def test_simple_error(self):
ts = msprime.simulate(
10, mutation_rate=10, recombination_rate=10, random_seed=2)
self.assertTrue(ts.num_sites > 1)
self.assertTrue(ts.num_trees > 1)
tsp = tsinfer.insert_errors(ts, 0.1)
# We should have some extra mutations
self.assertGreater(tsp.num_mutations, ts.num_mutations)
self.verify(ts, tsp)
def test_zero_error(self):
ts = msprime.simulate(
10, mutation_rate=10, recombination_rate=10, random_seed=1)
self.assertTrue(ts.num_sites > 1)
self.assertTrue(ts.num_trees > 1)
tsp = tsinfer.insert_errors(ts, 0)
t1 = ts.tables
t2 = tsp.tables
self.assertEqual(t1.nodes, t2.nodes)
self.assertEqual(t1.edges, t2.edges)
self.assertEqual(t1.sites, t2.sites)
self.assertEqual(t1.mutations, t2.mutations)
def test_zero_error(self):
ts = msprime.simulate(10,
mutation_rate=10,
recombination_rate=10,
random_seed=1)
assert ts.num_sites > 1
assert ts.num_trees > 1
tsp = tsinfer.insert_errors(ts, 0)
t1 = tsutil.mark_mutation_times_unknown(ts).tables
t2 = tsp.tables
assert t1.nodes == t2.nodes
assert t1.edges == t2.edges
assert t1.sites == t2.sites
assert t1.mutations == t2.mutations
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,
)