def test_add_genotypes(self, variant):
adapter = GeminiPlugin()
gemini_variant = {
'gts': ['G/A', 'G/A', './.', './.', './.'],
'gt_depths': [17, 19, -1, -1, -1],
'gt_ref_depths': [10, 13, -1, -1, -1],
'gt_alt_depths': [7, 6, -1, -1, -1],
'gt_quals': [99, 99, -1, -1, -1],
}
ind = DotDict()
ind.ind_index = 0
ind.ind_id = '1'
ind.case_id = 'Case_1'
ind.phenotype = 2
ind_objs = [ind]
adapter._add_genotypes(variant, gemini_variant, ind_objs)
genotype = variant.individuals[0]
assert genotype.sample_id == ind.ind_id
assert genotype.sample_id == ind.ind_id
assert genotype.genotype == 'G/A'
assert genotype.case_id == ind.case_id
assert genotype.phenotype == ind.phenotype
assert genotype.ref_depth == 10
assert genotype.alt_depth == 7
assert genotype.depth == 17
assert genotype.genotype_quality == 99
def test_get_genotypes(gemini_variant):
adapter = GeminiPlugin()
ind = DotDict()
ind.ind_index = 0
ind.ind_id = '1'
ind.case_id = 'Case_1'
ind.phenotype = 2
ind_objs = [ind]
individual = adapter._get_genotypes(gemini_variant, ind_objs)[0]
assert individual.sample_id == ind.ind_id
assert individual.sample_id == ind.ind_id
assert individual.genotype == 'G/A'
assert individual.case_id == ind.case_id
assert individual.phenotype == ind.phenotype
assert individual.ref_depth == 10
assert individual.alt_depth == 7
assert individual.depth == 17
assert individual.genotype_quality == 99
