def test_getAlignmentType_pairIsDeletion(self):
aligned_pair = AlignedPair(query_pos=10, ref_pos=None, ref_base=None)
actual = aligned_pair.get_alignment_type()
expected = AlignmentType.DELETION
assert actual == expected
def test_getAlignmentType_pairIsMismatch(self):
aligned_pair = AlignedPair(query_pos=10, ref_pos=15, ref_base="a")
actual = aligned_pair.get_alignment_type()
expected = AlignmentType.MISMATCH
assert actual == expected
def test_getAlignmentType_pairIsInsertion(self):
aligned_pair = AlignedPair(query_pos=None, ref_pos=10, ref_base="A")
actual = aligned_pair.get_alignment_type()
expected = AlignmentType.INSERTION
assert actual == expected
def test_getRefPositions_twoPairsOneNoneNoTransformReturnsTwoPositionsOneNone(self):
aligned_pairs = AlignedPairs(
[AlignedPair(4, None, None), AlignedPair(5, 11, "C")]
)
actual = aligned_pairs.get_ref_positions()
expected = [None, 11]
assert actual == expected
def test_getPairsInQueryInterval_nullIntervalReturnsEmpty(self):
interval = Interval(2, 2)
aligned_pairs = AlignedPairs(
[AlignedPair(1, 30, "A"), AlignedPair(2, 31, "C"), AlignedPair(3, 32, "T")]
)
actual = aligned_pairs.get_pairs_in_query_interval(interval)
expected = AlignedPairs()
assert actual == expected
def test_getIndexOfQueryInterval_intervalNotInPairsReturnsEmpty(self):
interval = Interval(5, 10)
aligned_pairs = AlignedPairs(
[AlignedPair(1, 30, "A"), AlignedPair(2, 31, "C"), AlignedPair(3, 32, "T")]
)
actual = aligned_pairs.get_index_of_query_interval(interval)
expected = (3, 3)
assert actual == expected
def test_getQueryPositions_twoPairsOneNoneNoTransformReturnsTwoPositionsOneNone(
self
):
aligned_pairs = AlignedPairs(
[AlignedPair(None, 10, "A"), AlignedPair(5, 11, "C")]
)
actual = aligned_pairs.get_query_positions()
expected = [None, 5]
assert actual == expected
def test_getRefPositions_twoPairsOneNoneTransformReturnsTwoPositionsOneHalfway(
self, *mocks
):
aligned_pairs = AlignedPairs(
[AlignedPair(1, None, None), AlignedPair(2, 5, "C")]
)
actual = aligned_pairs.get_ref_positions(
transform_Nones_into_halfway_positions=True
)
expected = [4.5, 5.0]
assert actual == expected
def test_getQueryPositions_twoPairsOneNoneTransformReturnsTwoPositionsOneHalfway(
self, *mocks
):
aligned_pairs = AlignedPairs(
[AlignedPair(None, 10, "A"), AlignedPair(5, 11, "C")]
)
actual = aligned_pairs.get_query_positions(
transform_Nones_into_halfway_positions=True
)
expected = [4.5, 5.0]
assert actual == expected
def test_getPairsInQueryInterval_intervalOverlapsRightOfPairs(self):
interval = Interval(4, 12)
aligned_pairs = AlignedPairs(
[
AlignedPair(3, 30, "A"),
AlignedPair(4, 31, "C"),
AlignedPair(None, 32, "T"),
]
)
actual = aligned_pairs.get_pairs_in_query_interval(interval)
expected = aligned_pairs[1:]
assert actual == expected
def test_getIndexOfQueryInterval_intervalOverlapsRightOfPairs(self):
interval = Interval(4, 12)
aligned_pairs = AlignedPairs(
[
AlignedPair(3, 30, "A"),
AlignedPair(4, 31, "C"),
AlignedPair(None, 32, "T"),
]
)
actual = aligned_pairs.get_index_of_query_interval(interval)
expected = (1, 3)
assert actual == expected
def test_getQueryPositions_allAlignedPairsAreNoneNoTransformReturnsNone(self):
aligned_pairs = AlignedPairs([AlignedPair(None, 10, "A")])
actual = aligned_pairs.get_query_positions()
expected = [None]
assert actual == expected
def test_getRefPositions_allAlignedPairsAreNoneNoTransformReturnsNone(self):
aligned_pairs = AlignedPairs([AlignedPair(1, None, None)])
actual = aligned_pairs.get_ref_positions()
expected = [None]
assert actual == expected
def test_getQueryPositions_allAlignedPairsAreNoneAndTransformRaisesException(
self, *mocks
):
aligned_pairs = AlignedPairs([AlignedPair(None, 10, "A")])
with pytest.raises(ValueError):
aligned_pairs.get_query_positions(
transform_Nones_into_halfway_positions=True
)
def test_getAlignmentTypes(self, alignedPairMocked):
aligned_pairs = AlignedPairs([AlignedPair()] * 4)
actual = aligned_pairs.get_alignment_types()
expected = [
AlignmentType.MATCH,
AlignmentType.MISMATCH,
AlignmentType.DELETION,
AlignmentType.INSERTION,
]
assert actual == expected
def test_initAlignedPairsListWith4AlignedPairs(self):
aligned_pairs_as_tuples = [
(0, 34, "A"),
(1, None, None),
(2, 35, "A"),
(None, 36, "A"),
]
actual = AlignedPairs(aligned_pairs_as_tuples)
expected = [
AlignedPair(*aligned_pair_as_tuple)
for aligned_pair_as_tuple in aligned_pairs_as_tuples
]
assert actual == expected
def test_getIndexOfQueryInterval_intervalEnvelopedInPairs(self):
interval = Interval(5, 7)
aligned_pairs = AlignedPairs(
[
AlignedPair(4, 30, "A"),
AlignedPair(None, 31, "A"),
AlignedPair(5, 32, "A"),
AlignedPair(None, 33, "A"),
AlignedPair(6, 34, "A"),
AlignedPair(None, 35, "A"),
]
)
actual = aligned_pairs.get_index_of_query_interval(interval)
expected = (2, 5)
assert actual == expected
def test_getIndexOfQueryInterval_intervalSpansPairs(self):
interval = Interval(1, 10)
aligned_pairs = AlignedPairs(
[
AlignedPair(4, 30, "A"),
AlignedPair(None, 31, "A"),
AlignedPair(5, 32, "A"),
AlignedPair(None, 33, "A"),
AlignedPair(6, 34, "A"),
AlignedPair(None, 35, "A"),
]
)
actual = aligned_pairs.get_index_of_query_interval(interval)
expected = (0, 6)
assert actual == expected
def test_getPairsInQueryInterval_intervalEnvelopedInPairs(self):
interval = Interval(5, 7)
aligned_pairs = AlignedPairs(
[
AlignedPair(4, 30, "A"),
AlignedPair(None, 31, "A"),
AlignedPair(5, 32, "A"),
AlignedPair(None, 33, "A"),
AlignedPair(6, 34, "A"),
AlignedPair(None, 35, "A"),
]
)
actual = aligned_pairs.get_pairs_in_query_interval(interval)
expected = aligned_pairs[2:5]
assert actual == expected
