Пример #1
0
def parse_intervals(genotype):
    records = {}
    for line in genotype.header:
        match = _VCF_DICT.match(line)
        if not match:
            continue

        key, values = match.groups()
        if key == "contig":
            values = dict(pair.split("=", 1) for pair in values.split(","))
            record = BEDRecord()
            record.contig = values["ID"]
            record.start = 0
            record.end = int(values["length"])
            record.name = record.contig
            record.strand = "+"

            records[record.contig] = [record]

    if not records:
        sys.stderr.write("ERROR: List of contigs not found in VCF header; "
                         "specifying --intervals is required!\n")
        return None

    return records
Пример #2
0
def parse_intervals(genotype):
    records = {}
    for line in genotype.header:
        match = _VCF_DICT.match(line)
        if not match:
            continue

        key, values = match.groups()
        if key == "contig":
            values = dict(pair.split("=", 1) for pair in values.split(","))
            record = BEDRecord()
            record.contig = values["ID"]
            record.start = 0
            record.end = int(values["length"])
            record.name = record.contig
            record.strand = "+"

            records[record.contig] = [record]

    if not records:
        sys.stderr.write("ERROR: List of contigs not found in VCF header; "
                         "specifying --intervals is required!\n")
        return None

    return records
Пример #3
0
def test_bedrecord__setters__type_errors():
    record = BEDRecord("my_contig\t12\t345\tname\t0\t+")

    with pytest.raises(ValueError):
        record.contig = 17
    with pytest.raises(ValueError):
        record.start = "foo"
    with pytest.raises(ValueError):
        record.end = "foo"
    with pytest.raises(ValueError):
        record.name = 17.3
    with pytest.raises(ValueError):
        record.score = "foo"
    with pytest.raises(ValueError):
        record.strand = "foo"