def test_multiple_recombinations(self):
ts = msprime.sim_ancestry(5,
sequence_length=10,
recombination_rate=10,
random_seed=1)
found = False
for _, e_out, _ in ts.edge_diffs():
if len(e_out) > 4:
found = True
break
assert found
with pytest.raises(ValueError):
tsinfer.insert_perfect_mutations(ts)
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_three_samples(self):
for seed in range(10):
ts = msprime.simulate(3,
recombination_rate=1,
random_seed=seed + 1,
model="smc_prime")
ts = tsinfer.insert_perfect_mutations(ts)
self.verify(ts)
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_twenty_samples(self):
for seed in range(5):
ts = msprime.simulate(10,
recombination_rate=0.1,
random_seed=seed + 500,
length=10,
model="smc_prime")
ts = tsinfer.insert_perfect_mutations(ts, delta=1 / 8192)
self.verify(ts)
def test_multiple_recombinations(self):
try:
recomb_map = msprime.RecombinationMap.uniform_map(length=10,
rate=10,
discrete=True)
except TypeError:
# Fallback for older versions of msprime, which use num_loci
recomb_map = msprime.RecombinationMap.uniform_map(length=10,
rate=10,
num_loci=10)
ts = msprime.simulate(10, recombination_map=recomb_map, random_seed=1)
found = False
for _, e_out, _ in ts.edge_diffs():
if len(e_out) > 4:
found = True
break
assert found
with pytest.raises(ValueError):
tsinfer.insert_perfect_mutations(ts)
def run_viz(
n,
L,
rate,
seed,
mutation_rate=0,
engine="C",
perfect_ancestors=True,
perfect_mutations=True,
path_compression=False,
time_chunking=True,
error_rate=0,
):
recomb_map = msprime.RecombinationMap.uniform_map(length=L,
rate=rate,
num_loci=L)
ts = msprime.simulate(
n,
recombination_map=recomb_map,
random_seed=seed,
model="smc_prime",
mutation_rate=mutation_rate,
)
if perfect_mutations:
ts = tsinfer.insert_perfect_mutations(ts, delta=1 / 512)
else:
ts = tsinfer.strip_singletons(
tsinfer.insert_errors(ts, error_rate, seed))
print("num_sites = ", ts.num_sites)
with open("tmp__NOBACKUP__/edges.svg", "w") as f:
f.write(draw_edges(ts))
with open("tmp__NOBACKUP__/ancestors.svg", "w") as f:
f.write(draw_ancestors(ts))
visualise(
ts,
rate,
0,
engine=engine,
box_size=26,
perfect_ancestors=perfect_ancestors,
path_compression=path_compression,
time_chunking=time_chunking,
)
def test_single_tree(self):
for seed in range(10):
ts = msprime.simulate(10, random_seed=seed + 1)
ts = tsinfer.insert_perfect_mutations(ts)
self.verify(ts)
def test_large_smc(self):
ts = get_smc_simulation(50, L=1, recombination_rate=100, seed=1)
ts = tsinfer.insert_perfect_mutations(ts)
self.assertGreater(ts.num_trees, 100)
self.verify_perfect_mutations(ts)
def test_small_smc(self):
for seed in range(1, 10):
ts = get_smc_simulation(5, L=1, recombination_rate=10, seed=seed)
ts = tsinfer.insert_perfect_mutations(ts)
self.assertGreater(ts.num_trees, 1)
self.verify_perfect_mutations(ts)
def test_single_tree(self):
ts = msprime.simulate(5, random_seed=234)
ts = tsinfer.insert_perfect_mutations(ts)
self.verify_perfect_mutations(ts)
def test_large_smc_perfect_mutations(self):
for seed in range(1, 10):
ts = get_smc_simulation(10, 100, 0.1, seed)
ts = tsinfer.insert_perfect_mutations(ts)
self.assertGreater(ts.num_trees, 1)
self.verify_many_trees_dense_mutations(ts)
def test_small_smc_perfect_mutations(self):
for seed in range(1, 10):
ts = get_smc_simulation(5, 100, 0.02, seed)
ts = tsinfer.insert_perfect_mutations(ts)
assert ts.num_trees > 1
self.verify_many_trees_dense_mutations(ts)
