def verify(self, ts, reference_sets, focal=None):
if focal is None:
focal = [u for refset in reference_sets for u in refset]
A1 = naive_genealogical_nearest_neighbours(ts, focal, reference_sets)
A2 = tsutil.genealogical_nearest_neighbours(ts, focal, reference_sets)
A3 = ts.genealogical_nearest_neighbours(focal, reference_sets)
A4 = ts.genealogical_nearest_neighbours(focal,
reference_sets,
num_threads=3)
A5 = windowed_genealogical_nearest_neighbours(ts, focal,
reference_sets)
assert np.array_equal(A3, A4)
assert A1.shape == A2.shape
assert A1.shape == A3.shape
assert np.allclose(A1, A2)
assert np.allclose(A1, A3)
mask = ~np.isnan(A5)
assert np.sum(mask) > 0 or ts.num_edges == 0
assert np.allclose(A1[mask], A5[mask])
assert np.allclose(A5[mask], A2[mask])
assert np.allclose(A5[mask], A3[mask])
if ts.num_edges > 0 and all(ts.node(u).is_sample() for u in focal):
# When the focal nodes are samples, we can assert some stronger properties.
assert np.allclose(np.sum(A1, axis=1), 1)
assert np.allclose(np.sum(A5, axis=1), 1)
return A1
def test_simple_example_internal_focal_node(self):
ts = tskit.load_text(nodes=io.StringIO(self.small_tree_ex_nodes),
edges=io.StringIO(self.small_tree_ex_edges),
strict=False)
focal = [7] # An internal node
reference_sets = [[4, 0, 1], [2, 3]]
GNN = naive_genealogical_nearest_neighbours(ts, focal, reference_sets)
self.assertTrue(np.allclose(GNN[0], np.array([1.0, 0.0])))
GNN = tsutil.genealogical_nearest_neighbours(ts, focal, reference_sets)
self.assertTrue(np.allclose(GNN[0], np.array([1.0, 0.0])))
GNN = ts.genealogical_nearest_neighbours(focal, reference_sets)
self.assertTrue(np.allclose(GNN[0], np.array([1.0, 0.0])))
focal = [8] # The root
GNN = naive_genealogical_nearest_neighbours(ts, focal, reference_sets)
self.assertTrue(np.allclose(GNN[0], np.array([0.6, 0.4])))
GNN = tsutil.genealogical_nearest_neighbours(ts, focal, reference_sets)
self.assertTrue(np.allclose(GNN[0], np.array([0.6, 0.4])))
GNN = ts.genealogical_nearest_neighbours(focal, reference_sets)
self.assertTrue(np.allclose(GNN[0], np.array([0.6, 0.4])))
def verify(self, ts, reference_sets, focal=None):
if focal is None:
focal = [u for refset in reference_sets for u in refset]
A1 = naive_genealogical_nearest_neighbours(ts, focal, reference_sets)
A2 = tsutil.genealogical_nearest_neighbours(ts, focal, reference_sets)
A3 = ts.genealogical_nearest_neighbours(focal, reference_sets)
A4 = ts.genealogical_nearest_neighbours(focal, reference_sets, num_threads=3)
self.assertTrue(np.array_equal(A3, A4))
self.assertEqual(A1.shape, A2.shape)
self.assertEqual(A1.shape, A3.shape)
self.assertTrue(np.allclose(A1, A2))
self.assertTrue(np.allclose(A1, A3))
if ts.num_edges > 0 and all(ts.node(u).is_sample() for u in focal):
# When the focal nodes are samples, we can assert some stronger properties.
self.assertTrue(np.allclose(np.sum(A1, axis=1), 1))
return A1
def verify(self, ts, reference_sets, focal=None):
if focal is None:
focal = [u for refset in reference_sets for u in refset]
A1 = naive_genealogical_nearest_neighbours(ts, focal, reference_sets)
A2 = tsutil.genealogical_nearest_neighbours(ts, focal, reference_sets)
A3 = ts.genealogical_nearest_neighbours(focal, reference_sets)
A4 = ts.genealogical_nearest_neighbours(focal,
reference_sets,
num_threads=3)
self.assertTrue(np.array_equal(A3, A4))
self.assertEqual(A1.shape, A2.shape)
self.assertEqual(A1.shape, A3.shape)
self.assertTrue(np.allclose(A1, A2))
self.assertTrue(np.allclose(A1, A3))
if all(ts.node(u).is_sample() for u in focal):
# When the focal nodes are samples, we can assert some stronger properties.
fully_rooted = True
for tree in ts.trees():
if tree.num_roots > 1:
fully_rooted = False
break
if fully_rooted:
self.assertTrue(np.allclose(np.sum(A1, axis=1), 1))
else:
all_refs = [u for refset in reference_sets for u in refset]
# Any node that hits a root before meeting a descendent of the reference
# nodes must have total zero.
coalescence_found = np.array([False for _ in all_refs])
for tree in ts.trees(tracked_samples=all_refs):
for j, u in enumerate(focal):
while u != tskit.NULL:
if tree.num_tracked_samples(u) > 1:
coalescence_found[j] = True
break
u = tree.parent(u)
self.assertTrue(
np.allclose(np.sum(A1[coalescence_found], axis=1), 1))
# Anything where there's no coalescence, ever is zero by convention.
self.assertTrue(
np.allclose(
np.sum(A1[np.logical_not(coalescence_found)], axis=1),
0))
return A1