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)