def get_handler(config, databases):
'''Build the TaskHandler for the annotation pipelines. The
handler will not have registered tasks when returned.
Args:
config (dict): Config dictionary, which contains the command
line arguments and the entries from the config file.
databases (dict): The dictionary of files from a database
TaskHandler.
Returns:
handler.TaskHandler: A constructed TaskHandler.
'''
logger = logging.getLogger('AnnotateHandler')
if config['output_dir'] is None:
out_dir = path.basename(config['transcriptome'] + '.dammit')
else:
out_dir = config['output_dir']
directory = path.abspath(out_dir)
handler = TaskHandler(directory, logger,
db='annotate',
backend=config['doit_backend'],
verbosity=config['verbosity'],
profile=config['profile'])
log.start_logging(path.join(directory, 'dammit.log'))
input_fn = path.join(directory, path.basename(config['transcriptome']))
name_map_fn = input_fn + '.dammit.namemap.csv'
handler.register_task('rename-transcriptome',
get_rename_transcriptome_task(
path.abspath(config['transcriptome']),
input_fn,
name_map_fn,
config['name'],
config['no_rename']
),
files={'transcriptome': input_fn,
'name_map': name_map_fn})
return handler
def get_handler(config):
'''Build the TaskHandler for the database prep pipeline. The
handler will not have registered tasks when returned.
Args:
config (dict): Config dictionary, which contains the command
line arguments and the entries from the config file.
databases (dict): The database dictionary from `databases.json`.
Returns:
handler.TaskHandler: A constructed TaskHandler.
'''
logger = logging.getLogger('DatabaseHandler')
logger.debug('get_handler')
handler = TaskHandler(config['database_dir'],
logger,
db='databases',
backend=config['doit_backend'],
verbosity=config['verbosity'],
n_threads=config['n_threads'])
return handler