def assemble(args): """Loop thru every blast/query pair and run an assembly for each one.""" with util.make_temp_dir(where=args['temp_dir'], prefix='atram_', keep=args['keep_temp_dir']) as temp_dir: util.update_temp_dir(temp_dir, args) queries = split_queries(args) for blast_db in args['blast_db']: with db.connect(blast_db, check_version=True) as cxn: for query in queries: db.aux_db(cxn, args['temp_dir'], blast_db, query) clean_database(cxn) log.setup(args['log_file'], blast_db, query) assembler = assembly.factory(args, cxn) try: assembly_loop(args, assembler, blast_db, query) except (TimeoutError, RuntimeError): pass except Exception as err: # pylint: disable=broad-except log.error('Exception: {}'.format(err)) finally: assembler.write_final_output(blast_db, query) db.aux_detach(cxn)
def assemble(args): """Loop thru every blast/query pair and run an assembly for each one.""" with util.make_temp_dir( where=args['temp_dir'], prefix='atram_', keep=args['keep_temp_dir']) as temp_dir: util.update_temp_dir(temp_dir, args) queries = split_queries(args) for blast_db in args['blast_db']: with db.connect(blast_db, check_version=True) as cxn: for query in queries: db.aux_db(cxn, args['temp_dir'], blast_db, query) clean_database(cxn) log.setup(args['log_file'], blast_db, query) assembler = assembly.factory(args, cxn) try: assembly_loop(args, assembler, blast_db, query) except (TimeoutError, RuntimeError): pass except Exception as err: log.error('Exception: {}'.format(err)) finally: assembler.write_final_output(blast_db, query) db.aux_detach(cxn)
def preprocess(args): """Run the preprocessor.""" log.setup(args['log_file'], args['blast_db']) with db.connect(args['blast_db'], clean=True) as db_conn: db.create_metadata_table(db_conn) db.create_sequences_table(db_conn) load_seqs(args, db_conn) log.info('Creating an index for the sequence table') db.create_sequences_index(db_conn) shard_list = assign_seqs_to_shards(db_conn, args['shard_count']) create_all_blast_shards(args, shard_list)
def main(debug: ("Enable debug output", 'flag', 'd'), connect: ("Force a new connection", 'flag', 'c')): """ Start the example script """ log.setup('eventlogger.log', debug) _LOG.info('EventLogger started with PID %i', _PID) _LOG.info('This example will end after it has been idle for %i seconds', _TIMEOUT) remote = FireRemote(_DEVICE_MAC if connect else _CONTROLLER_MAC) remote.events.listen(lambda k: _LOG.info('Pressed %s', k), 'down') remote.events.listen(lambda k: _LOG.info('Released %s', k), 'up') try: mode = remote.MODE_CONNECT if connect else remote.MODE_LISTEN remote.connect(mode, _TIMEOUT) remote.event_loop() except KeyboardInterrupt: print('') _LOG.info('EventLogger has been terminated...') remote.disconnect()
def preprocess(args): """Build the databases required by atram.""" log.setup(args['log_file'], args['blast_db']) with util.make_temp_dir(where=args['temp_dir'], prefix='atram_preprocessor_', keep=args['keep_temp_dir']) as temp_dir: util.update_temp_dir(temp_dir, args) with db.connect(args['blast_db'], clean=True) as cxn: db.create_metadata_table(cxn) db.create_sequences_table(cxn) load_seqs(args, cxn) log.info('Creating an index for the sequence table') db.create_sequences_index(cxn) shard_list = assign_seqs_to_shards(cxn, args['shard_count']) create_all_blast_shards(args, shard_list)
def preprocess(args): """Build the databases required by atram.""" log.setup(args['log_file'], args['blast_db']) with util.make_temp_dir( where=args['temp_dir'], prefix='atram_preprocessor_', keep=args['keep_temp_dir']) as temp_dir: util.update_temp_dir(temp_dir, args) with db.connect(args['blast_db'], clean=True) as cxn: db.create_metadata_table(cxn) db.create_sequences_table(cxn) load_seqs(args, cxn) log.info('Creating an index for the sequence table') db.create_sequences_index(cxn) shard_list = assign_seqs_to_shards(cxn, args['shard_count']) create_all_blast_shards(args, shard_list)
def main(ip_address: ("Host that runs Kodi"), debug: ("Enable debug output", 'flag', 'd'), connect: ("Force a new connection", 'flag', 'c'), timeout: ("Idle duration after which the remote disconnects", 'option', 't', int) = 300): """ Start the example script """ log.setup('kodi.log', debug) _LOG.info('Kodi remote proxy started with PID %i', _PID) reconnect = True remote = FireRemote(_DEVICE_MAC if connect else _CONTROLLER_MAC) evc = EventClient("Fire TV Remote", ip_address) remote.events.listen(evc.press, 'down') remote.events.listen(evc.release, 'up') while reconnect: try: mode = remote.MODE_CONNECT if connect else remote.MODE_LISTEN remote.connect(mode, timeout) remote.event_loop() except KeyboardInterrupt: print('') reconnect = False _LOG.info('Kodi remote proxy has been terminated...') remote.disconnect()
def assemble(args): """Loop thru every blast/query pair and run an assembly for each one.""" queries = split_queries(args) for blast_db in args['blast_db']: with db.connect(blast_db, check_version=True) as db_conn: for query in queries: db.aux_db(db_conn, args['temp_dir'], blast_db, query) clean_database(db_conn) log.setup(args['log_file'], blast_db, query) assembler = assembly.factory(args, db_conn) try: assembly_loop(assembler, blast_db, query) assembler.write_final_output(blast_db, query) except (TimeoutError, RuntimeError): pass except Exception as err: # pylint: disable=broad-except log.error('Exception: {}'.format(err)) db.aux_detach(db_conn)