def test_get_gene_info(): # test with HGNC symbol genes = list(get_gene_info(hgnc_symbols=['CHAT'])) assert len(genes) == 1 assert genes[0].symbol == 'CHAT' assert genes[0].ensembl_id == 'ENSG00000070748' # test with Ensembl id genes = list(get_gene_info(ensembl_ids=['ENSG00000156110'])) assert len(genes) == 1 assert genes[0].symbol == 'ADK' assert genes[0].ensembl_id == 'ENSG00000156110'
def _get_genes(self, variant): """Add the genes for a variant Get the hgnc symbols from all transcripts and add them to the variant Args: variant (dict): A variant dictionary Returns: genes (list): A list of Genes """ ensembl_ids = [] hgnc_symbols = [] for transcript in variant.transcripts: if transcript.ensembl_id: ensembl_ids.append(transcript.ensembl_id) if transcript.hgnc_symbol: hgnc_symbols.append(transcript.hgnc_symbol) genes = get_gene_info( ensembl_ids=ensembl_ids, hgnc_symbols=hgnc_symbols ) return genes
def _get_genes(self, variant): """Add the genes for a variant Get the hgnc symbols from all transcripts and add them to the variant Args: variant (dict): A variant dictionary Returns: genes (list): A list of Genes """ genes = get_gene_info(variant['transcripts']) return genes
def _get_genes(self, variant): """Add the genes for a variant Get the hgnc symbols from all transcripts and add them to the variant. Args: variant (dict): A variant dictionary Returns: genes (list): A list of Genes """ transcripts = variant['transcripts'] ensembl_ids = [transcript['ensembl_id'] for transcript in transcripts if transcript['ensembl_id']] hgnc_symbols = [transcript['hgnc_symbol'] for transcript in transcripts if transcript['hgnc_symbol']] genes = get_gene_info(ensembl_ids, hgnc_symbols) return genes
def _add_genes(self, variant_obj): """Add the Gene objects for a variant""" genes = [] ensembl_ids = [] hgnc_symbols = [] if variant_obj.transcripts: for transcript in variant_obj.transcripts: if transcript.ensembl_id: ensembl_ids.append(transcript.ensembl_id) if transcript.hgnc_symbol: hgnc_symbols.append(transcript.hgnc_symbol) else: hgnc_symbols = variant_obj.gene_symbols genes = get_gene_info(ensembl_ids=ensembl_ids, hgnc_symbols=hgnc_symbols) for gene in genes: variant_obj.add_gene(gene)
def _add_genes(self, variant_obj): """Add the Gene objects for a variant""" genes = [] ensembl_ids = [] hgnc_symbols = [] if variant_obj.transcripts: for transcript in variant_obj.transcripts: if transcript.ensembl_id: ensembl_ids.append(transcript.ensembl_id) if transcript.hgnc_symbol: hgnc_symbols.append(transcript.hgnc_symbol) else: hgnc_symbols = variant_obj.gene_symbols genes = get_gene_info( ensembl_ids=ensembl_ids, hgnc_symbols=hgnc_symbols ) for gene in genes: variant_obj.add_gene(gene)
def _get_genes(self, variant): """Add the genes for a variant Get the hgnc symbols from all transcripts and add them to the variant Args: variant (dict): A variant dictionary Returns: genes (list): A list of Genes """ ensembl_ids = [] hgnc_symbols = [] for transcript in variant.transcripts: if transcript.ensembl_id: ensembl_ids.append(transcript.ensembl_id) if transcript.hgnc_symbol: hgnc_symbols.append(transcript.hgnc_symbol) genes = get_gene_info(ensembl_ids=ensembl_ids, hgnc_symbols=hgnc_symbols) return genes