torchcell.datasets.scerevisiae.zelezniak2018.ProteomeZelezniak2018Dataset

class ProteomeZelezniak2018Dataset(root: str = 'data/torchcell/proteome_zelezniak2018', io_workers: int = 0, transform: Any | None = None, pre_transform: Any | None = None, **kwargs: Any)

Bases: ExperimentDataset

SWATH-MS proteome of the yeast kinase-knockout collection (97 strains).

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 Zenodo proteome matrix required before processing.

download() → None

Download the proteome matrix from Zenodo and verify its sha256.

process() → None

Aggregate the proteome matrix into per-strain experiments and write LMDB.

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

Preprocessing is handled inside process() for this dataset.

create_experiment(row: dict[str, Any]) → tuple[ProteinAbundanceExperiment, ProteinAbundanceExperimentReference, Publication]

Build the ProteinAbundance experiment/reference/publication for one strain.