def test_variant(): """ Test the variant class """ variant = setup_variant() assert variant.document_id == 'institute_genelist_caseid_variantid' assert variant.variant_id == generate_md5_key('1_132_A_C'.split('_')) assert variant.manual_rank == 5 assert variant.manual_rank_level == 'high'
def setup_variant(**kwargs): """ Setup a Variant object """ variant_id = kwargs.get('variant_id', '1_132_A_C') variant = Variant( document_id=kwargs.get('document_id', 'institute_genelist_caseid_variantid'), variant_id=generate_md5_key(variant_id.split('_')), display_name=variant_id, variant_type=kwargs.get('document_id', 'clinical'), case_id=kwargs.get('case_id', 'institute1_1'), chromosome=kwargs.get('chromosome', '1'), position=kwargs.get('position', 132), reference=kwargs.get('reference', 'A'), alternative=kwargs.get('alternative', 'C'), rank_score=kwargs.get('rank_score', 19), variant_rank=kwargs.get('variant_rank', 1), quality=kwargs.get('quality', 88), filters=kwargs.get('filters', ['PASS']), institute=kwargs.get('institute', setup_institute()), samples=kwargs.get('samples', []), genetic_models=kwargs.get('genetic_models', ['AD', 'AD_dn']), compounds=kwargs.get('compounds', []), genes=kwargs.get('genes', []), db_snp_ids=kwargs.get('db_snp_ids', ['rs0001']), # Gene ids: hgnc_symbols=kwargs.get('hgnc_symbols', ['ADK']), ensembl_gene_ids=kwargs.get('ensembl_gene_ids', ['ENSG00000156110']), # Frequencies: thousand_genomes_frequency=kwargs.get('thousand_genomes_frequency', 0.001), exac_frequency=kwargs.get('thousand_genomes_frequency', 0.002), local_frequency=kwargs.get('local_frequency', None), # Predicted deleteriousness: cadd_score=kwargs.get('cadd_score', 22), clnsig=kwargs.get('clnsig', 1), phast_conservation=kwargs.get('phast_conservation', []), gerp_conservation=kwargs.get('gerp_conservation', []), phylop_conservation=kwargs.get('phylop_conservation', []), # Database options: gene_lists=kwargs.get('gene_lists', ['gene_list_1', 'gene_list_2']), expected_inheritance=kwargs.get('expected_inheritance', ['AR']), manual_rank=kwargs.get('manual_rank', 5), acmg_evaluation=kwargs.get('acmg_evaluation', None)) return variant
def setup_variant(**kwargs): """ Setup a Variant object """ variant_id = kwargs.get('variant_id', '1_132_A_C') variant = Variant( document_id = kwargs.get('document_id', 'institute_genelist_caseid_variantid'), variant_id = generate_md5_key(variant_id.split('_')), display_name = variant_id, variant_type = kwargs.get('document_id', 'clinical'), case_id = kwargs.get('case_id', 'institute1_1'), chromosome = kwargs.get('chromosome', '1'), position = kwargs.get('position', 132), reference = kwargs.get('reference', 'A'), alternative = kwargs.get('alternative', 'C'), rank_score = kwargs.get('rank_score', 19), variant_rank = kwargs.get('variant_rank', 1), quality = kwargs.get('quality', 88), filters = kwargs.get('filters', ['PASS']), institute = kwargs.get('institute', setup_institute()), samples = kwargs.get('samples', []), genetic_models = kwargs.get('genetic_models', ['AD', 'AD_dn']), compounds = kwargs.get('compounds', []), genes = kwargs.get('genes', []), db_snp_ids = kwargs.get('db_snp_ids', ['rs0001']), # Gene ids: hgnc_symbols = kwargs.get('hgnc_symbols', ['ADK']), ensembl_gene_ids = kwargs.get('ensembl_gene_ids', ['ENSG00000156110']), # Frequencies: thousand_genomes_frequency = kwargs.get('thousand_genomes_frequency', 0.001), exac_frequency = kwargs.get('thousand_genomes_frequency', 0.002), local_frequency = kwargs.get('local_frequency', None), # Predicted deleteriousness: cadd_score = kwargs.get('cadd_score', 22), clnsig = kwargs.get('clnsig', 1), phast_conservation = kwargs.get('phast_conservation', []), gerp_conservation = kwargs.get('gerp_conservation', []), phylop_conservation = kwargs.get('phylop_conservation', []), # Database options: gene_lists = kwargs.get('gene_lists', ['gene_list_1', 'gene_list_2']), expected_inheritance = kwargs.get('expected_inheritance', ['AR']), manual_rank = kwargs.get('manual_rank', 5), acmg_evaluation = kwargs.get('acmg_evaluation', None) ) return variant