torchcell.datasets.scerevisiae.costanzo2016.DmiCostanzo2016Dataset

class DmiCostanzo2016Dataset(root: str = 'data/torchcell/dmi_costanzo2016', subset_n: int | None = None, batch_size: int = 10000, io_workers: int = 1, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

Double-mutant genetic interaction dataset from Costanzo et al. 2016.

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

download() → None

Download and unpack the Costanzo archive, keeping the SGA text files.

property experiment_class: type[GeneInteractionExperiment]

Return the GeneInteractionExperiment type for DMI data.

property reference_class: type[GeneInteractionExperimentReference]

Return the GeneInteractionExperimentReference type for DMI data.

property raw_file_names: list[str]

Return the SGA interaction text files used as raw input.

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

Concatenate and clean the SGA files into a genetic-interaction table.

process() → None

Preprocess the raw SGA files and write records into LMDB in batches.

static create_experiment(dataset_name: str, row: Series) → tuple[GeneInteractionExperiment, GeneInteractionExperimentReference, Publication]

Build DMI interaction experiment, reference, and publication objects.