def test_sim_wright_fisher_generations3(self):
# Uses the bespoke DTWF forward-time simulator.
number_of_gens = 10
tables = wf.wf_sim(10, number_of_gens, deep_history=False, seed=37)
tables.sort()
ts = tables.tree_sequence()
verify_equal_ibd(ts)
def test_wright_fisher_simplified_multiple_roots(self):
tables = wf.wf_sim(
31, 10, seed=1, deep_history=False, initial_generation_samples=False,
num_loci=5)
tables.sort()
ts = tables.tree_sequence()
samples = ts.samples()
self.verify(ts, [samples[:10], samples[10:]])
def test_wright_fisher_unsimplified(self):
tables = wf.wf_sim(
20, 15, seed=1, deep_history=True, initial_generation_samples=False,
num_loci=20)
tables.sort()
ts = tables.tree_sequence()
samples = ts.samples()
self.verify(ts, [samples[:10], samples[10:]])
def test_wright_fisher_unsimplified_all_sample_sets(self):
tables = wf.wf_sim(
4, 5, seed=1, deep_history=True, initial_generation_samples=False,
num_loci=10)
tables.sort()
ts = tables.tree_sequence()
for S in set_partitions(list(ts.samples())):
self.verify(ts, S)
def test_wright_fisher_simplified(self):
tables = wf.wf_sim(
9, 10, seed=1, deep_history=True, initial_generation_samples=False,
num_loci=5)
tables.sort()
ts = tables.tree_sequence().simplify()
ts = msprime.mutate(ts, rate=0.01, random_seed=1234)
self.assertGreater(ts.num_sites, 0)
self.verify(ts)
def test_wright_fisher_initial_generation(self):
tables = wf.wf_sim(
6, 5, seed=3, deep_history=True, initial_generation_samples=True,
num_loci=2)
tables.sort()
tables.simplify()
ts = msprime.mutate(tables.tree_sequence(), rate=0.08, random_seed=2)
self.assertGreater(ts.num_sites, 0)
self.verify(ts)
def test_wright_fisher_examples(self, N, T):
tables = wf.wf_sim(N, T, deep_history=False, seed=42)
tables.sort()
# NB this is essential! We get spurious breakpoints otherwise
tables.edges.squash()
tables.sort()
ts = tables.tree_sequence()
ibd0 = ibd_segments(ts)
ibd1 = naive_ibd_all_pairs(ts)
assert_ibd_equal(ibd0, ibd1)
def test_wright_fisher_initial_generation_no_deep_history(self):
tables = wf.wf_sim(
20, 15, seed=2, deep_history=False, initial_generation_samples=True,
num_loci=20)
tables.sort()
tables.simplify()
ts = tables.tree_sequence()
samples = ts.samples()
founders = [u for u in samples if ts.node(u).time > 0]
samples = [u for u in samples if ts.node(u).time == 0]
self.verify(ts, [founders[:10], founders[10:]], samples)
def test_wright_fisher_unsimplified_multiple_roots(self):
tables = wf.wf_sim(8,
15,
seed=1,
deep_history=False,
initial_generation_samples=False,
num_loci=20)
tables.sort()
ts = msprime.mutate(tables.tree_sequence(), rate=0.006, random_seed=2)
self.assertGreater(ts.num_sites, 0)
ts = tsutil.insert_individuals(ts, ploidy=2)
self.verify(ts)
def test_wright_fisher_initial_generation(self):
tables = wf.wf_sim(6,
5,
seed=3,
deep_history=True,
initial_generation_samples=True,
num_loci=2)
tables.sort()
tables.simplify()
ts = msprime.mutate(tables.tree_sequence(), rate=0.08, random_seed=2)
assert ts.num_sites > 0
ts = tsutil.insert_individuals(ts, ploidy=3)
self.verify(ts)
def test_forward_time_wright_fisher_simplified(self):
tables = wf.wf_sim(
30,
10,
seed=1,
deep_history=False,
initial_generation_samples=False,
num_loci=5,
)
tables.sort()
ts = tables.tree_sequence()
samples = ts.samples()
self.verify_topologies(ts, sample_sets=[samples[:10], samples[10:]])
def test_forward_time_wright_fisher_unsimplified_all_sample_sets(self):
tables = wf.wf_sim(
4,
5,
seed=1,
deep_history=False,
initial_generation_samples=False,
num_loci=10,
)
tables.sort()
ts = tables.tree_sequence()
for S in test_stats.set_partitions(list(ts.samples())):
self.verify_topologies(ts, sample_sets=S)
def test_wright_fisher_unsimplified(self):
tables = wf.wf_sim(
4,
5,
seed=1,
deep_history=True,
initial_generation_samples=False,
num_loci=10,
)
tables.sort()
ts = msprime.mutate(tables.tree_sequence(), rate=0.05, random_seed=234)
assert ts.num_sites > 0
ts = tsutil.insert_individuals(ts, ploidy=4)
self.verify(ts)
def test_wright_fisher_initial_generation_no_deep_history(self):
tables = wf.wf_sim(20,
15,
seed=2,
deep_history=False,
initial_generation_samples=True,
num_loci=20)
tables.sort()
tables.simplify()
ts = tables.tree_sequence()
samples = ts.samples()
founders = [u for u in samples if ts.node(u).time > 0]
samples = [u for u in samples if ts.node(u).time == 0]
A = self.verify(ts, [founders[:10], founders[10:]], samples)
# Because the founders are all isolated, the stat must be zero.
self.assertTrue(np.all(A == 0))
