view SMART/Java/Python/ @ 71:d96f6c9a39e0 draft default tip

Removed pyc files.
author m-zytnicki
date Thu, 07 Apr 2016 09:25:18 -0400
parents 769e306b7933
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#! /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
# "".
# 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.

from optparse import OptionParser
from commons.core.parsing.FastaParser import FastaParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc.RPlotter import RPlotter
from SMART.Java.Python.misc.Utils import *

class GetGenomeCoverage(object):

    def __init__(self, verbosity = 1):
        self.verbosity       = verbosity
        self.inputContainer  = None
        self.referenceParser = None
        self.outputFileName  = None
        self.genomeSize      = None
        self.coverage        = {}
        self.distribution    = {}

    def setInputFile(self, fileName, format):
        self.inputContainer = TranscriptContainer(fileName, format, self.verbosity)

    def setOutputFile(self, fileName):
        self.outputFileName = fileName

    def setReference(self, fileName):
        self.referenceParser = FastaParser(fileName, self.verbosity)

    def getReferenceSizes(self):
        self.genomeSize = 0
        for chromosome in self.referenceParser.getRegions():
            self.genomeSize += self.referenceParser.getSizeOfRegion(chromosome)

    def getCoverage(self):
        progress = Progress(self.inputContainer.getNbTranscripts(), "Reading reads", self.verbosity)
        for transcript in self.inputContainer.getIterator():
            chromosome = transcript.getChromosome()
            if chromosome not in self.coverage:
                self.coverage[chromosome] = {}
            for exon in transcript.getExons():
                for pos in range(exon.getStart(), exon.getEnd() + 1):
                    if pos not in self.coverage[chromosome]:
                        self.coverage[chromosome][pos] = 1
                        self.coverage[chromosome][pos] += 1

    def getDistribution(self):
        nbNucleotides = sum([len(self.coverage[chromosome].keys()) for chromosome in self.coverage])
        progress      = Progress(nbNucleotides, "Building distribution", self.verbosity)
        for chromosome in self.coverage:
            for num in self.coverage[chromosome].values():
                if num not in self.distribution:
                    self.distribution[num] = 1
                    self.distribution[num] += 1
        self.distribution[0] = self.genomeSize - nbNucleotides

    def plotDistribution(self):
        plotter = RPlotter(self.outputFileName, self.verbosity)
        print "min/avg/med/max reads per base: %d/%.2f/%.1f/%d" % getMinAvgMedMax(self.distribution)

    def run(self):

if __name__ == "__main__":
    # parse command line
    description = "Plot Genome Coverage v1.0.1: Get the coverage of a genome. [Category: Personal]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",               type="string", help="reads file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format",    dest="format",         action="store",               type="string", help="format of file [compulsory] [format: transcript file format]")
    parser.add_option("-r", "--reference", dest="reference",      action="store",               type="string", help="sequences 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 PNG format]")
    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    getGenomeCoverage = GetGenomeCoverage(options.verbosity)
    getGenomeCoverage.setInputFile(options.inputFileName, options.format)