view smart_toolShed/SMART/Java/Python/ @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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#! /usr/bin/env python
# Copyright INRA-URGI 2009-2010
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Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.

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

if __name__ == "__main__":
    # parse command line
    description = "Get WIG Data v1.0.2: Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome). [Category: WIG Tools]"

    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", "--inputFormat", dest="inputFormat",    action="store",                     type="string", help="format of the input file [compulsory] [format: transcript file format]")
    parser.add_option("-w", "--wig",         dest="wig",            action="store",                     type="string", help="wig file name [compulsory] [format: file in WIG format]")    
    parser.add_option("-d", "--distance",    dest="distance",       action="store",      default=1000,  type="int",    help="distance around position [compulsory] [format: int] [default: 1000]")    
    parser.add_option("-s", "--strands",     dest="strands",        action="store_true", default=False,                help="consider both strands separately [format: boolean] [default: False]")    
    parser.add_option("-o", "--output",      dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in PNG format]")
    parser.add_option("-a", "--default",     dest="defaultValue",   action="store",      default=0.0,   type="float",  help="default value (when value is NA) [default: 0.0] [format: float]")
    parser.add_option("-l", "--log",         dest="log",            action="store_true", default=False,                help="use log scale for y-axis [format: boolean] [default: False]")
    parser.add_option("-k", "--keep",        dest="keep",           action="store_true", default=False,                help="keep temporary files [format: boolean] [default: False]")
    parser.add_option("-v", "--verbosity",   dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    # create parsers and writers
    transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
    wigParser        = WigParser(options.wig)
    # allocate data
    strands = (1, -1) if options.strands else (1, )
    values    = {}
    for strand in strands:
        values[strand] = dict([(i, 0.0) for i in range(-options.distance, options.distance+1)])

    # read transcripts
    progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
    for transcript in transcriptParser.getIterator():
        theseValues = transcript.extractWigData(wigParser)
        if len(strands) == 1:
            theseValues = {1: theseValues}
        for strand in strands:
            if len(theseValues[strand]) < 2 * options.distance + 1:
                theseValues[strand] = [options.defaultValue] * (2 * options.distance + 1 - len(theseValues[strand])) + theseValues[strand]
            if len(theseValues[strand]) != 2 * options.distance + 1:
				raise Exception("Got something wrong with the size of the WIG data concerning %s: %d found instead of %d" % (transcript, len(theseValues[strand]), 2 * options.distance + 1))
            for i in range(-options.distance, options.distance+1):
                values[strand][i] += theseValues[strand][i + options.distance]

    for strand in strands:
        for i in range(-options.distance, options.distance+1):
            values[strand][i] /= transcriptParser.getNbTranscripts() * strand

    # draw plot
    plotter = RPlotter(options.outputFileName, options.verbosity, options.keep)
    for strand in strands:
    if options.log: