def test_line_with_no_tags(self):
fields = [
"query_name",
"1239",
"65",
"1239",
"+",
"target_name",
"4378340",
"2555250",
"2556472",
"1139",
"1228",
"60",
]
line = "\t".join(fields)
actual = PafRecord.from_str(line)
expected = PafRecord(
"query_name",
1239,
65,
1239,
Strand.Forward,
"target_name",
4378340,
2555250,
2556472,
1139,
1228,
60,
)
assert actual == expected
def test_line_with_invalid_tag_raises_error(self):
fields = [
"query_name",
"1239",
"65",
"1239",
"-",
"target_name",
"4378340",
"2555250",
"2556472",
"1139",
"1228",
"60",
"NMX:i:89",
]
line = "\t".join(fields)
with pytest.raises(InvalidTagFormat):
PafRecord.from_str(line)
def test_line_with_dupliacte_tag_returns_last_one(self):
fields = [
"query_name",
"1239",
"65",
"1239",
"-",
"target_name",
"4378340",
"2555250",
"2556472",
"1139",
"1228",
"60",
"NM:i:89",
"NM:i:2",
]
line = "\t".join(fields)
actual = PafRecord.from_str(line)
expected_tags = {"NM": Tag.from_str("NM:i:2")}
expected = PafRecord(
"query_name",
1239,
65,
1239,
Strand.Reverse,
"target_name",
4378340,
2555250,
2556472,
1139,
1228,
60,
expected_tags,
)
assert actual == expected
def test_line_with_tags(self):
fields = [
"query_name",
"1239",
"65",
"1239",
"-",
"target_name",
"4378340",
"2555250",
"2556472",
"1139",
"1228",
"60",
"NM:i:89",
"ms:i:1906",
]
line = "\t".join(fields)
actual = PafRecord.from_str(line)
tags = {"NM": Tag.from_str("NM:i:89"), "ms": Tag.from_str("ms:i:1906")}
expected = PafRecord(
"query_name",
1239,
65,
1239,
Strand.Reverse,
"target_name",
4378340,
2555250,
2556472,
1139,
1228,
60,
tags,
)
assert actual == expected
def __next__(self) -> PafRecord:
if self.closed:
raise IOError("PAF file is closed - cannot get next element.")
return PafRecord.from_str(next(self._stream))
def test_line_has_too_few_fields_raises_error(self):
line = "qname\t1\t3"
with pytest.raises(MalformattedRecord):
PafRecord.from_str(line)
def test_empty_str_raises_error(self):
line = ""
with pytest.raises(MalformattedRecord):
PafRecord.from_str(line)