def test_from_single_locus_decapitated(self):
ts = msprime.simulate(10, random_seed=5)
from_ts = tsutil.decapitate(ts, ts.num_edges // 2)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(
from_ts=from_ts, start_time=start_time, random_seed=2)
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def test_decapitated_mutations(self):
ts = msprime.simulate(10, random_seed=5, mutation_rate=10)
from_ts = tsutil.decapitate(ts, ts.num_edges // 2)
self.assertGreater(from_ts.num_mutations, 0)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(
from_ts=from_ts, start_time=start_time, random_seed=2)
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def test_from_multi_locus_old_recombination(self):
ts = msprime.simulate(10, recombination_rate=2, random_seed=5)
self.assertGreater(ts.num_trees, 1)
from_ts = tsutil.decapitate(ts, ts.num_edges // 2)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(
from_ts=from_ts, start_time=start_time, random_seed=2,
recombination_rate=2)
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def test_from_multi_locus_old_recombination(self):
ts = msprime.simulate(10, recombination_rate=2, random_seed=5)
self.assertGreater(ts.num_trees, 1)
from_ts = tsutil.decapitate(ts, ts.num_edges // 2)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(from_ts=from_ts,
start_time=start_time,
random_seed=2,
recombination_rate=2)
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def get_example_base(self, num_populations=1, length=1):
N = num_populations
population_configurations = [
msprime.PopulationConfiguration() for _ in range(N)]
migration_matrix = np.ones((N, N))
np.fill_diagonal(migration_matrix, 0)
ts = msprime.simulate(
samples=[msprime.Sample(0, 0) for _ in range(10)],
length=length,
random_seed=155,
population_configurations=population_configurations,
migration_matrix=migration_matrix)
return tsutil.decapitate(ts, ts.num_edges // 2)
def get_example_base(self, num_populations=1, length=1):
N = num_populations
population_configurations = [
msprime.PopulationConfiguration() for _ in range(N)
]
migration_matrix = np.ones((N, N))
np.fill_diagonal(migration_matrix, 0)
ts = msprime.simulate(
samples=[msprime.Sample(0, 0) for _ in range(10)],
length=length,
random_seed=155,
population_configurations=population_configurations,
migration_matrix=migration_matrix)
return tsutil.decapitate(ts, ts.num_edges // 2)
def get_mutations_over_roots_tree(self):
ts = msprime.simulate(15, random_seed=1)
ts = tsutil.decapitate(ts, 20)
tables = ts.dump_tables()
delta = 1.0 / (ts.num_nodes + 1)
x = 0
for node in range(ts.num_nodes):
site_id = tables.sites.add_row(x, ancestral_state="0")
x += delta
tables.mutations.add_row(site_id, node=node, derived_state="1")
ts = tables.tree_sequence()
tree = ts.first()
assert any(
tree.parent(mut.node) == tskit.NULL for mut in tree.mutations())
return tree
def get_mutations_over_roots_tree(self):
ts = msprime.simulate(15, random_seed=1)
ts = tsutil.decapitate(ts, 20)
tables = ts.tables
sites = msprime.SiteTable()
mutations = msprime.MutationTable()
delta = 1.0 / (ts.num_nodes + 1)
x = 0
for node in range(ts.num_nodes):
site_id = sites.add_row(x, ancestral_state="0")
x += delta
mutations.add_row(site_id, node=node, derived_state="1")
ts = msprime.load_tables(
nodes=tables.nodes, edges=tables.edges,
sites=sites, mutations=mutations)
tree = ts.first()
assert any(
tree.parent(mut.node) == msprime.NULL_NODE
for mut in tree.mutations())
return tree
def test_from_two_populations_decapitated(self):
from_ts = msprime.simulate(
recombination_rate=2, random_seed=5,
population_configurations=[
msprime.PopulationConfiguration(5),
msprime.PopulationConfiguration(5)],
migration_matrix=[[0, 1], [1, 0]])
from_ts = tsutil.decapitate(from_ts, from_ts.num_edges // 3)
self.assertTrue(any(tree.num_roots > 1 for tree in from_ts.trees()))
self.assertGreater(from_ts.num_trees, 1)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(
from_ts=from_ts, start_time=start_time,
random_seed=2, recombination_rate=2,
population_configurations=[
msprime.PopulationConfiguration(),
msprime.PopulationConfiguration()],
migration_matrix=[[0, 1], [1, 0]])
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def test_many_populations(self):
for N in range(1, 6):
population_configurations = [
msprime.PopulationConfiguration() for _ in range(N)]
migration_matrix = np.ones((N, N))
np.fill_diagonal(migration_matrix, 0)
from_ts = msprime.simulate(
samples=[msprime.Sample(0, 0) for _ in range(10)],
recombination_rate=2, random_seed=15,
population_configurations=population_configurations,
migration_matrix=migration_matrix)
from_ts = tsutil.decapitate(from_ts, from_ts.num_edges // 3)
self.assertTrue(any(tree.num_roots > 1 for tree in from_ts.trees()))
self.assertGreater(from_ts.num_trees, 1)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(
from_ts=from_ts, start_time=start_time,
random_seed=8, recombination_rate=2,
population_configurations=population_configurations,
migration_matrix=migration_matrix)
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def test_from_two_populations_decapitated(self):
from_ts = msprime.simulate(recombination_rate=2,
random_seed=5,
population_configurations=[
msprime.PopulationConfiguration(5),
msprime.PopulationConfiguration(5)
],
migration_matrix=[[0, 1], [1, 0]])
from_ts = tsutil.decapitate(from_ts, from_ts.num_edges // 3)
self.assertTrue(any(tree.num_roots > 1 for tree in from_ts.trees()))
self.assertGreater(from_ts.num_trees, 1)
start_time = from_ts.tables.nodes.time.max()
final_ts = msprime.simulate(from_ts=from_ts,
start_time=start_time,
random_seed=2,
recombination_rate=2,
population_configurations=[
msprime.PopulationConfiguration(),
msprime.PopulationConfiguration()
],
migration_matrix=[[0, 1], [1, 0]])
self.verify_from_tables(from_ts, final_ts, start_time)
self.verify_simulation_completed(final_ts)
def test_jukes_cantor_n50_multiroot(self):
ts = msprime.simulate(50, random_seed=1)
ts = tsutil.decapitate(ts, ts.num_edges // 2)
ts = tsutil.jukes_cantor(ts, 5, 2, seed=2)
self.verify(ts)
def test_jukes_cantor_n15_multiroot(self):
ts = msprime.simulate(15, random_seed=1)
ts = tsutil.decapitate(ts, ts.num_edges // 3)
ts = tsutil.jukes_cantor(ts, 15, 2, seed=3)
self.verify(ts)
def test_infinite_sites_n20_multiroot(self):
ts = msprime.simulate(20, mutation_rate=3, random_seed=3)
self.verify(tsutil.decapitate(ts, ts.num_edges // 2))