annotate smart_toolShed/SMART/Java/Python/getDifference.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /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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"""Restrict a transcript list with some parameters (regions)"""

from optparse import OptionParser
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
from commons.core.writer.Gff3Writer import Gff3Writer
from commons.core.parsing.FastaParser import FastaParser
from SMART.Java.Python.misc.Progress import Progress

class DifferenceGetter(object):

    def __init__(self, verbosity):
        self.verbosity        = verbosity
        self.annotationParser = None
        self.referenceParser  = None
        self.sequenceParser   = None
        self.transcriptCount  = 1
        self.split            = False

    def createTranscript(self, chromosome, start, end):
        transcript = Transcript()
        transcript.setChromosome(chromosome)
        transcript.setDirection("+")
        transcript.setStart(start)
        transcript.setEnd(end)
        transcript.setName("region_%d" % self.transcriptCount)
        transcript.setTagValue("ID", "region_%d" % self.transcriptCount)
        self.transcriptCount += 1
        return transcript

    def setSplit(self, split):
        self.split = split

    def setAnnotationFile(self, fileName, format):
        if fileName != None:
            self.annotationParser = TranscriptContainer(fileName, format, self.verbosity)

    def setReferenceFile(self, fileName, format):
        if fileName != None:
            self.referenceParser = TranscriptContainer(fileName, format, self.verbosity)

    def setSequenceFile(self, fileName):
        if fileName != None:
            self.sequenceParser = FastaParser(fileName, self.verbosity)

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

    def initialize(self):
        self.presence = {}
        for chromosome in self.sequenceParser.getRegions():
            self.presence[chromosome] = [[1, self.sequenceParser.getSizeOfRegion(chromosome)]]

    def readTranscripts(self):
        nbTranscripts = self.annotationParser.getNbTranscripts()
        progress      = Progress(nbTranscripts, "Parsing annotation file" , self.verbosity)
        for transcript in self.annotationParser.getIterator():
            chromosome   = transcript.getChromosome()
            toBeDeleted  = []
            toBeAppended = []
            for i, element in enumerate(self.presence[chromosome]):
                start, end = element
                if start <= transcript.getEnd() and transcript.getStart() <= end:
                    toBeDeleted.append(i)
                    if start < transcript.getStart():
                        toBeAppended.append([start, transcript.getStart() - 1])
                    if end > transcript.getEnd():
                        toBeAppended.append([transcript.getEnd() + 1, end])
            for i in reversed(toBeDeleted):
                del self.presence[chromosome][i]
            self.presence[chromosome].extend(toBeAppended)
            progress.inc()
        progress.done()

    def writeOutput(self):
        for chromosome in self.presence:
            for element in self.presence[chromosome]:
                start, end = element
                self.writer.addTranscript(self.createTranscript(chromosome, start, end))
        self.writer.write()

    def compareToSequence(self):
        self.initialize()
        self.readTranscripts()
        self.writeOutput()

    def compareToAnnotation(self):
        transcriptListComparator = TranscriptListsComparator(None, self.verbosity)
        transcriptListComparator.setSplitDifference(self.split)
        transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, self.annotationParser)
        transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, self.referenceParser)
        transcriptListComparator.setOutputWriter(self.writer)
        transcriptListComparator.getDifferenceTranscriptList()

    def run(self):
        if self.referenceParser != None:
            self.compareToAnnotation()
        else:
            self.compareToSequence()


if __name__ == "__main__":
    
    # parse command line
    description = "Get Difference v1.0.1: Get all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level). [Category: Data Comparison]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input1",    dest="inputFileName1",   action="store",                     type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format1",   dest="format1",          action="store",                     type="string", help="format [compulsory] [format: transcript file format]")
    parser.add_option("-j", "--input2",    dest="inputFileName2",   action="store",      default=None,  type="string", help="reference file [format: file in transcript format given by -g]")
    parser.add_option("-g", "--format2",   dest="format2",          action="store",      default=None,  type="string", help="format of the reference file [format: transcript file format]")
    parser.add_option("-s", "--sequence",  dest="sequenceFileName", action="store",      default=None,  type="string", help="sequence file [format: file in FASTA format]")
    parser.add_option("-p", "--split",     dest="split",            action="store_true", default=False,                help="when comparing to a set of genomic coordinates, do not join [format: boolean] [default: False")
    parser.add_option("-o", "--output",    dest="outputFileName",   action="store",                     type="string", help="output file [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()

    getter = DifferenceGetter(options.verbosity)
    getter.setSplit(options.split)
    getter.setAnnotationFile(options.inputFileName1, options.format1)
    getter.setSequenceFile(options.sequenceFileName)
    getter.setReferenceFile(options.inputFileName2, options.format2)
    getter.setOutputFile(options.outputFileName)
    getter.run()