def __init__(self, tree_sequence, breakpoints=None):
self._tree_sequence = tree_sequence
self._num_samples = tree_sequence.get_num_samples()
self._breakpoints = breakpoints
self._sites = []
def make_mutation(id_):
site, node, derived_state, parent, metadata = tree_sequence.get_mutation(
id_)
return msprime.Mutation(id_=id_,
site=site,
node=node,
derived_state=derived_state,
parent=parent,
metadata=metadata)
for j in range(tree_sequence.get_num_sites()):
pos, ancestral_state, ll_mutations, id_, metadata = tree_sequence.get_site(
j)
self._sites.append(
msprime.Site(id_=id_,
position=pos,
ancestral_state=ancestral_state,
mutations=[
make_mutation(ll_mut)
for ll_mut in ll_mutations
],
metadata=metadata))
def test_single_tree_regular_mutations(self):
ts = msprime.simulate(self.num_test_sites, length=self.num_test_sites)
# TODO change this to use branch_mutations from tsutil.
sites = [
msprime.Site(
position=j, index=j, ancestral_state="0",
mutations=[msprime.Mutation(site=j, node=j, derived_state="1")])
for j in range(self.num_test_sites)]
ts = ts.copy(sites)
self.verify_matrix(ts)
self.verify_max_distance(ts)
def recurrent_mutation_example():
ts = msprime.simulate(10, recombination_rate=1, length=10, random_seed=2)
sites = [
msprime.Site(position=j,
index=j,
ancestral_state="0",
mutations=[
msprime.Mutation(site=j, node=k, derived_state="1")
for k in range(j + 1)
]) for j in range(ts.sample_size)
]
return ts.copy(sites)
def test_tree_sequence_regular_mutations(self):
ts = msprime.simulate(self.num_test_sites,
recombination_rate=1,
length=self.num_test_sites)
self.assertGreater(ts.get_num_trees(), 10)
sites = [
msprime.Site(position=j,
index=j,
ancestral_state="0",
mutations=[
msprime.Mutation(site=j,
node=j,
derived_state="1")
]) for j in range(self.num_test_sites)
]
ts = ts.copy(sites)
self.verify_matrix(ts)
self.verify_max_distance(ts)