def test_no_tags_returns_default(self):
record = PafRecord()
tag = "NM"
actual = record.get_tag(tag)
assert actual is None
def test_unmapped_record_returns_zero(self):
record = PafRecord()
actual = record.blast_identity()
expected = 0.0
assert actual == expected
def test_alignment_block_same_length_as_matches(self):
record = PafRecord(mlen=5, blen=5)
actual = record.blast_identity()
expected = 1.0
assert actual == expected
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_alignment_block_longer_than_matches(self):
record = PafRecord(mlen=4, blen=5)
actual = record.blast_identity()
expected = 0.8
assert actual == expected
def test_no_matches_returns_zero(self):
record = PafRecord(mlen=0, blen=5)
actual = record.blast_identity()
expected = 0.0
assert actual == expected
def test_tag_present(self):
expected = Tag.from_str("de:f:0.1")
tags = {"de": expected}
record = PafRecord(tags=tags)
tag = "de"
actual = record.get_tag(tag)
assert actual == expected
def test_tag_not_present_returns_default(self):
tags = {"de": Tag.from_str("de:f:0.1")}
record = PafRecord(tags=tags)
tag = "NM"
default = Tag.from_str("NM:i:0")
actual = record.get_tag(tag, default=default)
expected = default
assert actual == expected
def test_for_loop_returns_pafrecords(self):
with tempfile.TemporaryDirectory() as tmpdirname:
record1 = PafRecord()
record2 = PafRecord(qname="record2")
path = Path(f"{tmpdirname}/test.paf")
path.write_text(f"{str(record1)}\n{str(record2)}")
with PafFile(path) as paf:
actual = [record for record in paf]
expected = [record1, record2]
assert actual == expected
def test_unmapped_record_returns_zero(self):
record = PafRecord(tlen=0)
actual = record.target_coverage
expected = 0.0
assert actual == expected
def test_tend_less_than_tstart(self):
record = PafRecord(tstart=5, tend=2)
actual = record.target_aligned_length
expected = 3
assert actual == expected
def test_tend_greater_than_tstart(self):
record = PafRecord(tstart=2, tend=5)
actual = record.target_aligned_length
expected = 3
assert actual == expected
def test_unmapped_record_returns_zero(self):
record = PafRecord()
actual = record.target_aligned_length
expected = 0
assert actual == expected
def test_qend_less_than_qstart(self):
record = PafRecord(qstart=5, qend=2)
actual = record.query_aligned_length
expected = 3
assert actual == expected
def test_qend_greater_than_qstart(self):
record = PafRecord(qstart=2, qend=5)
actual = record.query_aligned_length
expected = 3
assert actual == expected
def test_unmapped_record_returns_zero(self):
record = PafRecord()
actual = record.relative_length
expected = 0.0
assert actual == expected
def test_next_after_end_raises_error(self):
with tempfile.TemporaryDirectory() as tmpdirname:
record = PafRecord()
path = Path(f"{tmpdirname}/test.paf")
path.write_text(str(record))
with PafFile(path) as paf:
next(paf)
with pytest.raises(StopIteration):
next(paf)
def test_mapped_record(self):
record = PafRecord(
qname="05f868dc-6760-47ec-b7e7-ab4054b0e4fe",
qlen=4641,
qstart=5,
qend=4640,
strand=Strand.Reverse,
tname="NODE_1_length_4378477_cov_60.093643",
tlen=4378340,
tstart=1069649,
tend=1074329,
mlen=4499,
blen=4740,
mapq=60,
tags={"tp": Tag.from_str("tp:A:P")},
)
assert not record.is_unmapped()
def test_no_tags(self):
record = PafRecord()
actual = str(record)
expected = DELIM.join(
str(x) for x in PafRecord._field_defaults.values()
if x is not None)
assert actual == expected
def test_next_returns_pafrecord(self):
with tempfile.TemporaryDirectory() as tmpdirname:
record = PafRecord()
path = Path(f"{tmpdirname}/test.paf")
path.write_text(str(record))
with PafFile(path) as paf:
actual = next(paf)
expected = record
assert actual == expected
def test_with_tags(self):
tags = {"NM": Tag.from_str("NM:i:1"), "ms": Tag.from_str("ms:i:1906")}
record = PafRecord(tags=tags)
actual = str(record)
expected = (DELIM.join(
str(x)
for x in PafRecord._field_defaults.values() if x is not None) +
DELIM + DELIM.join(tags))
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_part_of_query_aligned(self):
qlen = 10
qalen = 4
patch_target = "pafpy.pafrecord.PafRecord.query_aligned_length"
with patch(patch_target, new_callable=PropertyMock) as mocked_qalen:
mocked_qalen.return_value = qalen
record = PafRecord(qlen=qlen)
actual = record.query_coverage
mocked_qalen.assert_called_once()
expected = 0.4
assert actual == expected
def test_all_of_target_aligned(self):
tlen = 10
talen = 10
patch_target = "pafpy.pafrecord.PafRecord.target_aligned_length"
with patch(patch_target, new_callable=PropertyMock) as mocked_talen:
mocked_talen.return_value = talen
record = PafRecord(tlen=tlen)
actual = record.target_coverage
mocked_talen.assert_called_once()
expected = 1.0
assert actual == expected
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 test_query_and_target_same_length(self):
talen = 10
qalen = 10
patch_talen = "pafpy.pafrecord.PafRecord.target_aligned_length"
patch_qalen = "pafpy.pafrecord.PafRecord.query_aligned_length"
with ExitStack() as stack:
mocked_talen = stack.enter_context(
patch(patch_talen, new_callable=PropertyMock))
mocked_qalen = stack.enter_context(
patch(patch_qalen, new_callable=PropertyMock))
mocked_talen.return_value = talen
mocked_qalen.return_value = qalen
record = PafRecord()
actual = record.relative_length
mocked_talen.assert_called_once()
mocked_qalen.assert_called_once()
expected = 1.0
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_unknown_char_raises_error(self):
tag = Tag.from_str("tp:A:?")
with pytest.raises(ValueError):
PafRecord(strand=Strand.Forward, tags={
tag.tag: tag
}).is_inversion()
def test_tp_tag_not_present_in_mapped_record_raises_error(self):
with pytest.raises(ValueError):
PafRecord(strand=Strand.Reverse).is_inversion()