputFileName, options.verbosity) writer = FastaWriter(options.outputFileName, options.verbosity) elif options.format == "fastq": parser = FastqParser(options.inputFileName, options.verbosity) writer = FastqWriter(options.outputFileName, options.verbosity) else: parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity) writer = TranscriptWriter(options.outputFileName, options.format, options.verbosity) # treat items nbItems = parser.getNbItems() progress = Progress(nbItems, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity) nbKept = 0 nbRead = 0 nbClKept = 0 nbClRead = 0 for item in parser.getIterator(): size = item.getSize() nb = 1 if options.format in ("fasta", "fastq") or "nbElements" not in item.getTagNames() else float(item.getTagValue("nbElements")) nbRead += nb nbClRead += 1 if (options.minSize == None or options.minSize <= size) and (options.maxSize == None or options.maxSize >= size): writer.addElement(item) nbKept += nb nbClKept += 1 progress.inc() progress.done() writer.write() print "%d items, %d kept (%.2f%%)" % (nbRead, nbKept, 0 if nbItems == 0 else float(nbKept) / nbItems * 100) if nbKept != nbClKept or nbRead != nbClRead: print "%d clusters, %d kept (%.2f%%)" % (nbClRead, nbClKept, 0 if nbClRead == 0 else float(nbClKept) / nbClRead * 100)