def test_wright_fisher_trees(self):
tables = wf.wf_sim(20, 10, seed=1, deep_history=False)
tables.sort()
ts = tables.tree_sequence()
self.verify(ts, rate=10)
ts = ts.simplify()
self.verify(ts, rate=10)
def test_wright_fisher_trees(self):
tables = wf.wf_sim(20, 10, seed=1, deep_history=False)
tables.sort()
ts = tables.tree_sequence()
self.verify(ts, rate=10)
ts = ts.simplify()
self.verify(ts, rate=10)
def get_wf_base(N, ngens, survival=0.0, num_loci=10, seed=1):
"""
Returns a forward time simulation suitable for using with simulate-from.
"""
tables = wf.wf_sim(
N, ngens, seed=seed, survival=survival, deep_history=False,
initial_generation_samples=True, num_loci=num_loci)
tables.sort()
tables.simplify()
# Unmark the ancient samples
flags = tables.nodes.flags
flags = np.zeros_like(flags)
flags[tables.nodes.time == 0] = msprime.NODE_IS_SAMPLE
tables.nodes.set_columns(
flags=flags,
population=tables.nodes.population,
time=tables.nodes.time)
return tables.tree_sequence()
def get_wf_base(N, ngens, survival=0.0, num_loci=10, seed=1):
"""
Returns a forward time simulation suitable for using with simulate-from.
"""
tables = wf.wf_sim(N,
ngens,
seed=seed,
survival=survival,
deep_history=False,
initial_generation_samples=True,
num_loci=num_loci)
tables.sort()
tables.simplify()
# Unmark the ancient samples
flags = tables.nodes.flags
flags = np.zeros_like(flags)
flags[tables.nodes.time == 0] = msprime.NODE_IS_SAMPLE
tables.nodes.set_columns(flags=flags,
population=tables.nodes.population,
time=tables.nodes.time)
return tables.tree_sequence()