def test_compute_distances12(adata_cdr3, adata_cdr3_mock_distance_calculator):
"""Test for #174. Gracefully handle the case when there are no distances. """
adata_cdr3.obs["IR_VJ_1_cdr3"] = np.nan
adata_cdr3.obs["IR_VDJ_1_cdr3"] = np.nan
# test both receptor arms, primary chain only
tn = IrNeighbors(
adata_cdr3,
metric=adata_cdr3_mock_distance_calculator,
receptor_arms="all",
dual_ir="primary_only",
sequence="aa",
cutoff=0,
)
tn.compute_distances()
print(tn.dist.toarray())
npt.assert_equal(tn.dist.toarray(), np.zeros((5, 5)))
def test_compute_distances11(adata_cdr3, adata_cdr3_mock_distance_calculator):
tn = IrNeighbors(
adata_cdr3,
metric=adata_cdr3_mock_distance_calculator,
receptor_arms="all",
dual_ir="all",
sequence="aa",
)
tn.compute_distances()
print(tn.dist.toarray())
npt.assert_equal(
tn.dist.toarray(),
np.array(
[
[1, 0, 0, 0, 0],
[0, 1, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 1, 0],
[0, 0, 0, 0, 1],
]
),
)
def test_compute_distances6(adata_cdr3, adata_cdr3_mock_distance_calculator):
# test both receptor arms, primary chain only
tn = IrNeighbors(
adata_cdr3,
metric=adata_cdr3_mock_distance_calculator,
receptor_arms="all",
dual_ir="primary_only",
sequence="aa",
)
tn.compute_distances()
print(tn.dist.toarray())
npt.assert_equal(
tn.dist.toarray(),
np.array(
[
[1, 13, 0, 0, 0],
[13, 1, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 1, 0],
[0, 0, 0, 0, 1],
]
),
)
def test_compute_distances3(adata_cdr3, adata_cdr3_mock_distance_calculator):
# test single chain with custom distance
tn = IrNeighbors(
adata_cdr3,
metric=adata_cdr3_mock_distance_calculator,
receptor_arms="VJ",
dual_ir="primary_only",
sequence="aa",
)
tn.compute_distances()
assert tn.dist.nnz == 9
npt.assert_equal(
tn.dist.toarray(),
np.array(
[
[1, 4, 0, 1, 0],
[4, 1, 0, 4, 0],
[0] * 5,
[1, 4, 0, 1, 0],
[0] * 5,
]
),
)
def test_compute_distances2(adata_cdr3, adata_cdr3_mock_distance_calculator):
# test single receptor arm with multiple chains and identity distance
tn = IrNeighbors(
adata_cdr3,
metric="identity",
cutoff=0,
receptor_arms="VJ",
dual_ir="any",
sequence="aa",
)
tn.compute_distances()
npt.assert_equal(
tn.dist.toarray(),
np.array(
[
[1, 1, 0, 1, 1],
[1, 1, 0, 0, 0],
[0] * 5,
[1, 0, 0, 1, 1],
[1, 0, 0, 1, 1],
]
),
)
def test_compute_distances5(adata_cdr3, adata_cdr3_mock_distance_calculator):
# test single receptor arm with multiple chains and custom distance
tn = IrNeighbors(
adata_cdr3,
metric=adata_cdr3_mock_distance_calculator,
receptor_arms="VJ",
dual_ir="all",
sequence="aa",
)
tn.compute_distances()
print(tn.dist.toarray())
npt.assert_equal(
tn.dist.toarray(),
np.array(
[
[1, 0, 0, 4, 0],
[0, 1, 0, 0, 4],
[0, 0, 0, 0, 0],
[4, 0, 0, 1, 0],
[0, 4, 0, 0, 1],
]
),
)