checkQC.config module

class checkQC.config.Config(config)

Bases: object

A Config object wraps the configuration for all handlers, so that the correct config can be passed to a handler depending on e.g. which read length and run type has been used for a sequencing run.

get(key, default=None)

get_handler_configs(instrument_and_reagent_type, read_length, downgrade_errors_for=(), use_closest_read_length=False)

Get the handler configurations for the specified parameters.

Parameters:

• instrument_and_reagent_type – type of instrument and reagents to match from config
• read_length – give the read length either as str or int

Returns:

the corresponding handler configuration(s)

class checkQC.config.ConfigFactory

Bases: object

The ConfigFactory provides methods for creating a Config instance.

static from_config_path(config_path)

Creates a Config instance from the provided config_path

Parameters:config_path – path to the configuration, or None. If no config_path is provided the default config file will be used :returns: Config instance based on the specified file path

static get_logging_config_dict(config_path)

Loads the specified logger config. This is useful when CheckQC is used more like a library, so that the default logging configuration can be overridden.

Parameters:config_path – Path to the logging config. Returns:The content of the logging config file.