def test_refDoesntMatch_raisesError(self, mocked_variant):
name = "foo"
comment = ""
seq = "hello world"
record = Record(name, comment, seq)
relative_start = 1
mocked_variant.POS = 1
mocked_variant.REF = "hall"
with pytest.raises(ValueError):
record.apply_variant(mocked_variant, relative_start)
def test_noAlt_returnsEmpty(self, mocked_variant):
name = "foo"
comment = ""
seq = "hello world"
record = Record(name, comment, seq)
relative_start = 1
mocked_variant.POS = 1
mocked_variant.REF = "hell"
mocked_variant.ALT = []
actual = record.apply_variant(mocked_variant, relative_start)
expected = []
assert actual == expected
def test_variantEndsInNextLoci_skips(self, mocked_variant):
name = "foo"
comment = ""
seq = "yyACG"
record = Record(name, comment, seq)
relative_start = 5
mocked_variant.POS = 7
mocked_variant.REF = "ACGTACGT"
mocked_variant.ALT = ["abcdefgh"]
with patch("uuid.uuid4", return_value=name) as mocked_uuid4:
actual = record.apply_variant(mocked_variant, relative_start)
assert mocked_uuid4.call_count == 0
expected = []
assert actual == expected
def test_oneAlt_returnsOneRecord(self, mocked_variant):
name = "foo"
comment = ""
seq = "hello world"
record = Record(name, comment, seq)
relative_start = 1
mocked_variant.POS = 1
mocked_variant.REF = "hello"
mocked_variant.ALT = ["hola"]
with patch("uuid.uuid4", return_value=name) as mocked_uuid4:
actual = record.apply_variant(mocked_variant, relative_start)
assert mocked_uuid4.call_count == 1
expected_comment = f"POS=1|ALT=0|ALT_POS_IN_SEQ=[0,4)"
expected = [Record(name, expected_comment, "hola world")]
assert actual == expected
def test_twoAltsOneTooLong_returnsOneRecord(self, mocked_variant):
name = "foo"
comment = ""
seq = "hello world"
record = Record(name, comment, seq)
max_indel_len = 3
relative_start = 2
mocked_variant.POS = 4
mocked_variant.REF = "l"
mocked_variant.ALT = ["ins", "longlong"]
with patch("uuid.uuid4", return_value=name) as mocked_uuid4:
actual = record.apply_variant(
mocked_variant, relative_start, max_indel_len=max_indel_len
)
assert mocked_uuid4.call_count == 1
expected_comment1 = f"POS=4|ALT=0|ALT_POS_IN_SEQ=[2,5)"
expected = [
Record(name, expected_comment1, "heinslo world"),
]
assert actual == expected