mutcleaner.cleaners.rbd_ace2_cleaner#

Functions

`clean_rbd_ace2_dataset`(pipeline)	Execute the RBD ACE2 cleaning pipeline.
`create_rbd_ace2_cleaner`([dataset_or_path, ...])	Create the RBD ACE2 cleaning pipeline.

Classes

RBDACE2CleanerConfig([pipeline_name, ...])

Configuration for the RBD ACE2 cleaner.

class mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig(pipeline_name='RBDACE2 pipeline', num_workers=16, validate_config=True, reference_sequences=<factory>, target_name_aliases=<factory>, column_mapping=<factory>, drop_na_columns=<factory>, type_conversions=<factory>, validate_mut_workers=16, process_workers=16, label_columns=<factory>, primary_label_column='label')[source]#

Bases: BaseCleanerConfig

Configuration for the RBD ACE2 cleaner.

Attributes:

reference_sequencesDict[str, str]: Canonical RBD target reference sequences.
target_name_aliasesDict[str, str]: RBD target alias-to-canonical-name mapping.
column_mappingDict[str, str]: Mapping from raw source column names to the standardized column names consumed by the RBD ACE2 cleaner.
validate_mut_workersint: Worker count for mutation validation.
process_workersint: Worker count for sequence materialization.
label_columnsList[str]: Label columns retained through the pipeline.
primary_label_columnstr: Label column written into the final MutationDataset.
pipeline_namestr: Pipeline name.

Methods

`from_dict`(config_dict)	Create configuration object from dictionary
`from_json`(json_path)	Load configuration from JSON file
`get_summary`()	Get a human-readable summary of the configuration
`merge`(partial_config)	Merge partial configuration with current configuration
`to_dict`([exclude_callables])	Convert configuration to dictionary
`to_json`(json_path, **json_kwargs)	Save configuration to JSON file
`validate`()	Validate RBD ACE2 cleaner configuration values.

column_mapping: Dict[str, str]#

drop_na_columns: List[str]#

label_columns: List[str]#

pipeline_name: str = 'RBDACE2 pipeline'#

primary_label_column: str = 'label'#

process_workers: int = 16#

reference_sequences: Dict[str, str]#

target_name_aliases: Dict[str, str]#

type_conversions: Dict[str, str]#

validate()[source]#

Validate RBD ACE2 cleaner configuration values.

Raises:: ValueError – If the configuration is internally inconsistent.
Return type:: None

validate_mut_workers: int = 16#

mutcleaner.cleaners.rbd_ace2_cleaner.clean_rbd_ace2_dataset(pipeline)[source]#

Execute the RBD ACE2 cleaning pipeline.

Parameters:: pipeline (Pipeline) – Pipeline created by create_rbd_ace2_cleaner().
Return type:: Tuple[Pipeline, MutationDataset]
Returns:: Executed pipeline and cleaned mutation dataset.

mutcleaner.cleaners.rbd_ace2_cleaner.create_rbd_ace2_cleaner(dataset_or_path=None, config=None)[source]#

Create the RBD ACE2 cleaning pipeline.

Parameters:

dataset_or_path (Union[DataFrame, str, Path, None]) – Raw RBD ACE2 dataframe or input file path.
config (Union[RBDACE2CleanerConfig, Dict[str, Any], str, Path, None]) – Cleaner configuration object, partial configuration dictionary, JSON path, or None to use the built-in default configuration.

Return type:

Pipeline

Returns:

Delayed cleaning pipeline.

Raises:

TypeError – If dataset_or_path or config uses an unsupported type.