def test_simulation_runs(self):
model = drosophila_melanogaster.LiStephanTwoPopulation()
samples = [
msprime.Sample(population=0, time=0),
msprime.Sample(population=1, time=0)
]
ts = msprime.simulate(samples=samples, **model.asdict())
self.assertEqual(ts.num_populations, 2)
"""
Example of using the stdpopsim library with msprime.
"""
import msprime
import stdpopsim
from stdpopsim import drosophila_melanogaster
chrom = drosophila_melanogaster.genome.chromosomes["chr2R"]
recomb_map = chrom.recombination_map()
print("Testing Li and Stephan (2006) model")
model = drosophila_melanogaster.LiStephanTwoPopulation()
model.debug()
samples = [msprime.Sample(population=0, time=0),
msprime.Sample(population=0, time=0),
msprime.Sample(population=1, time=0),
msprime.Sample(population=1, time=0)]
ts = msprime.simulate(
samples=samples,
# recombination rate placeholder for quick runtime
recombination_rate=1e-09,
mutation_rate=chrom.default_mutation_rate,
**model.asdict())
print("simulated:", ts.num_trees, ts.num_sites)
print("====================\n")
def test_qc_model_equal(self):
model = drosophila_melanogaster.LiStephanTwoPopulation()
model_qc = drosophlia_melanogaster_qc.LiStephanTwoPopulation()
self.assertTrue(model.equals(model_qc))
def test_debug_runs(self):
model = drosophila_melanogaster.LiStephanTwoPopulation()
output = io.StringIO()
model.debug(output)
s = output.getvalue()
self.assertGreater(len(s), 0)