def test_diversity__windowed(sample_size):
ts = simulate_ts(sample_size, length=200)
ds = ts_to_dataset(ts) # type: ignore[no-untyped-call]
ds, subsets = add_cohorts(
ds, ts, cohort_key_names=["cohorts"]) # type: ignore[no-untyped-call]
ds = window(ds, size=25)
ds = diversity(ds)
div = ds["stat_diversity"].sel(cohorts="co_0").compute()
# Calculate diversity using tskit windows
# Find the variant positions so we can have windows with a fixed number of variants
positions = ts.tables.sites.position
windows = np.concatenate(([0], positions[::25][1:], [ts.sequence_length]))
ts_div = ts.diversity(windows=windows, span_normalise=False)
np.testing.assert_allclose(div, ts_div)
# Calculate diversity using scikit-allel moving_statistic
# (Don't use windowed_diversity, since it treats the last window differently)
ds = count_variant_alleles(
ts_to_dataset(ts)) # type: ignore[no-untyped-call]
ac = ds["variant_allele_count"].values
mpd = allel.mean_pairwise_difference(ac, fill=0)
ska_div = allel.moving_statistic(mpd, np.sum, size=25)
np.testing.assert_allclose(
div[:-1], ska_div) # scikit-allel has final window missing
def test_diversity(sample_size, chunks, cohort_allele_count):
ts = simulate_ts(sample_size)
ds = ts_to_dataset(ts, chunks)
ds, subsets = add_cohorts(ds, ts, cohort_key_names=["cohorts"])
if cohort_allele_count is not None:
ds = count_cohort_alleles(ds, merge=False).rename(
{variables.cohort_allele_count: cohort_allele_count})
ds = ds.assign_coords({"cohorts": ["co_0"]})
ds = diversity(ds, cohort_allele_count=cohort_allele_count)
else:
ds = ds.assign_coords({"cohorts": ["co_0"]})
ds = diversity(ds)
div = ds.stat_diversity.sum(axis=0,
skipna=False).sel(cohorts="co_0").values
ts_div = ts.diversity(span_normalise=False)
np.testing.assert_allclose(div, ts_div)
def test_diversity(sample_size, chunks, cohort_allele_count):
ts = msprime.simulate(sample_size,
length=100,
mutation_rate=0.05,
random_seed=42)
ds = ts_to_dataset(ts, chunks) # type: ignore[no-untyped-call]
ds, subsets = add_cohorts(
ds, ts, cohort_key_names=["cohorts"]) # type: ignore[no-untyped-call]
if cohort_allele_count is not None:
ds = count_cohort_alleles(ds, merge=False).rename(
{variables.cohort_allele_count: cohort_allele_count})
ds = ds.assign_coords({"cohorts": ["co_0"]})
ds = diversity(ds, cohort_allele_count=cohort_allele_count)
else:
ds = ds.assign_coords({"cohorts": ["co_0"]})
ds = diversity(ds)
div = ds.stat_diversity.sum(axis=0,
skipna=False).sel(cohorts="co_0").values
ts_div = ts.diversity(span_normalise=False)
np.testing.assert_allclose(div, ts_div)
def test_diversity__missing_call_genotype():
ds = xr.Dataset()
with pytest.raises(ValueError, match="call_genotype not present"):
diversity(ds)
