import logging logging.basicConfig(level=logging.DEBUG, filemode='w', format="%(asctime)s - %(name)s:%(funcName)s:%(lineno)d - %(levelname)s - %(message)s", datefmt="%H:%M:%S") warnings.simplefilter("error") logging.info("Moving 'glycomedb.db' to 'old_glycomedb.db'") try: os.remove("old_glycomedb.db") except: pass os.rename("glycomedb.db", "old_glycomedb.db") logging.info("Downloading all structures to 'glycomedb.db'") db = glycomedb.download_all_structures("glycomedb.db") db._patch_querymethods() logging.info("Extracting Human glycans to 'human_glycans.db'") hdb = database.dbopen("human_glycans.db", record_type=db.record_type, flag='w') hdb.load_data(db.query_by_taxon_id(9606), set_id=False) hdb.apply_indices() logging.info("Extracting Human N-glycans to 'human_n_glycans.db'") nhdb = database.dbopen("human_n_glycans.db", record_type=db.record_type, flag='w') nhdb.load_data(hdb.from_sql(hdb.execute("SELECT * FROM {table_name} WHERE is_n_glycan=1;")), set_id=False) nhdb.apply_indices() try: from glypy.search.hypothesis import ms2_fragment_database_hypothesis logging.info("De-duplicating human_n_glycans.db") keepers = ms2_fragment_database_hypothesis.duplicate_check(nhdb) ddnhdb = database.dbopen("human_n_glycans_deduplicated.db", record_type=db.record_type, flag='w') ddnhdb.load_data(keepers, set_id=False) ddnhdb.apply_indices() except ImportError: pass