def test_calc_base_stats():
count, mean, std = PhenoTool._calc_base_stats([1, 2, 3, 4, 5, 6, 7, 8, 9])
assert count == 9
assert mean == 5
assert std == pytest.approx(1.686899413014786, abs=1e-15)
def test_join_pheno_df_with_empty_pheno_df():
pheno_df = pd.DataFrame([], columns=["person_id", "measure_value"])
variants = Counter({112233: 1})
with pytest.raises(AssertionError):
PhenoTool.join_pheno_df_with_variants(pheno_df, variants)
def test_init_empty_person_ids(fake_phenotype_data):
pheno_tool = PhenoTool(fake_phenotype_data, "i1.m1", person_ids=[])
assert pheno_tool
def test_get_normalize_measure_id_measure_dict_no_keys(fake_phenotype_data):
pheno_tool = PhenoTool(fake_phenotype_data, "i1.m1")
with pytest.raises(AssertionError):
pheno_tool._get_normalize_measure_id({"measure_name": "something"})
with pytest.raises(AssertionError):
pheno_tool._get_normalize_measure_id({"instrument_name": "something"})