torchcell.datasets.scerevisiae.caudal2024.CaudalPanTranscriptome2024Dataset

class CaudalPanTranscriptome2024Dataset(root: str = 'data/torchcell/caudal_pantranscriptome2024', io_workers: int = 0, transform: Any | None = None, pre_transform: Any | None = None, **kwargs: Any)

Bases: ExperimentDataset

Natural-isolate pan-transcriptome: each isolate a perturbation set off S288C.

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 Caudal + Peter raw files (symlinked from the library mirror).

download() → None

Symlink the Caudal zip and the six Peter-tier genotype files into raw_dir.

Large artifacts are referenced in place (never copied). The Caudal zip is hash-verified against its module pin; each Peter file against the genomes tier’s manifest (natural_isolate.link_genotype_files). process re-verifies all seven in raw/ before reading them.

process() → None

Build the 943 per-isolate pan-transcriptome experiments and write LMDB.

Every file in raw/ is verified before a row is read: the Caudal zip against this module’s pin, the six Peter files against the genomes tier’s manifest. A mismatch raises RawSha256MismatchError. Each isolate’s genotype comes from NaturalIsolateGenotypes; what the genotypes carry is counted in preprocess/natural_isolate_genotype_ledger.json.

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[RNASeqExpressionExperiment, RNASeqExpressionExperimentReference, Publication]

Build the RNA-seq experiment/reference/publication for one isolate.