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

Added simple test BED file.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
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"""
Merge sliding windows of two different clusterings
"""

import sys
import re
import os
from optparse import OptionParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from commons.core.writer.Gff3Writer import Gff3Writer
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.structure.Transcript import Transcript

class MergeSlidingWindowsClusters(object):
    """
    Merge the ouptput of several sets of sliding windows
    """

    def __init__(self, verbosity = 0):
        self.verbosity     = verbosity
        self.inputs        = []
        self.outputData    = {}
        self.nbData        = 0
        self.nbWrittenData = 0
        self.chromosomes   = []
        self.writer        = None

    def __del__(self):
        if self.writer != None:
            self.writer.close()

    def addInput(self, fileName, fileFormat):
        self.inputs.append(TranscriptContainer(fileName, fileFormat, self.verbosity))
        self.chromosomes = list(set(self.chromosomes).union(set(self.inputs[-1].getChromosomes())))

    def setOutput(self, fileName):
        self.writer = Gff3Writer(fileName, self.verbosity)

    def readInput(self, i, chromosome):
        progress = Progress(self.inputs[i].getNbTranscripts(), "Reading file #%d -- chromosome %s" % (i+1, chromosome), self.verbosity)
        for transcript in self.inputs[i].getIterator():
            progress.inc()
            if chromosome != transcript.getChromosome(): continue
            start     = transcript.getStart()
            end       = transcript.getEnd()
            direction = transcript.getDirection()
            tags      = transcript.tags
            if chromosome not in self.outputData:
                self.outputData[chromosome] = {}
            if direction not in self.outputData[chromosome]:
                self.outputData[chromosome][direction] = {}
            if start not in self.outputData[chromosome][direction]:
                self.outputData[chromosome][direction][start] = {}
            if end in self.outputData[chromosome][direction][start]:
                ends = self.outputData[chromosome][direction][start].keys()
                if ends[0] != end:
                    sys.exit("Error! Two regions starting at %d end are not consistent (%d and %d) in %s on strand %d" % (start, end, ends[0], chromosome, direction))
                self.outputData[chromosome][direction][start][end].update(tags)
            else:
                self.outputData[chromosome][direction][start][end] = tags
                self.nbData += 1
        progress.done()


    def writeOutput(self, chromosome):
        progress = Progress(self.nbData - self.nbWrittenData, "Writing output for chromosome %s" % (chromosome), self.verbosity)
        for direction in self.outputData[chromosome]:
            for start in self.outputData[chromosome][direction]:
                for end in self.outputData[chromosome][direction][start]:
                    transcript = Transcript()
                    transcript.setChromosome(chromosome)
                    transcript.setStart(start)
                    transcript.setEnd(end)
                    transcript.setDirection(direction)
                    transcript.tags = self.outputData[chromosome][direction][start][end]
                    transcript.setName("region_%d" % (self.nbWrittenData + 1))
                    tags = transcript.getTagNames()
                    for tag in tags:
                        if tag.startswith("Name_") or tag.startswith("ID_"):
                            del transcript.tags[tag]
                    self.nbWrittenData += 1
                    self.writer.addTranscript(transcript)
                    progress.inc()
        self.writer.write()
        progress.done()
        self.outputData = {}

    def merge(self):
        for chromosome in self.chromosomes:
            for i, input in enumerate(self.inputs):
                self.readInput(i, chromosome)
            self.writeOutput(chromosome)
        self.writer.close()


if __name__ == "__main__":
    
    # parse command line
    description = "Merge Sliding Windows Clusters v1.0.2: Merge two files containing the results of a sliding windows clustering. [Category: Sliding Windows]"

    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", "--inputFormat1", dest="inputFormat1",   action="store",                     type="string", help="format of the input 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", "--inputFormat2", dest="inputFormat2",   action="store",                     type="string", help="format of the input file 2 [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("-v", "--verbosity",    dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    merger = MergeSlidingWindowsClusters(options.verbosity)
    merger.addInput(options.inputFileName1, options.inputFormat1)
    merger.addInput(options.inputFileName2, options.inputFormat2)
    merger.setOutput(options.outputFileName)
    merger.merge()