torchcell.datasets.scerevisiae.dasilveira2014.MetaboliteDaSilveira2014Dataset

class MetaboliteDaSilveira2014Dataset(root: str = 'data/torchcell/metabolite_dasilveira2014', io_workers: int = 0, transform: Any | None = None, pre_transform: Any | None = None, **kwargs: Any)

Bases: ExperimentDataset

MS lipidome of the yeast kinase/phosphatase deletion collection (127 mutants).

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 Table S4 lipid matrix + Table S10 ChEBI ids required before processing.

download() → None

Copy the pinned Table S4 + Table S10 from the library mirror and verify.

process() → None

Parse the Quant sheet into per-mutant Metabolite experiments and write LMDB.

Every record is built and every refusal raised BEFORE lipid_chebi.csv, data.csv or the store is written, so a refused matrix writes nothing under preprocess/ or processed/. Refusals (each 0 in the pinned Table S4, 2026.10.01: 147 lipids, 127 mutant rows): a lipid that no WT control row measured (it would have no reference value), two mutant rows naming one ORF, and a mutant row with every lipid blank. No row is refused or dropped for its gene name: each is stored under the names the release gives it.

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[MetaboliteExperiment, MetaboliteExperimentReference, Publication]

Build the Metabolite experiment/reference/publication for one mutant.