def root(context, config, database, verbose, log_file):
"""Clinical sequencing coverage analysis tool."""
# setup logging
loglevel = LEVELS.get(min(verbose, 2), 'WARNING')
init_log(logging.getLogger(), loglevel=loglevel, filename=log_file)
logger.info("version {0}".format(__version__))
# avoid setting global defaults in Click options, do it below when
# updating the config object
context.obj = Config(config, markup=markup)
context.obj['database'] = (database or context.obj.get(
'database', 'coverage.sqlite3'))
# update the context with new defaults from the config file
context.default_map = context.obj
def root(context, config, database, verbose, log_file):
"""Clinical sequencing coverage analysis tool."""
# setup logging
loglevel = LEVELS.get(min(verbose, 2), 'WARNING')
init_log(logging.getLogger(), loglevel=loglevel, filename=log_file)
logger.info("version {0}".format(__version__))
# avoid setting global defaults in Click options, do it below when
# updating the config object
context.obj = Config(config, markup=markup)
context.obj['database'] = (database or
context.obj.get('database', 'coverage.sqlite3'))
# update the context with new defaults from the config file
context.default_map = context.obj
def root(context, config, database, log_level, log_file):
"""Clinical sequencing coverage analysis tool."""
init_log(logging.getLogger(), loglevel=log_level, filename=log_file)
logger.debug("version {0}".format(__version__))
# avoid setting global defaults in Click options, do it below when
if os.path.exists(config):
with open(config) as conf_handle:
context.obj = yaml.load(conf_handle)
else:
context.obj = {}
context.obj['database'] = (database or context.obj.get('database'))
# update the context with new defaults from the config file
context.default_map = context.obj
def root(context, config, database, log_level, log_file):
"""Clinical sequencing coverage analysis tool."""
init_log(logging.getLogger(), loglevel=log_level, filename=log_file)
logger.debug("version {0}".format(__version__))
# avoid setting global defaults in Click options, do it below when
if os.path.exists(config):
with open(config) as conf_handle:
context.obj = yaml.load(conf_handle)
else:
context.obj = {}
context.obj['database'] = (database or context.obj.get('database'))
# update the context with new defaults from the config file
context.default_map = context.obj
