def test_hwep_dataset__raise_on_missing_alleles():
with pytest.raises(
ValueError,
match="`alleles` parameter must be set when not present as dataset dimension.",
):
ds = xr.Dataset({"x": (("ploidy"), np.zeros((2,)))})
hwep_test(ds)
def test_hwep_dataset__precomputed_counts(ds_neq: Dataset) -> None:
ds = ds_neq
ac = ds["call_genotype"].sum(dim="ploidy")
cts = [1, 0, 2] # arg order: hets, hom1, hom2
gtc = xr.concat([(ac == ct).sum(dim="samples") for ct in cts], dim="counts").T
ds = ds.assign(**{"variant_genotype_counts": gtc})
p = hwep_test(ds, genotype_counts="variant_genotype_counts", merge=False)
assert np.all(p < 1e-8)
def test_hwep_dataset__raise_on_nonbiallelic():
with pytest.raises(
NotImplementedError, match="HWE test only implemented for biallelic genotypes"
):
ds = xr.Dataset({"x": (("ploidy", "alleles"), np.zeros((2, 3)))})
hwep_test(ds)
def test_hwep_dataset__out_of_eq(ds_neq: Dataset) -> None:
p = hwep_test(ds_neq)["variant_hwe_p_value"].values
assert np.all(p < 1e-8)
def test_hwep_dataset__in_eq(ds_eq: Dataset) -> None:
p = hwep_test(ds_eq)["variant_hwe_p_value"].values
assert np.all(p > 1e-8)