server.adaptor.execute(sql1, ) server.adaptor.execute(sql2, ) server.adaptor.execute(sql3, ) if __name__ == '__main__': import argparse from chlamdb.biosqldb import manipulate_biosqldb import chlamdb_setup_utils parser = argparse.ArgumentParser() parser.add_argument("-i", '--PMID_sqlite_db', type=str, help="input PMID sqlite3 db file") parser.add_argument("-d", '--database_name', type=str, help="database name") parser.add_argument("-c", '--corresp_table', type=str, help="hash to locus correspondance table") args = parser.parse_args() hash2locus_list = chlamdb_setup_utils.get_hash2locus_list( args.corresp_table) load_PMID(args.PMID_sqlite_db, hash2locus_list, args.database_name)
help= "Tab separated file with correspondance between sequence hashes and locus tags" ) parser.add_argument("-l", '--legacy_table', action="store_true", help="Create legacy table in biosqldb") args = parser.parse_args() biodb = args.database_name server, db = manipulate_biosqldb.load_db(biodb) if args.hash2locus_tag: import chlamdb_setup_utils hash2locus_list = chlamdb_setup_utils.get_hash2locus_list( args.hash2locus_tag) if args.input_interpro: if not args.legacy_table: print("creating locus_tag2seqfeature_id") sql = 'select locus_tag, seqfeature_id from annotation.seqfeature_id2locus_%s' % biodb locus_tag2seqfeature_id = manipulate_biosqldb.to_dict( server.adaptor.execute_and_fetchall(sql, )) print("make table v1") interpro2biosql(server, hash2locus_list, locus_tag2seqfeature_id, biodb, *args.input_interpro) else: print("creating locus_tag2seqfeature_id") locus_tag2seqfeature_id = manipulate_biosqldb.locus_tag2seqfeature_id_dict( server, biodb)