def get_uniprot_to_entrez_map(all_pws_map=None):
if all_pws_map is None:
all_pws_map = cx_pathway_reader.read_pathways()
all_alias = get_alias_set(all_pws_map)
mapped, missing = fetch_uniprot_to_entrez(all_alias)
json_data = {
'mapped': mapped,
'missing': missing,
}
path = os.path.join(config.data_dir, 'gene-map-uniprot-entrez.json')
with open(path, 'w') as f:
json.dump(json_data, f)
def read_pathways():
# get all pathways
return cx_pw.read_pathways()