def test_keep_mutation_parent(self):
ts = msprime.simulate(12, recombination_rate=3, random_seed=3)
ts = tsutil.insert_branch_mutations(ts)
self.assertGreater(ts.num_sites, 2)
other = msprime.mutate(ts, rate=1, random_seed=1, keep=True)
self.assertGreater(other.num_sites, ts.num_sites)
self.verify_sites(ts, other)
def test_keep_mutation_parent(self):
ts = msprime.simulate(12, recombination_rate=3, random_seed=3)
ts = tsutil.insert_branch_mutations(ts)
self.assertGreater(ts.num_sites, 2)
other = msprime.mutate(ts, rate=1, random_seed=1, keep=True)
self.assertGreater(other.num_sites, ts.num_sites)
self.verify_sites(ts, other)
def test_single_tree_regular_mutations(self):
ts = msprime.simulate(self.num_test_sites, length=self.num_test_sites)
ts = tsutil.insert_branch_mutations(ts)
# We don't support back mutations, so this should fail.
with pytest.raises(_tskit.LibraryError):
self.verify_matrix(ts)
with pytest.raises(_tskit.LibraryError):
self.verify_max_distance(ts)
def test_keep_mutation_parent_zero_rate(self):
ts = msprime.simulate(12, recombination_rate=3, random_seed=3)
ts = tsutil.insert_branch_mutations(ts)
self.assertGreater(ts.num_sites, 2)
other = msprime.mutate(ts, rate=0, random_seed=1, keep=True)
t1 = ts.dump_tables()
t2 = other.dump_tables()
t1.provenances.clear()
t2.provenances.clear()
self.assertEqual(t1, t2)
def test_keep_mutation_parent_zero_rate(self):
ts = msprime.simulate(12, recombination_rate=3, random_seed=3)
ts = tsutil.insert_branch_mutations(ts)
self.assertGreater(ts.num_sites, 2)
other = msprime.mutate(ts, rate=0, random_seed=1, keep=True)
t1 = ts.dump_tables()
t2 = other.dump_tables()
t1.provenances.clear()
t2.provenances.clear()
self.assertEqual(t1, t2)
def test_back_mutations(self):
base_ts = msprime.simulate(10, random_seed=2)
for j in [1, 2, 3]:
ts = tsutil.insert_branch_mutations(base_ts,
mutations_per_branch=j)
self.verify_tree_sequence(ts)
def recurrent_mutation_example():
ts = msprime.simulate(10, recombination_rate=1, length=10, random_seed=2)
return tsutil.insert_branch_mutations(ts)
def test_single_tree_regular_mutations(self):
ts = msprime.simulate(self.num_test_sites, length=self.num_test_sites)
ts = tsutil.insert_branch_mutations(ts)
# We don't support back mutations, so this should fail.
self.assertRaises(_msprime.LibraryError, self.verify_matrix, ts)
self.assertRaises(_msprime.LibraryError, self.verify_max_distance, ts)
def test_branch_mutations(self):
ts = tsutil.insert_branch_mutations(
msprime.simulate(10, recombination_rate=1, random_seed=2))
self.assertGreater(ts.num_sites, 1)
self.verify(ts, 3, random_seed=7)
def test_branch_mutations(self):
ts = tsutil.insert_branch_mutations(
msprime.simulate(10, recombination_rate=1, random_seed=2))
self.assertGreater(ts.num_sites, 1)
self.verify(ts, 3, random_seed=7)
