def alignment_example(sequence_length, include_reference=True):
ts = msprime.sim_ancestry(
samples=5, sequence_length=sequence_length, random_seed=123
)
ts = msprime.sim_mutations(ts, rate=0.1, random_seed=1234)
tables = ts.dump_tables()
if include_reference:
tables.reference_sequence.data = tskit.random_nucleotides(
ts.sequence_length, seed=1234
)
ts = tables.tree_sequence()
assert ts.num_sites > 5
return ts
def test_length_bad_type(self, length):
with pytest.raises(TypeError, match="argument must be a string"):
tskit.random_nucleotides(length)
def test_length_bad_value(self, length):
with pytest.raises(ValueError, match="must be an integer"):
tskit.random_nucleotides(length)
def test_no_seed_different_values(self):
s1 = tskit.random_nucleotides(20)
s2 = tskit.random_nucleotides(20)
assert s1 != s2
def test_different_seed_not_equal(self):
s1 = tskit.random_nucleotides(20, seed=1)
s2 = tskit.random_nucleotides(20, seed=2)
assert s1 != s2
def test_seed_equality(self, seed):
s1 = tskit.random_nucleotides(10, seed=seed)
s2 = tskit.random_nucleotides(10, seed=seed)
assert s1 == s2
def test_seed_keyword_only(self):
with pytest.raises(TypeError, match="1 positional"):
tskit.random_nucleotides(10, 42)
def test_length_required(self):
with pytest.raises(TypeError, match="required positional"):
tskit.random_nucleotides()
def test_length_keyword(self):
s1 = tskit.random_nucleotides(length=10, seed=42)
s2 = tskit.random_nucleotides(length=10, seed=42)
assert s1 == s2
def test_default_alphabet(self):
s = tskit.random_nucleotides(100, seed=42)
assert "".join(sorted(set(s))) == "ACGT"
def test_length(self, length):
s = tskit.random_nucleotides(length, seed=42)
assert len(s) == length
assert isinstance(s, str)
