torchcell.datasets.scerevisiae.ohnuki2018.ScmdOhnuki2018Dataset

class ScmdOhnuki2018Dataset(root: str = 'data/torchcell/scmd_ohnuki2018', io_workers: int = 0, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None, **kwargs: Any)

Bases: ExperimentDataset

CalMorph morphology of essential-gene heterozygous diploid deletions (Ohnuki 2018).

Diploid BY4743 HIP-style heterozygous (50%-dosage) deletions of 1,112 essential genes, phenotyped in liquid YPD at 25 C; the diploid essential-gene counterpart of the haploid Ohya 2005 full-deletion CalMorph screen.

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]

Return the experiment schema class for this dataset.

property reference_class: type[ExperimentReference]

Return the experiment-reference schema class for this dataset.

property raw_file_names: list[str]

Return the raw mutant and wildtype TSV filenames.

download() → None

Copy both matrices from the sha256-pinned library mirror and verify hashes.

process() → None

Load raw TSVs, build CalMorph experiments, and write the LMDB store.

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

Preprocess raw data - for CalMorph this is handled in process().

preprocess_calmorph_data(df_mutant: DataFrame) → DataFrame

Clean the mutant matrix and name every strain as released (no genome).

create_experiment() → None

Not used: records are built by create_calmorph_experiment.

static create_calmorph_experiment(dataset_name: str, row: Series, wt_reference_phenotype: dict[str, Any]) → tuple[CalMorphExperiment, CalMorphExperimentReference, Publication]

Build a CalMorph experiment and reference pair from one data row.