def test_substitutions_changes(self):
"""Test that substitions occur at the expected rate."""
cfg = AppSettings()
reps = 1000
deltas = []
for _ in range(0, reps):
seq = "a" * 100
dna = Chromosome(seq)
dna.substitutions()
deltas.append(sum(1 for a, b in zip(seq, dna.sequence) if a != b))
# Expand the conf_99 to compensate for repeated mutations in the same place
expected_delta = cfg.genetics.mutation_rate * 100 * \
(1 - 1/len(Chromosome.nucleotides()))
# Because there is a little slop around synonymous substitions I multiply
# the confidence by 10 just to limit the number of failing tests.
conf_99 = ((poisson.var(cfg.genetics.mutation_rate * 100) / 1000)
**(1 / 2)) * 10
observed_delta = sum(deltas) / reps
assert (expected_delta - conf_99) < observed_delta < (expected_delta +
conf_99)
def test_substitutions_length(self):
"""Ensure the substitions don't change sequence length."""
dna = Chromosome("a" * 100)
dna.substitutions()
assert len(dna.sequence) == 100