def setUpClass(cls): cls.parent_dir = os.path.dirname(os.path.realpath(__file__)) if 'hpo' not in config.sections(): config.add_section('hpo') config.set('hpo', 'obo_file', os.path.join(cls.parent_dir, 'data/hp.obo')) config.set('hpo', 'disease_to_phenotype_file', os.path.join(cls.parent_dir, 'data/phenotype.hpoa')) cls.obo_file = os.path.join(cls.parent_dir, 'data/hp.obo')
def setUp(cls): # parent dir cls.parent_dir = os.path.dirname(os.path.realpath(__file__)) cls.obo_file = os.path.join(cls.parent_dir, 'data/hp.obo') cls.pheno2genes_file = os.path.join(cls.parent_dir, 'data/phenotypes_to_genes.txt') cls.hpo_network_file = os.path.join(cls.parent_dir, 'data/hpo_network.pickle') config.set('hpo', 'data_directory', os.path.join(cls.parent_dir, 'data')) terms_to_genes, genes_to_terms, cls.annotations_count = load_p2g( cls.pheno2genes_file) # choose an HPO id that is in the custom annotations file, so it should have different information content cls.hpo_id = 'HP:0000545'
def setUp(cls): # parent dir cls.parent_dir = os.path.dirname(os.path.realpath(__file__)) if 'hpo' not in config.sections(): config.add_section('hpo') config.set('hpo', 'obo_file', os.path.join(cls.parent_dir, 'data/hp.obo')) config.set('hpo', 'disease_to_phenotype_file', os.path.join(cls.parent_dir, 'data/phenotype.hpoa')) cls.obo_file = config.get('hpo', 'obo_file') cls.disease_to_phenotype_file = config.get('hpo', 'disease_to_phenotype_file') cls.hpo_network, cls.alt2prim, cls.disease_records = generate_annotated_hpo_network( cls.obo_file, cls.disease_to_phenotype_file, ) cls.phenotype_groups = read_phenotype_groups()
def setUpClass(cls): cls.parent_dir = os.path.dirname(os.path.realpath(__file__)) config.set('hpo', 'data_directory', os.path.join(cls.parent_dir, 'data')) cls.obo_file = os.path.join(cls.parent_dir, 'data/hp.obo')