torchcell.datasets.scerevisiae.smith2016.CrispriChemgenSmith2016Dataset

class CrispriChemgenSmith2016Dataset(root: str = 'data/torchcell/crispri_chemgen_smith2016', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

Smith 2016 per-guide dCas9-Mxi1 CRISPRi chemical-genetic env x geno dataset.

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 experiment_class: type[Experiment]

Experiment schema class produced by this dataset.

property reference_class: type[ExperimentReference]

Experiment-reference schema class produced by this dataset.

property raw_file_names: list[str]

The two sha256-pinned SI workbooks (effect table + guide->spacer map).

download() → None

Link the mirror files into raw/ after verifying each against its pin.

EFFECT_SHA256 and GUIDE_SHA256 are the pins; the manifest is the retrieval record and must carry the same digests, else ManifestPinMismatchError names both.

process() → None

Build one env x geno -> A record per (pool, guide, drug, condition); write LMDB.

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

Preprocessing is handled inside process() for this dataset.

create_experiment() → None

Experiment construction is handled inline in process() for this dataset.