def test_observed_heterozygosity__scikit_allel_comparison(
n_variant, n_sample, missing_pct, window_size, seed):
ds = simulate_genotype_call_dataset(
n_variant=n_variant,
n_sample=n_sample,
n_ploidy=2,
missing_pct=missing_pct,
seed=seed,
)
ds["sample_cohort"] = (
["samples"],
np.zeros(n_sample, int),
)
ds = window(ds, size=window_size)
ho_sg = observed_heterozygosity(ds)["stat_observed_heterozygosity"].values
if n_sample % window_size:
# scikit-allel will drop the ragged end
ho_sg = ho_sg[0:-1]
# calculate with scikit-allel
ho_sa = allel.moving_statistic(
allel.heterozygosity_observed(ds["call_genotype"]),
np.sum,
size=window_size,
)
# add cohort dimension to scikit-allel result
np.testing.assert_almost_equal(ho_sg, ho_sa[..., None])
def test_observed_heterozygosity(chunks):
ds = simulate_genotype_call_dataset(
n_variant=4,
n_sample=6,
n_ploidy=4,
)
ds["call_genotype"] = (
["variants", "samples", "ploidy"],
da.asarray([
[
[0, 0, 0, 0],
[0, 0, 0, 0],
[1, 1, 1, 1],
[1, 1, 1, 1],
[0, 0, 0, 0],
[1, 1, 1, 1],
],
[
[0, 0, 0, 0],
[0, 0, 0, 1],
[0, 0, 1, 1],
[0, 0, 1, 1],
[1, 0, 1, 0],
[0, 1, 0, 1],
],
[
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 1, 2, 3],
[0, 1, 2, 3],
[0, 1, 2, 3],
[4, 5, 6, 7],
],
[
[0, 0, -1, -1],
[0, 1, -1, -1],
[0, 0, 1, 1],
[-1, -1, -1, -1],
[0, -1, -1, -1],
[-1, -1, -1, -1],
],
]).rechunk(chunks),
)
ds.call_genotype_mask.values = ds.call_genotype < 0
ds["sample_cohort"] = (
["samples"],
da.asarray([0, 0, 1, 1, 2, 2]).rechunk(chunks[1]),
)
ho = observed_heterozygosity(ds)["stat_observed_heterozygosity"]
np.testing.assert_almost_equal(
ho,
np.array([
[0, 0, 0],
[1 / 4, 2 / 3, 2 / 3],
[0, 1, 1],
[1 / 2, 4 / 6, np.nan],
]),
)
def test_observed_heterozygosity__windowed(chunks, cohorts, expectation):
ds = simulate_genotype_call_dataset(
n_variant=4,
n_sample=6,
n_ploidy=4,
)
ds["call_genotype"] = (
["variants", "samples", "ploidy"],
da.asarray([
[
[0, 0, 0, 0],
[0, 0, 0, 0],
[1, 1, 1, 1],
[1, 1, 1, 1],
[0, 0, 0, 0],
[1, 1, 1, 1],
],
[
[0, 0, 0, 0],
[0, 0, 0, 1],
[0, 0, 1, 1],
[0, 0, 1, 1],
[1, 0, 1, 0],
[0, 1, 0, 1],
],
[
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 1, 2, 3],
[0, 1, 2, 3],
[0, 1, 2, 3],
[4, 5, 6, 7],
],
[
[0, 0, -1, -1],
[0, 1, -1, -1],
[0, 0, 1, 1],
[-1, -1, -1, -1],
[0, -1, -1, -1],
[-1, -1, -1, -1],
],
]).rechunk(chunks),
)
ds.call_genotype_mask.values = ds.call_genotype < 0
ds["sample_cohort"] = (
["samples"],
da.asarray(cohorts).rechunk(chunks[1]),
)
ds = window(ds, size=2)
ho = observed_heterozygosity(ds)["stat_observed_heterozygosity"]
np.testing.assert_almost_equal(
ho,
np.array(expectation),
)