def test_transformNonesToHalfwayPositions_allNonesButOneReturnsTransformedArray(
self
):
array = [None, None, 0, None, None]
actual = AlignedPairs.transform_Nones_to_halfway_positions(array)
expected = [-0.5, -0.5, 0, 0.5, 0.5]
assert actual == expected
def test_getPairsInQueryInterval_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_pairs_in_query_interval(interval)
expected = aligned_pairs
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_initAlignedPairsEmptyList(self):
actual = AlignedPairs([])
expected = []
assert actual == expected
def test_initAlignedPairsNoArguments(self):
actual = AlignedPairs()
expected = []
assert actual == expected
def test_transformNonesToHalfwayPositions_allNonesRaisesException(self):
with pytest.raises(ValueError):
AlignedPairs.transform_Nones_to_halfway_positions([None, None])
def test_transformNonesToHalfwayPositions_severalNonesReturnsTransformedArray(self):
array = [None, 5, None, None, 6, None, None]
actual = AlignedPairs.transform_Nones_to_halfway_positions(array)
expected = [4.5, 5, 5.5, 5.5, 6, 6.5, 6.5]
assert actual == expected
def test_transformNonesToHalfwayPositions_noNonesReturnsInput(self):
array = [1, 2]
actual = AlignedPairs.transform_Nones_to_halfway_positions(array)
expected = array
assert actual == expected
def test_transformNonesToHalfwayPositions_emptyReturnsEmpty(self):
actual = AlignedPairs.transform_Nones_to_halfway_positions([])
expected = []
assert actual == expected
def test_getRefPositions_allAlignedPairsAreNoneAndTransformRaisesException(
self, *mocks
):
aligned_pairs = AlignedPairs([AlignedPair(10, None, None)])
with pytest.raises(ValueError):
aligned_pairs.get_ref_positions(transform_Nones_into_halfway_positions=True)
class TestPrecisionMasker:
@patch.object(
Classification, "is_unmapped", return_value=True, new_callable=PropertyMock
)
def test_getIntervalWhereProbeAlignsToTruth_ProbeIsUnmappedReturnsNone(self, *mock):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = None
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs(
[(0, 34, "A"), (1, None, None), (2, 35, "A"), (None, 36, "A")]
),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(0, 4))
def test_getIntervalWhereProbeAlignsToTruth_probeMapsReturnsInterval(self, *mock):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = Interval(34, 37, "chrom1")
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs(
[
(8, 50, "A"),
(9, None, None),
(10, None, None),
(11, None, None),
(12, 51, "C"),
]
),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(1, 2))
def test_getIntervalWhereProbeAlignsToTruth_probeIsInsertionWithTwoNonesAfterReturnsIntervalAroundInsertion(
self, *mock
):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = Interval(50, 52, "chrom1")
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs(
[
(8, 50, "A"),
(9, None, None),
(10, None, None),
(11, None, None),
(12, 51, "C"),
]
),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(2, 3))
def test_getIntervalWhereProbeAlignsToTruth_probeIsInsertionFlankedByNoneReturnsIntervalAroundInsertion(
self, *mock
):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = Interval(50, 52, "chrom1")
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs(
[
(8, 50, "A"),
(9, None, None),
(10, None, None),
(11, None, None),
(12, 51, "C"),
]
),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(3, 4))
def test_getIntervalWhereProbeAlignsToTruth_probeIsInsertionWithTwoNonesBeforeReturnsIntervalAroundInsertion(
self, *mock
):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = Interval(50, 52, "chrom1")
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs([(5, None, None), (6, 4, "A"), (7, None, None)]),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(0, 3))
def test_getIntervalWhereProbeAlignsToTruth_refPositionsWhereProbeMapsFlankedByNoneReturnsInterval(
self, *mock
):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = Interval(3, 6, "chrom1")
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs([(5, None, None), (6, 0, "A"), (7, None, None)]),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(0, 3))
def test_getIntervalWhereProbeAlignsToTruth_refPositionsWhereProbeMapsContainsZeroDontReturnNegative(
self, *mock
):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = Interval(0, 2, "chrom1")
assert actual == expected
@patch.object(
Classification, "is_unmapped", return_value=False, new_callable=PropertyMock
)
@patch.object(
Classification,
"get_aligned_pairs",
return_value=AlignedPairs([(5, 0, "A"), (6, 1, "C"), (7, 2, "G"), (8, 3, "G")]),
)
@patch.object(AlignedPairs, "get_index_of_query_interval", return_value=(0, 0))
@patch.object(AlignedPairs, "get_ref_positions", return_value=[])
def test_getIntervalWhereProbeAlignsToTruth_refPositionsQueryAlignsToIsEmpty_returnsNone(
self, *mock
):
classification = Classification()
actual = PrecisionMasker.get_interval_where_probe_aligns_to_truth(
classification
)
expected = None
assert actual == expected
def get_aligned_pairs(self,
matches_only: bool = False,
with_seq: bool = False) -> AlignedPairs:
return AlignedPairs(
self.record.get_aligned_pairs(matches_only=matches_only,
with_seq=with_seq))