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Description
Sex calls weren't calculated for Amin1 and Adir1 due to fragmented assembly and difficulty finding the sex chromosome contigs.
The test for diplotype clustering fails accordingly
fixture = <tests.anoph.conftest.Adir1Simulator object at 0x156944c70>, api = <malariagen_data.anoph.dipclust.AnophelesDipClustAnalysis object at 0x1684fdc60>, distance_metric = 'cityblock'
@pytest.mark.parametrize("distance_metric", ["cityblock", "euclidean"])
@parametrize_with_cases("fixture,api", cases=".")
def test_plot_diplotype_clustering(
fixture, api: AnophelesDipClustAnalysis, distance_metric
):
# Set up test parameters.
all_sample_sets = api.sample_sets()["sample_set"].to_list()
linkage_methods = (
"single",
"complete",
"average",
"weighted",
"centroid",
"median",
"ward",
)
sample_queries = (None, "sex_call == 'F'")
dipclust_params = dict(
region=fixture.random_region_str(region_size=5000),
sample_sets=[random.choice(all_sample_sets)],
linkage_method=random.choice(linkage_methods),
distance_metric=distance_metric,
sample_query=random.choice(sample_queries),
show=False,
)
Amin1 hasn't been pushed yet but will fail in the same way.
For amin1 and adir1, these tests either need to be omitted, modified, or new ones added.