TranscriptProcessingConfig

class VmaxBuilder.config.dataclasses.TranscriptProcessingConfig(protein_coding_only: bool = False, protein_coding_aggregation_policy: str = 'sum', id_translation_provider: str = 'auto', id_translation_species: str | None = None, id_translation_max_workers: int = 8, id_translation_batch_size: int = 500)[source]

Generated: validation needed.

Description:

Transcript-level processing options shared across expression preprocessing and model-stage transcript metadata retrieval.

Parameters:

  • protein_coding_only (bool) – Whether transcript->gene aggregation should keep only transcript rows marked as protein-coding when annotation is available.

  • protein_coding_aggregation_policy (str) – Aggregation policy for protein-coding transcript rows. Supported values: sum, mean.

  • id_translation_provider (str) – Translation provider key used when building model gene->transcript metadata.

  • id_translation_species (str | None) – Optional species hint for transcript lookup.

  • id_translation_max_workers (int) – Worker thread count for transcript lookup.

  • id_translation_batch_size (int) – Query batch size for transcript lookup.

Public Methods

protein_coding_only

protein_coding_aggregation_policy

id_translation_provider

id_translation_species

id_translation_max_workers

id_translation_batch_size