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_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.phenotype = 2
ind_objs = [ind]
adapter._add_genotypes(variant, gemini_variant, 'dummy', 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 == 'dummy'
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
def cyvcf_variant(request):
"Return dictionary to mock a cyvcf variant"
variant = DotDict()
variant.CHROM = 'X'
variant.POS = 84563218
variant.REF = 'C'
variant.ALT = ['G']
variant.FILTER = 'PASS'
variant.ID = 'rs1'
variant.QUAL = 360.829986572
variant.INFO = {
'CADD': 25,
'CSQ': "G|missense_variant|MODERATE|POF1B|ENSG00000124429|"\
"Transcript|ENST00000373145|protein_coding|10/16||ENST00000373145"\
".3:c.962G>C|ENSP00000362238.3:p.Arg321Thr|1082|962|321|R/T|aGg/"\
"aCg|||-1|HGNC|13711|||ENSP00000362238|POF1B_HUMAN||UPI00001AE9F1"\
"|deleterious|possibly_damaging|hmmpanther:PTHR22546|||||,G|"\
"missense_variant|MODERATE|POF1B|ENSG00000124429|Transcript|"\
"ENST00000262753|protein_coding|10/17||ENST00000262753.4:c.962G"\
">C|ENSP00000262753.4:p.Arg321Thr|1108|962|321|R/T|aGg/aCg|||-"\
"1|HGNC|13711||CCDS14452.1|ENSP00000262753|POF1B_HUMAN||"\
"UPI0000212116|deleterious|probably_damaging|hmmpanther:PTHR22546|||||",
'Compounds': '643594:X_84615532_GTA_G>12',
'Ensembl_gene_id': 'ENSG00000124429',
'GeneticModels': '643594:XD_dn|AR_comp_dn|XR_dn',
'ModelScore': '643594:16.0',
'RankScore': '643594:19',
}
variant.start = 84563217
variant.end = 84563218
variant.var_type = 'snp'
variant.sub_vartype = 'tv'
variant.gt_types = ['C/C', 'C/G', 'C/C']
variant.gt_types = [0, 1, 0]
variant.gt_depths = [20, 7, 20]
variant.gt_ref_depths = [20, 1, 20]
variant.gt_alt_depths = [0, 6, 0]
variant.gt_quals = [57., 16., 54.]
variant.aaf = 0.16666666666666666
variant.call_rate = 1.0
variant.gt_phases = [False, False, False]
variant.gt_phred_ll_het = [57, 0, 54]
variant.gt_phred_ll_homalt = [855, 16, 810]
variant.gt_phred_ll_homref = [0, 154, 0]
variant.is_deletion = False
variant.is_indel = False
variant.is_snp = True
variant.is_sv = False
variant.is_transition = False
variant.nucl_diversity = 0.3333333333333333
variant.num_called = 3
variant.num_het = 1
variant.num_hom_alt = 0
variant.num_hom_ref = 2
variant.num_unknown = 0
return variant
def cyvcf_variant(request):
"Return dictionary to mock a cyvcf variant"
variant = DotDict()
variant.CHROM = 'X'
variant.POS = 84563218
variant.REF = 'C'
variant.ALT = ['G']
variant.FILTER = 'PASS'
variant.ID ='rs1'
variant.QUAL = 360.829986572
variant.INFO = {
'CADD': 25,
'CSQ': "G|missense_variant|MODERATE|POF1B|ENSG00000124429|"\
"Transcript|ENST00000373145|protein_coding|10/16||ENST00000373145"\
".3:c.962G>C|ENSP00000362238.3:p.Arg321Thr|1082|962|321|R/T|aGg/"\
"aCg|||-1|HGNC|13711|||ENSP00000362238|POF1B_HUMAN||UPI00001AE9F1"\
"|deleterious|possibly_damaging|hmmpanther:PTHR22546|||||,G|"\
"missense_variant|MODERATE|POF1B|ENSG00000124429|Transcript|"\
"ENST00000262753|protein_coding|10/17||ENST00000262753.4:c.962G"\
">C|ENSP00000262753.4:p.Arg321Thr|1108|962|321|R/T|aGg/aCg|||-"\
"1|HGNC|13711||CCDS14452.1|ENSP00000262753|POF1B_HUMAN||"\
"UPI0000212116|deleterious|probably_damaging|hmmpanther:PTHR22546|||||",
'Compounds': '643594:X_84615532_GTA_G>12',
'Ensembl_gene_id': 'ENSG00000124429',
'GeneticModels': '643594:XD_dn|AR_comp_dn|XR_dn',
'ModelScore': '643594:16.0',
'RankScore': '643594:19',
}
variant.start = 84563217
variant.end = 84563218
variant.var_type = 'snp'
variant.sub_vartype = 'tv'
variant.gt_types = ['C/C', 'C/G', 'C/C']
variant.gt_types = [0, 1, 0]
variant.gt_depths = [20, 7, 20]
variant.gt_ref_depths = [20, 1, 20]
variant.gt_alt_depths = [0, 6, 0]
variant.gt_quals = [ 57., 16., 54.]
variant.aaf = 0.16666666666666666
variant.call_rate = 1.0
variant.gt_phases = [False, False, False]
variant.gt_phred_ll_het = [57,0,54]
variant.gt_phred_ll_homalt = [855,16,810]
variant.gt_phred_ll_homref = [0,154,0]
variant.is_deletion = False
variant.is_indel = False
variant.is_snp = True
variant.is_sv = False
variant.is_transition = False
variant.nucl_diversity = 0.3333333333333333
variant.num_called = 3
variant.num_het = 1
variant.num_hom_alt = 0
variant.num_hom_ref = 2
variant.num_unknown = 0
return variant
