def test_multichar_alleles(self):
ts = tsutil.insert_multichar_mutations(self.get_tree_sequence())
for var in ts.variants():
assert len(var.alleles) == 2
assert var.site.ancestral_state == var.alleles[0]
assert var.site.mutations[0].derived_state == var.alleles[1]
assert all(0 <= var.genotypes)
assert all(var.genotypes <= 1)
def test_multichar_alleles(self):
ts = tsutil.insert_multichar_mutations(self.get_tree_sequence())
for var in ts.variants():
self.assertEqual(len(var.alleles), 2)
self.assertEqual(var.site.ancestral_state, var.alleles[0])
self.assertEqual(var.site.mutations[0].derived_state, var.alleles[1])
self.assertTrue(all(0 <= var.genotypes))
self.assertTrue(all(var.genotypes <= 1))
def test_multichar_mutations(self):
ts = msprime.simulate(6, random_seed=1, recombination_rate=2)
ts = tsutil.insert_multichar_mutations(ts)
assert ts.num_sites > 5
all_alleles = set()
for var in ts.variants():
all_alleles.update(var.alleles)
all_alleles = tuple(all_alleles)
self.verify(ts, all_alleles)
self.verify(ts, all_alleles[::-1])
def test_single_tree_multichar_mutations(self):
ts = msprime.simulate(6, random_seed=1, mutation_rate=1)
ts = tsutil.insert_multichar_mutations(ts)
self.verify(ts)
def test_as_bytes_fails(self):
ts = tsutil.insert_multichar_mutations(self.get_tree_sequence())
with pytest.raises(ValueError):
list(ts.variants(as_bytes=True))
def test_as_bytes_fails(self):
ts = tsutil.insert_multichar_mutations(self.get_tree_sequence())
self.assertRaises(ValueError, list, ts.variants(as_bytes=True))
def multichar_mutation_example():
ts = msprime.simulate(10, recombination_rate=1, length=10, random_seed=2)
return tsutil.insert_multichar_mutations(ts)
def test_multichar_mutations(self):
ts = tsutil.insert_multichar_mutations(
msprime.simulate(12, recombination_rate=4, random_seed=3))
self.assertGreater(ts.num_sites, 5)
self.verify(ts, 3, random_seed=7)
def test_multichar_mutations(self):
ts = tsutil.insert_multichar_mutations(
msprime.simulate(12, recombination_rate=4, random_seed=3))
self.assertGreater(ts.num_sites, 5)
self.verify(ts, 3, random_seed=7)
