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
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
def test_bedrecord__setters__3_fields():
record = BEDRecord("my_contig\t12\t345")
record.contig = "chrZ"
assert_equal(record.contig, "chrZ")
record.end += 20
assert_equal(record.end, 365)
assert_equal(str(record), "chrZ\t12\t365")
assert_equal(repr(record), "BEDRecord(contig='chrZ', start=12, end=365)")
def test_bedrecord__setters__3_fields():
record = BEDRecord("my_contig\t12\t345")
record.contig = "chrZ"
assert record.contig == "chrZ"
record.end += 20
assert record.end == 365
assert str(record) == "chrZ\t12\t365"
assert repr(record) == "BEDRecord(contig='chrZ', start=12, end=365)"
def test_bedrecord__setters__3_fields():
record = BEDRecord("my_contig\t12\t345")
record.contig = "chrZ"
assert_equal(record.contig, "chrZ")
record.end += 20
assert_equal(record.end, 365)
assert_equal(str(record), "chrZ\t12\t365")
assert_equal(repr(record),
"BEDRecord(contig='chrZ', start=12, end=365)")
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"