torchcell.datasets.scerevisiae.baryshnikova2010.SmfBaryshnikova2010Dataset

class SmfBaryshnikova2010Dataset(root: str = 'data/torchcell/smf_baryshnikova2010', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

Baryshnikova 2010 genome-scale single-mutant fitness dataset (6023 alleles).

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 publisher’s Supplementary Data 1 workbook.

download() → None

Symlink the mirror file into raw/ after verifying it against XLS_SHA256.

XLS_SHA256 is the one pin; the manifest is the retrieval record and must carry the same digest, else ManifestPinMismatchError names both.

static environment(kind: str) → Environment

The SGA final-selection plate for one allele kind (30 C, or 26 C for TS).

process() → None

Convert each SMF row into a fitness record; 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.