def test_bedrecord__accessors__3_fields():
record = BEDRecord("my_contig\t12\t345")
assert record.contig == "my_contig"
assert record.start == 12
assert record.end == 345
with pytest.raises(IndexError):
record.name()
with pytest.raises(IndexError):
record.score()
with pytest.raises(IndexError):
record.strand()
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__unset_fields__after_end():
record = BEDRecord("")
record.strand = "-"
assert_equal(str(record), "\t0\t0\t\t0\t-")
record = BEDRecord("my_name")
record.strand = "-"
assert_equal(str(record), "my_name\t0\t0\t\t0\t-")
record = BEDRecord("my_name\t17")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t0\t\t0\t-")
record = BEDRecord("my_name\t17\t258")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\t\t0\t-")
record = BEDRecord("my_name\t17\t258\tregion")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t0\t-")
record = BEDRecord("my_name\t17\t258\tregion\t33")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t33\t-")
record = BEDRecord("my_name\t17\t258\tregion\t33\t+")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t33\t-")
def test_bedrecord__setters__unset_fields__after_end():
record = BEDRecord("")
record.strand = "-"
assert_equal(str(record), "\t0\t0\t\t0\t-")
record = BEDRecord("my_name")
record.strand = "-"
assert_equal(str(record), "my_name\t0\t0\t\t0\t-")
record = BEDRecord("my_name\t17")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t0\t\t0\t-")
record = BEDRecord("my_name\t17\t258")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\t\t0\t-")
record = BEDRecord("my_name\t17\t258\tregion")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t0\t-")
record = BEDRecord("my_name\t17\t258\tregion\t33")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t33\t-")
record = BEDRecord("my_name\t17\t258\tregion\t33\t+")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t33\t-")
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"
def test_bedrecord__setters__unset_fields__at_end():
record = BEDRecord("my_contig\t12\t345")
record.name = "my_region"
assert_equal(record.name, "my_region")
record.score = -13
assert_equal(record.score, -13)
record.strand = '-'
assert_equal(record.strand, '-')
assert_equal(str(record), "my_contig\t12\t345\tmy_region\t-13\t-")
assert_equal(
repr(record), "BEDRecord(contig='my_contig', start=12, end=345, "
"name='my_region', score=-13, strand='-')")
def test_bedrecord__setters__unset_fields__at_end():
record = BEDRecord("my_contig\t12\t345")
record.name = "my_region"
assert_equal(record.name, "my_region")
record.score = -13
assert_equal(record.score, -13)
record.strand = '-'
assert_equal(record.strand, '-')
assert_equal(str(record), "my_contig\t12\t345\tmy_region\t-13\t-")
assert_equal(repr(record),
"BEDRecord(contig='my_contig', start=12, end=345, "
"name='my_region', score=-13, strand='-')")
def test_bedrecord__setters__unset_fields__at_end():
record = BEDRecord("my_contig\t12\t345")
record.name = "my_region"
assert record.name == "my_region"
record.score = -13
assert record.score == -13
record.strand = "-"
assert record.strand == "-"
assert str(record) == "my_contig\t12\t345\tmy_region\t-13\t-"
assert (
repr(record) == "BEDRecord(contig='my_contig', start=12, end=345, "
"name='my_region', score=-13, strand='-')"
)