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)