def test_raise_on_both_path_types():
with pytest.raises(
ValueError,
match=
"Either `path` or all 3 of `{bed,bim,fam}_path` must be specified but not both",
):
read_plink(path="x", bed_path="x")
def test_same_as_the_reference_implementation() -> None:
"""
This test validates that our implementation gets exactly
the same results as the reference R implementation.
"""
d = Path(__file__).parent
ds = read_plink(path="hapmap_JPT_CHB_r23a_filtered")
pcs = da.from_array(
pd.read_csv(d.joinpath("pcs.csv").as_posix(), usecols=[1, 2]).to_numpy()
)
ds[sample_pca_projection] = (("samples", "components"), pcs)
phi = pc_relate(ds).pc_relate_phi.compute()
n_samples = 90
assert isinstance(phi, xr.DataArray)
assert phi.shape == (n_samples, n_samples)
# Get genesis/reference results:
genesis_phi = pd.read_csv(d.joinpath("kinbtwe.csv"))
genesis_phi = genesis_phi[["kin"]].to_numpy()
phi_s = phi.data[np.triu_indices_from(phi.data, 1)] # type: ignore[no-untyped-call]
assert phi_s.size == genesis_phi.size
assert np.allclose(phi_s, genesis_phi.T)
def test_read_multi_path(shared_datadir, ds1):
path = shared_datadir / example_dataset_1
ds2 = read_plink(
bed_path=path.with_suffix(".bed"),
bim_path=path.with_suffix(".bim"),
fam_path=path.with_suffix(".fam"),
bim_sep="\t",
fam_sep="\t",
)
xr.testing.assert_equal(ds1, ds2)
def load_plink(paths: PLINKPaths, contig: Contig) -> Dataset:
logger.info(
f"Loading PLINK dataset for contig {contig} from {paths.bed_path}")
with dask.config.set(scheduler="threads"):
ds = read_plink(
bed_path=paths.bed_path,
bim_path=paths.bim_path,
fam_path=paths.fam_path,
bim_int_contig=False,
count_a1=False,
)
ds["sample_id"] = ds["sample_id"].astype("int32")
# All useful sample metadata will come from the
# main UKB dataset instead
ds = ds.drop_vars([
"sample_family_id",
"sample_paternal_id",
"sample_maternal_id",
"sample_phenotype",
])
# Update contig index/names
ds = transform_contig(ds, contig)
return ds
import urllib.request
from sgkit.io.plink import read_plink
if __name__ == "__main__":
for ext in (".bed", ".bim", ".fam"):
urllib.request.urlretrieve(
f"https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/plink/data/plink_sim_10s_100v_10pmiss{ext}",
f"plink_sim_10s_100v_10pmiss{ext}",
)
ds = read_plink(path="plink_sim_10s_100v_10pmiss")
print(ds)
def ds1(shared_datadir, request):
path = shared_datadir / example_dataset_1
return read_plink(path=path, bim_sep="\t", fam_sep="\t", **request.param)