def test_smc_variants(self):
for model in ["smc", "smc_prime"]:
threshold = 20
sim = ancestry._parse_simulate(sample_size=10,
recombination_rate=5,
model=model)
sim.run()
self.assertGreater(sim.num_rejected_common_ancestor_events, 0)
self.assertGreater(sim.num_common_ancestor_events, threshold)
self.assertGreater(sim.num_recombination_events, threshold)
def test_smc_variants(self):
for model in ["smc", "smc_prime"]:
threshold = 20
sim = ancestry._parse_simulate(sample_size=10,
recombination_rate=5,
model=model,
random_seed=432)
sim.run()
assert sim.num_rejected_common_ancestor_events > 0
assert sim.num_common_ancestor_events > threshold
assert sim.num_recombination_events > threshold
def test_hudson(self):
threshold = 20
sim = ancestry._parse_simulate(
sample_size=10,
recombination_rate=10,
random_seed=32,
)
sim.run()
assert sim.num_common_ancestor_events > threshold
assert sim.num_recombination_events > threshold
assert sim.num_rejected_common_ancestor_events == 0
sim2 = ancestry._parse_simulate(
sample_size=10,
recombination_rate=10,
model="hudson",
random_seed=32,
)
sim2.run()
assert sim2.num_common_ancestor_events == sim.num_common_ancestor_events
assert sim2.num_recombination_events == sim.num_recombination_events
assert sim2.num_rejected_common_ancestor_events == 0
def test_hudson(self):
threshold = 20
sim = ancestry._parse_simulate(
sample_size=10,
recombination_rate=10,
random_generator=_msprime.RandomGenerator(2),
)
sim.run()
self.assertGreater(sim.num_common_ancestor_events, threshold)
self.assertGreater(sim.num_recombination_events, threshold)
self.assertEqual(sim.num_rejected_common_ancestor_events, 0)
sim2 = ancestry._parse_simulate(
sample_size=10,
recombination_rate=10,
model="hudson",
random_generator=_msprime.RandomGenerator(2),
)
sim2.run()
self.assertEqual(sim2.num_common_ancestor_events,
sim.num_common_ancestor_events)
self.assertEqual(sim2.num_recombination_events,
sim.num_recombination_events)
self.assertEqual(sim2.num_rejected_common_ancestor_events, 0)