def test_single_tree_perfect_mutations(self):
ts = msprime.simulate(5, random_seed=234)
ts = tsinfer.insert_perfect_mutations(ts)
A = tsinfer.get_ancestral_haplotypes(ts)
B = self.get_matrix(ts)
self.assertTrue(np.array_equal(A, B))
self.verify_single_tree(ts, A)
def test_many_trees_perfect_mutations(self):
ts = get_smc_simulation(10, 100, 0.1, 1234)
self.assertGreater(ts.num_trees, 1)
ts = tsinfer.insert_perfect_mutations(ts)
A = tsinfer.get_ancestral_haplotypes(ts)
B = self.get_matrix(ts)
self.assertTrue(np.array_equal(A, B))
self.verify_haplotypes(ts, A)
def test_many_trees(self):
ts = msprime.simulate(
8, recombination_rate=10, mutation_rate=10, random_seed=234)
self.assertGreater(ts.num_trees, 1)
self.assertGreater(ts.num_sites, 1)
A = tsinfer.get_ancestral_haplotypes(ts)
B = self.get_matrix(ts)
self.assertTrue(np.array_equal(A, B))
self.verify_haplotypes(ts, A)
def verify_single_tree_dense_mutations(self, ts):
A = tsinfer.get_ancestral_haplotypes(ts)
A = A[ts.num_samples:][::-1]
n, m = A.shape
ancestors, start, end, focal_sites = tsinfer.get_ancestor_descriptors(A)
self.assertTrue(np.array_equal(A, ancestors[-n:]))
self.assertEqual(start, [0 for _ in range(ancestors.shape[0])])
self.assertTrue(end, [m for _ in range(ancestors.shape[0])])
for j in range(1, ancestors.shape[0]):
self.assertGreaterEqual(len(focal_sites[j]), 0)
for site in focal_sites[j]:
self.assertEqual(ancestors[j, site], 1)
def verify_single_tree_dense_mutations(self, ts):
A = tsinfer.get_ancestral_haplotypes(ts)
A = A[ts.num_samples:][::-1]
n, m = A.shape
ancestors, start, end, focal_sites = tsinfer.get_ancestor_descriptors(
A)
assert np.array_equal(A, ancestors[-n:])
assert start == [0 for _ in range(ancestors.shape[0])]
assert end, [m for _ in range(ancestors.shape[0])]
for j in range(1, ancestors.shape[0]):
assert len(focal_sites[j]) >= 0
for site in focal_sites[j]:
assert ancestors[j, site] == 1
def verify_many_trees_dense_mutations(self, ts):
A = tsinfer.get_ancestral_haplotypes(ts)
A = A[ts.num_samples:][::-1]
tsinfer.get_ancestor_descriptors(A)
ancestors, start, end, focal_sites = tsinfer.get_ancestor_descriptors(A)
n, m = ancestors.shape
self.assertEqual(m, ts.num_sites)
self.assertTrue(np.all(ancestors[0, :] == 0))
for a, s, e, focal in zip(ancestors[1:], start[1:], end[1:], focal_sites[1:]):
self.assertTrue(0 <= s < e <= m)
self.assertTrue(np.all(a[:s] == tskit.MISSING_DATA))
self.assertTrue(np.all(a[e:] == tskit.MISSING_DATA))
self.assertTrue(np.all(a[s:e] != tskit.MISSING_DATA))
for site in focal:
self.assertEqual(a[site], 1)
def test_single_tree(self):
ts = msprime.simulate(5, mutation_rate=10, random_seed=234)
A = tsinfer.get_ancestral_haplotypes(ts)
B = self.get_matrix(ts)
assert np.array_equal(A, B)
self.verify_single_tree(ts, A)
