torchcell.datasets.FungalUpDownTransformerDataset

class FungalUpDownTransformerDataset(root: str, genome: SCerevisiaeGenome, model_name: str | None = None, transform: Callable[[...], Any] | None = None, pre_transform: Callable[[...], Any] | None = None)

Bases: BaseEmbeddingDataset

Per-gene embeddings from the fungal up/down-stream sequence transformer.

static parse_genome(genome: SCerevisiaeGenome | None) → ParsedGenome | None

Return a ParsedGenome holding the gene set, or None if genome is None.

initialize_model() → FungalUpDownTransformer | None

Build the up/down-stream transformer for the configured model name.

process() → None

Embed each gene’s sequence window and save the collated dataset.