torchcell.datasets.scerevisiae.synth_leth_db.SynthLethalityYeastSynthLethDbDataset

class SynthLethalityYeastSynthLethDbDataset(root: str = 'data/torchcell/syn_leth_db_yeast', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None)

Bases: ExperimentDataset

Yeast synthetic lethality gene-pair experiments from SynLethDB.

organism: ClassVar[Organism] = 'scerevisiae'

each loader declares its own, the build’s organism switch reads it off the class (dataset_organism), and a loader that forgot it is refused by name instead of inheriting an organism it may not have.

Type:

The host organism every record describes. Annotated here WITHOUT a value

property raw_file_names: list[str]

Return the raw synthetic-lethality CSV filename.

property processed_file_names: list[str]

Return the processed LMDB directory name.

property experiment_class: type[SyntheticLethalityExperiment]

Return the synthetic-lethality experiment schema class.

property reference_class: type[SyntheticLethalityExperimentReference]

Return the synthetic-lethality experiment-reference schema class.

download() → None

Download the synthetic-lethality CSV from Google Drive.

preprocess_raw(df: DataFrame, preprocess: dict[str, Any] | None = None) → DataFrame

Return the released rows unchanged; nothing is resolved (#1045).

process() → None

Verify the raw CSV, ledger its rows, and write the LMDB.

static create_experiment(dataset_name: str, row: Series) → tuple[SyntheticLethalityExperiment, SyntheticLethalityExperimentReference, Publication]

Build the experiment, reference, and publication objects for one row.