Python getListDefault 예제들

예제 #1

파일: vcf.py 프로젝트: MMesbahU/svviz

def parseInsertion(record, dataHub):
    altchars = set(record.alt.upper())
    breakpoint = utilities.Locus(record.chrom, record.start, record.end, "+")

    if altchars <= set("ACGTN"):
        insertSeq = record.alt.upper()

        variant = variants.Insertion(breakpoint, insertSeq, dataHub.alignDistance, dataHub.genome)
    elif "MEINFO" in record.info:
        meinfo = record.info["MEINFO"].split(",")
        meName = meinfo[0]
        meStart = utilities.getListDefault(meinfo, 1, 0)
        meEnd = utilities.getListDefault(meinfo, 2, 1e100)
        meStrand = utilities.getListDefault(meinfo, 3, "+")

        meLocus = utilities.Locus(meName, meStart, meEnd, meStrand)
        variant = variants.MobileElementInsertion(breakpoint, meLocus, getMobileElementFasta(dataHub), 
            dataHub.alignDistance, dataHub.genome)
    else:
        raise VCFParserError("Unknown insertion sequence")

    return variant

예제 #2

def parseInsertion(record, dataHub):
    altchars = set(record.alt.upper())
    breakpoint = utilities.Locus(record.chrom, record.start, record.end, "+")

    if altchars <= set("ACGTN"):
        insertSeq = record.alt.upper()

        variant = variants.Insertion(breakpoint, insertSeq,
                                     dataHub.alignDistance, dataHub.genome)
    elif "MEINFO" in record.info:
        meinfo = record.info["MEINFO"].split(",")
        meName = meinfo[0]
        meStart = utilities.getListDefault(meinfo, 1, 0)
        meEnd = utilities.getListDefault(meinfo, 2, 1e100)
        meStrand = utilities.getListDefault(meinfo, 3, "+")

        meLocus = utilities.Locus(meName, meStart, meEnd, meStrand)
        variant = variants.MobileElementInsertion(
            breakpoint, meLocus, getMobileElementFasta(dataHub),
            dataHub.alignDistance, dataHub.genome)
    else:
        raise VCFParserError("Unknown insertion sequence")

    return variant

예제 #3

파일: variants.py 프로젝트: apregier/svviz

def getVariant(dataHub):
    if dataHub.args.type.lower().startswith("del"):
        assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("del")
        chrom = dataHub.args.breakpoints[0]
        start = int(dataHub.args.breakpoints[1])
        end = int(dataHub.args.breakpoints[2])
        assert start < end
        variant = Deletion.from_breakpoints(chrom, start-1, end-1, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower() in ["ldel", "largedeletion"]:
        assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("ldel")
        chrom = dataHub.args.breakpoints[0]
        start = int(dataHub.args.breakpoints[1])
        end = int(dataHub.args.breakpoints[2])
        assert start < end
        variant = LargeDeletion.from_breakpoints(chrom, start-1, end-1, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("ins"):
        assert len(dataHub.args.breakpoints) in [3,4], getBreakpointFormatsStr("ins")
        chrom = dataHub.args.breakpoints[0]
        pos = int(dataHub.args.breakpoints[1])
        if len(dataHub.args.breakpoints) == 3:
            seq = dataHub.args.breakpoints[2]
            end = pos
        else:
            end = int(dataHub.args.breakpoints[2])
            seq = dataHub.args.breakpoints[3]
        variant = Insertion(Locus(chrom, pos, end, "+"), seq, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("inv"):
        assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("inv")
        chrom = dataHub.args.breakpoints[0]
        start = int(dataHub.args.breakpoints[1])
        end = int(dataHub.args.breakpoints[2])
        if dataHub.args.min_mapq is None:
            dataHub.args.min_mapq = -1
        variant = Inversion(Locus(chrom, start, end, "+"), dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("mei"):
        assert len(dataHub.args.breakpoints) >= 4, getBreakpointFormatsStr("mei")

        insertionBreakpoint = Locus(dataHub.args.breakpoints[1], dataHub.args.breakpoints[2], dataHub.args.breakpoints[2], "+")

        meName = dataHub.args.breakpoints[3]
        meStrand = getListDefault(dataHub.args.breakpoints, 4, "+")
        meStart = getListDefault(dataHub.args.breakpoints, 5, 0)
        meEnd = getListDefault(dataHub.args.breakpoints, 6, 1e100)

        meCoords = Locus(meName, meStart, meEnd, meStrand)
        meFasta = genomesource.FastaGenomeSource(dataHub.args.breakpoints[0])

        variant = MobileElementInsertion(insertionBreakpoint, meCoords, meFasta, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("tra"):
        assert len(dataHub.args.breakpoints) == 5, getBreakpointFormatsStr("tra")
        chrom1 = dataHub.args.breakpoints[0]
        start1 = int(dataHub.args.breakpoints[1])

        chrom2 = dataHub.args.breakpoints[2]
        start2 = int(dataHub.args.breakpoints[3])

        orientation = dataHub.args.breakpoints[4]

        if dataHub.args.min_mapq is None:
            dataHub.args.min_mapq = -1

        variant = Translocation(Locus(chrom1, start1, start1, "+"), 
                                Locus(chrom2, start2, start2, orientation), 
                                dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower() in ["bkend", "breakend"]:
        assert len(dataHub.args.breakpoints) == 6, getBreakpointFormatsStr("bkend")
        chrom1 = dataHub.args.breakpoints[0]
        start1 = int(dataHub.args.breakpoints[1])
        strand1 = dataHub.args.breakpoints[2]

        chrom2 = dataHub.args.breakpoints[3]
        start2 = int(dataHub.args.breakpoints[4])
        strand2 = dataHub.args.breakpoints[5]

        if dataHub.args.min_mapq is None:
            dataHub.args.min_mapq = -1

        variant = Breakend(Locus(chrom1, start1, start1, strand1), 
                           Locus(chrom2, start2, start2, strand2), 
                           dataHub.alignDistance, dataHub.genome)
    else:
        raise Exception("only accept event types of deletion, insertion, mei, translocation or breakend")
    logging.info(" Variant: {}".format(variant))

    return variant

예제 #4

def getVariant(dataHub):
    if dataHub.args.type.lower().startswith("del"):
        assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("del")
        chrom = dataHub.args.breakpoints[0]
        start = int(dataHub.args.breakpoints[1])
        end = int(dataHub.args.breakpoints[2])
        assert start < end
        variant = Deletion.from_breakpoints(chrom, start-1, end-1, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower() in ["ldel", "largedeletion"]:
        assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("ldel")
        chrom = dataHub.args.breakpoints[0]
        start = int(dataHub.args.breakpoints[1])
        end = int(dataHub.args.breakpoints[2])
        assert start < end
        variant = LargeDeletion.from_breakpoints(chrom, start-1, end-1, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("ins"):
        assert len(dataHub.args.breakpoints) in [3,4], getBreakpointFormatsStr("ins")
        chrom = dataHub.args.breakpoints[0]
        pos = int(dataHub.args.breakpoints[1])
        if len(dataHub.args.breakpoints) == 3:
            seq = dataHub.args.breakpoints[2]
            end = pos
        else:
            end = int(dataHub.args.breakpoints[2])
            seq = dataHub.args.breakpoints[3]
        variant = Insertion(Locus(chrom, pos, end, "+"), seq, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("inv"):
        assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("inv")
        chrom = dataHub.args.breakpoints[0]
        start = int(dataHub.args.breakpoints[1])
        end = int(dataHub.args.breakpoints[2])
        if dataHub.args.min_mapq is None:
            dataHub.args.min_mapq = -1
        variant = Inversion(Locus(chrom, start, end, "+"), dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("mei"):
        assert len(dataHub.args.breakpoints) >= 4, getBreakpointFormatsStr("mei")

        insertionBreakpoint = Locus(dataHub.args.breakpoints[1], dataHub.args.breakpoints[2], dataHub.args.breakpoints[2], "+")

        meName = dataHub.args.breakpoints[3]
        meStrand = getListDefault(dataHub.args.breakpoints, 4, "+")
        meStart = getListDefault(dataHub.args.breakpoints, 5, 0)
        meEnd = getListDefault(dataHub.args.breakpoints, 6, 1e100)

        meCoords = Locus(meName, meStart, meEnd, meStrand)
        meFasta = genomesource.FastaGenomeSource(dataHub.args.breakpoints[0])

        variant = MobileElementInsertion(insertionBreakpoint, meCoords, meFasta, dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower().startswith("tra"):
        assert len(dataHub.args.breakpoints) == 5, getBreakpointFormatsStr("tra")
        chrom1 = dataHub.args.breakpoints[0]
        start1 = int(dataHub.args.breakpoints[1])

        chrom2 = dataHub.args.breakpoints[2]
        start2 = int(dataHub.args.breakpoints[3])

        orientation = dataHub.args.breakpoints[4]

        if dataHub.args.min_mapq is None:
            dataHub.args.min_mapq = -1

        variant = Translocation(Locus(chrom1, start1, start1, "+"), 
                                Locus(chrom2, start2, start2, orientation), 
                                dataHub.alignDistance, dataHub.genome)

    elif dataHub.args.type.lower() in ["bkend", "breakend"]:
        assert len(dataHub.args.breakpoints) == 6, getBreakpointFormatsStr("bkend")
        chrom1 = dataHub.args.breakpoints[0]
        start1 = int(dataHub.args.breakpoints[1])
        strand1 = dataHub.args.breakpoints[2]

        chrom2 = dataHub.args.breakpoints[3]
        start2 = int(dataHub.args.breakpoints[4])
        strand2 = dataHub.args.breakpoints[5]

        if dataHub.args.min_mapq is None:
            dataHub.args.min_mapq = -1

        variant = Breakend(Locus(chrom1, start1, start1, strand1), 
                           Locus(chrom2, start2, start2, strand2), 
                           dataHub.alignDistance, dataHub.genome)
    else:
        raise Exception("only accept event types of deletion, insertion, mei, translocation or breakend")
    logging.info(" Variant: {}".format(variant))

    return variant