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

Added simple test BED file.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
# 
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"""Compare overlap of a transcript list and list of read, and get some info depending on the coverage"""

import os
from optparse import OptionParser
from commons.core.parsing.SequenceListParser import *
from commons.core.writer.Gff3Writer import *
from SMART.Java.Python.mySql.MySqlConnection import *
from SMART.Java.Python.structure.TranscriptListsComparator import *
from SMART.Java.Python.misc.RPlotter import *
from SMART.Java.Python.misc.Progress import *


if __name__ == "__main__":
    
    # parse command line
    description = "Get Info per Coverage v1.0.1: Get a list of information clustered by the density of the coverage on a genome. [Category: Personnal]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input1",                     dest="inputFileName1", action="store",                                         type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format1",                    dest="format1",                action="store",                                         type="string", help="format of file 1 [compulsory] [format: transcript file format]")
    parser.add_option("-j", "--input2",                     dest="inputFileName2", action="store",                                         type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
    parser.add_option("-g", "--format2",                    dest="format2",                action="store",                                         type="string", help="format of file 2 [compulsory] [format: transcript file format]")
    parser.add_option("-o", "--output",                     dest="output",                 action="store",            default=None,    type="string", help="output file [compulsory] [format: output file in TXT format]")
    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",            default=None,    type="string", help="write a log file [format: bool] [default: false]")
    (options, args) = parser.parse_args()

    logHandle = None
    if options.log != None:
        logHandle = open(options.log, "w")
        
    transcriptContainer1 = TranscriptContainer(options.inputFileName1, options.format1, options.verbosity)
    transcriptContainer2 = TranscriptContainer(options.inputFileName2, options.format2, options.verbosity)
    
    transcriptListComparator = TranscriptListsComparator(logHandle, options.verbosity)
    transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, 10)
    transcriptListComparator.getColinearOnly(True)
    transcriptListComparator.computeOddsPerTranscript(True)
    transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1)
    transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2)
    transcriptListComparator.compareTranscriptList()
    transcriptTables = transcriptListComparator.getOutputTables()
    
    sizesWithIntrons                     = {}
    sizesWithoutIntrons                = {}
    nbExons                                        = {}
    averageSizesWithIntrons        = {}
    averageSizesWithoutIntrons = {}
    averageNbExons                         = {}
    sumSizesWithIntrons                = {}
    sumSizesWithoutIntrons         = {}
    sumSizesNbExons                        = {}
    coverages                                    = transcriptListComparator.getOddsPerTranscript()

    progress = Progress(transcriptContainer2.getNbTranscripts(), "Reading transcript file again", options.verbosity)
    for transcript in transcriptContainer2.getIterator():
        if transcript.name in coverages:
            if transcript.getSizeWithIntrons() not in averageSizesWithIntrons:
                averageSizesWithIntrons[transcript.getSizeWithIntrons()] = coverages[transcript.name]
            else:
                averageSizesWithIntrons[transcript.getSizeWithIntrons()] += coverages[transcript.name]
            if transcript.getSizeWithIntrons() not in sumSizesWithIntrons:
                sumSizesWithIntrons[transcript.getSizeWithIntrons()] = 1
            else:
                sumSizesWithIntrons[transcript.getSizeWithIntrons()] += 1
            if transcript.getSize() not in averageSizesWithoutIntrons:
                averageSizesWithoutIntrons[transcript.getSize()] = coverages[transcript.name]
            else:
                averageSizesWithoutIntrons[transcript.getSize()] += coverages[transcript.name]
            if transcript.getSize() not in sumSizesWithoutIntrons:
                sumSizesWithoutIntrons[transcript.getSize()] = 1
            else:
                sumSizesWithoutIntrons[transcript.getSize()] += 1
            if transcript.getNbExons() not in averageNbExons:
                averageNbExons[transcript.getNbExons()] = coverages[transcript.name]
            else:
                averageNbExons[transcript.getNbExons()] += coverages[transcript.name]
            if transcript.getNbExons() not in sumSizesNbExons:
                sumSizesNbExons[transcript.getNbExons()] = 1
            else:
                sumSizesNbExons[transcript.getNbExons()] += 1
            sizesWithIntrons[transcript.name]        = (transcript.getSizeWithIntrons(), coverages[transcript.name])
            sizesWithoutIntrons[transcript.name] = (transcript.getSize(), coverages[transcript.name])
            nbExons[transcript.name]                         = (transcript.getNbExons(), coverages[transcript.name])
        progress.inc()
    progress.done()
        
    plotterSizeWithIntrons = RPlotter("%sWithIntrons.png" % (options.output), options.verbosity)
    plotterSizeWithIntrons.setPoints(True)
    plotterSizeWithIntrons.setMaximumX(10000)
    plotterSizeWithIntrons.setMaximumY(1000)    
    plotterSizeWithIntrons.setLog("y")
    plotterSizeWithIntrons.addLine(sizesWithIntrons)
    plotterSizeWithIntrons.plot()
    
    plotterSizeWithoutIntrons = RPlotter("%sWithoutIntrons.png" % (options.output), options.verbosity)
    plotterSizeWithoutIntrons.setPoints(True)
    plotterSizeWithoutIntrons.setMaximumX(10000)    
    plotterSizeWithoutIntrons.setMaximumY(1000)
    plotterSizeWithoutIntrons.setLog("y")
    plotterSizeWithoutIntrons.addLine(sizesWithoutIntrons)
    plotterSizeWithoutIntrons.plot()
    
    plotterNbExons = RPlotter("%sNbExons.png" % (options.output), options.verbosity)
    plotterNbExons.setPoints(True)
    plotterNbExons.addLine(nbExons)
    plotterNbExons.plot()
    
    for element in averageSizesWithIntrons:
        averageSizesWithIntrons[element] = int(float(averageSizesWithIntrons[element]) / sumSizesWithIntrons[element])
    plotterAverageSizeWithIntrons = RPlotter("%sAverageWithIntrons.png" % (options.output), options.verbosity)
    plotterAverageSizeWithIntrons.setMaximumX(10000)
    plotterAverageSizeWithIntrons.setMaximumY(1000)    
    plotterAverageSizeWithIntrons.setLog("y")
    plotterAverageSizeWithIntrons.addLine(averageSizesWithIntrons)
    plotterAverageSizeWithIntrons.plot()
    print "min/avg/med/max sizes with introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithIntrons)

    for element in averageSizesWithoutIntrons:
        averageSizesWithoutIntrons[element] = int(float(averageSizesWithoutIntrons[element]) / sumSizesWithoutIntrons[element])
    plotterAverageSizeWithoutIntrons = RPlotter("%sAverageWithoutIntrons.png" % (options.output), options.verbosity)
    plotterAverageSizeWithoutIntrons.setMaximumX(10000)
    plotterAverageSizeWithoutIntrons.setMaximumY(1000)    
    plotterAverageSizeWithoutIntrons.setLog("y")
    plotterAverageSizeWithoutIntrons.addLine(averageSizesWithoutIntrons)
    plotterAverageSizeWithoutIntrons.plot()
    print "min/avg/med/max sizes without introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithoutIntrons)

    for element in averageNbExons:
        averageNbExons[element] = int(float(averageNbExons[element]) / sumSizesNbExons[element])
    plotterAverageNbExons = RPlotter("%sAverageNbExons.png" % (options.output), options.verbosity)
    plotterAverageNbExons.addLine(averageNbExons)
    plotterAverageNbExons.plot()
    print "min/avg/med/max # exons: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageNbExons)

    if options.log:
        logHandle.close()