annotate SMART/Java/Python/getDistribution.py @ 22:1e3f2c2657a3

Deleted selected 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".
# 
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# 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
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# software by the user in light of its specific status of free software,
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"""Get the repartition of some elements in a chromosomes"""

import os
from optparse import OptionParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.structure.Transcript import Transcript
from commons.core.writer.Gff3Writer import Gff3Writer
from SMART.Java.Python.misc.RPlotter import RPlotter
from SMART.Java.Python.misc.Progress import Progress
from math import *

def divideKeyDict(dictionary, ratio):
    return dict([(key / ratio, dictionary[key]) for key in dictionary])


def setTranscript(chromosome, direction, start, end, name, value):
    transcript = Transcript()
    transcript.setChromosome(chromosome)
    transcript.setDirection(direction)
    transcript.setStart(start)
    transcript.setEnd(end)
    transcript.setName(name)
    transcript.setTagValue("nbElements", value)
    return transcript



if __name__ == "__main__":
    
    magnifyingFactor = 1000
    
    # parse command line
    description = "Get Distribution v1.0.1: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",       dest="inputFileName",     action="store",                           type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format",      dest="format",            action="store",                           type="string", help="format of the input file [compulsory] [format: transcript file format]")
    parser.add_option("-o", "--output",      dest="outputFileName",    action="store",                           type="string", help="output file [compulsory] [format: output file in GFF3 format]")
    parser.add_option("-r", "--reference",   dest="referenceFileName", action="store",      default=None,        type="string", help="file containing the genome [compulsory] [format: file in FASTA format]")
    parser.add_option("-n", "--nbBins",      dest="nbBins",            action="store",      default=1000,        type="int",    help="number of bins [default: 1000] [format: int]")
    parser.add_option("-2", "--bothStrands", dest="bothStrands",       action="store_true", default=False,                      help="plot one curve per strand [format: bool] [default: false]")
    parser.add_option("-w", "--raw",         dest="raw",               action="store_true", default=False,                      help="plot raw number of occurrences instead of density [format: bool] [default: false]")
    parser.add_option("-x", "--csv",         dest="csv",               action="store_true", default=False,                      help="write a .csv file [format: bool]")
    parser.add_option("-c", "--chromosome",  dest="chromosome",        action="store",      default=None,        type="string", help="plot only a chromosome [format: string]")
    parser.add_option("-s", "--start",       dest="start",             action="store",      default=None,        type="int",    help="start from a given region [format: int]")
    parser.add_option("-e", "--end",         dest="end",               action="store",      default=None,        type="int",    help="end from a given region [format: int]")
    parser.add_option("-y", "--yMin",        dest="yMin",              action="store",      default=None,        type="int",    help="minimum value on the y-axis to plot [format: int]")
    parser.add_option("-Y", "--yMax",        dest="yMax",              action="store",      default=None,        type="int",    help="maximum value on the y-axis to plot [format: int]")
    parser.add_option("-g", "--gff",         dest="gff",               action="store_true", default=False,                      help="also write GFF3 file [format: bool] [default: false]")
    parser.add_option("-H", "--height",      dest="height",            action="store",      default=None,        type="int",    help="height of the graphics [format: int] [default: 300]")
    parser.add_option("-W", "--width",       dest="width",             action="store",      default=None,        type="int",    help="width of the graphics [format: int] [default: 1000]")
    parser.add_option("-v", "--verbosity",   dest="verbosity",         action="store",      default=1,           type="int",    help="trace level [default: 1] [format: int]")
    parser.add_option("-l", "--log",         dest="log",               action="store_true", default=False,                      help="write a log file [format: bool]")
    parser.add_option("-D", "--directory",   dest="working_Dir",       action="store",      default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
    (options, args) = parser.parse_args()

    sizes = {}
    if options.referenceFileName != None:
        # get the sizes of the chromosomes
        referenceHandle = open(options.referenceFileName)
        name            = None
        size            = 0
        maxSize         = 0
        for line in referenceHandle:
            line = line.strip()
            if line == "": continue
            if line[0] == ">":
                if name != None:
                    if options.verbosity > 10:
                        print name
                    sizes[name] = size
                    maxSize     = max(maxSize, size)
                    size        = 0
                name = line[1:]
            else:
                size += len(line)
        sizes[name] = size
        maxSize     = max(maxSize, size)
        if options.verbosity > 1:
            print "done"
        start = 0
        end   = maxSize
    else:
        if options.chromosome == None or options.start == None or options.end == None:
            raise Exception("Missing chromosome or start and end positions, or reference file")
        maxSize                   = options.end
        sizes[options.chromosome] = options.end
        start                     = options.start
        end                       = options.end

    
    tmp1      = int(maxSize / float(options.nbBins))
    tmp2      = 10 ** (len("%d" % (tmp1))-2)
    sliceSize = int((tmp1 / tmp2) * tmp2)
    
    bins      = dict()
    binsPlus  = dict()
    binsMinus = dict()
    for chromosome in sizes:
        bins[chromosome]      = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
        binsPlus[chromosome]  = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
        binsMinus[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])

    parser   = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
    progress = Progress(parser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
    maxSlice = 0
    # count the number of reads
    for transcript in parser.getIterator():
        if options.chromosome == None or (transcript.getChromosome() == options.chromosome and transcript.getStart() >= start and transcript.getStart() <= end):
            if transcript.getDirection() == 1:
                binsPlus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
            else:
                binsMinus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
            bins[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
            maxSlice = max(maxSlice, transcript.getStart() / sliceSize)
        progress.inc()
    progress.done()

    # compute densities
    densityPlus = dict()
    for chromosome in bins:
        densityPlus[chromosome] = dict([(bin, 0) for bin in binsPlus[chromosome]])
        for bin in binsPlus[chromosome]:
            densityPlus[chromosome][bin] = float(binsPlus[chromosome][bin]) / sliceSize * magnifyingFactor
        # correct densities for first and last bins
        if start % sliceSize != 0:
            densityPlus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
        if sizes[chromosome] % sliceSize != 0:
            densityPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
    densityMinus = dict()
    for chromosome in binsMinus:
        densityMinus[chromosome] = dict([(bin, 0) for bin in binsMinus[chromosome]])
        for bin in binsMinus[chromosome]:
            densityMinus[chromosome][bin] = float(binsMinus[chromosome][bin]) / sliceSize * magnifyingFactor
        # correct densities for first and last bins
        if start % sliceSize != 0:
            densityMinus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
        if sizes[chromosome] % sliceSize != 0:
            densityMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
    density = dict()
    for chromosome in bins:
        density[chromosome] = dict([(bin, 0) for bin in bins[chromosome]])
        for bin in bins[chromosome]:
            density[chromosome][bin] = densityPlus[chromosome][bin] + densityMinus[chromosome][bin]

    for chromosome in densityMinus:
        for bin in densityMinus[chromosome]:
            densityMinus[chromosome][bin] *= -1
        for bin in binsMinus[chromosome]:
            binsMinus[chromosome][bin] *= -1

    for chromosome in density:
        maxX = max(bins[chromosome].keys())
        if maxX <= 1000:
            unit  = "nt."
            ratio = 1.0
        elif maxX <= 1000000:
            unit  = "kb"
            ratio = 1000.0
        else:
            unit  = "Mb"
            ratio = 1000000.0
        outputFileName = "%s_%s" % (options.outputFileName, chromosome)
        if options.start != None and options.end != None:
            outputFileName += ":%d-%d" % (options.start, options.end)
        outputFileName += ".png"
        plotter = RPlotter(outputFileName, options.verbosity)
        plotter.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
        plotter.setYLabel("# reads")
        if options.bothStrands:
            plotter.setImageSize(1000, 300)
        else:
            plotter.setImageSize(1000, 200)
        if options.height != None:
            plotter.setHeight(options.height)
        if options.width != None:
            plotter.setWidth(options.width)
        if options.yMax != None:
            plotter.setMinimumY(options.yMin)
        if options.yMax != None:
            plotter.setMaximumY(options.yMax)
        if options.bothStrands :
            if options.raw:
                plotter.addLine(divideKeyDict(binsPlus[chromosome], ratio))
            else:
                plotter.addLine(divideKeyDict(densityPlus[chromosome], ratio))
            if options.raw:
                plotter.addLine(divideKeyDict(binsMinus[chromosome], ratio))
            else:
                plotter.addLine(divideKeyDict(densityMinus[chromosome], ratio))
        else:
            if options.raw:
                plotter.addLine(divideKeyDict(bins[chromosome], ratio))
            else:
                plotter.addLine(divideKeyDict(density[chromosome], ratio))
        plotter.plot()
        
    if options.csv:
        outputFileName = "%s" % (options.outputFileName)
        if options.chromosome != None:
            outputFileName += "_%s" % (options.chromosome)
        if options.start != None and options.end != None:
            outputFileName += ":%d-%d" % (options.start, options.end)
        outputFileName += ".csv"
        csvHandle = open(outputFileName, "w")
        for slice in range(start / sliceSize, maxSlice + 1):
            csvHandle.write(";%d-%d" % (slice * sliceSize + 1, (slice+1) * sliceSize))
        csvHandle.write("\n")
        if options.bothStrands:
            for chromosome in densityPlus:
                if len(densityPlus[chromosome]) > 0:
                    csvHandle.write("%s [+]" % (chromosome))
                    for slice in sorted(densityPlus[chromosome].keys()):
                        csvHandle.write(";%.2f" % (densityPlus[chromosome][slice]))
                    csvHandle.write("\n")            
                if len(densityMinus[chromosome]) > 0:
                    csvHandle.write("%s [-]" % (chromosome))
                    for slice in sorted(densityPlus[chromosome].keys()):
                        csvHandle.write(";%.2f" % (-densityMinus[chromosome][slice]))
                    csvHandle.write("\n")            
        else:
            for chromosome in density:
                if len(density[chromosome]) > 0:
                    csvHandle.write(chromosome)
                    for slice in sorted(density[chromosome].keys()):
                        csvHandle.write(";%.2f" % (density[chromosome][slice]))
                    csvHandle.write("\n")
        csvHandle.close()
             
    if options.gff:
        chromosome = "" if options.chromosome == None                         else options.chromosome.capitalize()
        start      = "" if options.start      == None                         else "%d" % (options.start)
        end        = "" if options.end        == None                         else "%d" % (options.end)
        link1      = "" if options.start      == None and options.end == None else ":"
        link2      = "" if options.start      == None and options.end == None else "-"
        writer     = Gff3Writer("%s%s%s%s%s.gff3" % (options.outputFileName, link1, start, link2, end), options.verbosity)
        cpt = 1
        if options.raw:
            valuesPlus  = binsPlus
            valuesMinus = binsMinus
            values      = bins
        else:
            valuesPlus  = densityPlus
            valuesMinus = densityMinus
            values      = density
        if options.bothStrands:
            for chromosome in values:
                for slice in valuesPlus[chromosome]:
                    writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), valuesPlus[chromosome][slice]))
                    cpt += 1
                for slice in valuesMinus[chromosome]:
                    writer.addTranscript(setTranscript(chromosome, -1, slice, slice + sliceSize, "region%d" % (cpt), - valuesMinus[chromosome][slice]))
                    cpt += 1
        else:
            for chromosome in values:
                for slice in values[chromosome]:
                    writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), values[chromosome][slice]))
                    cpt += 1
        writer.write()