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')