score_ism_variants

score_ism_variants#

DnaClient.score_ism_variants(interval, ism_interval, condition=None, variant_scorers=(), *, interval_variant=None, organism=Organism.HOMO_SAPIENS, progress_bar=True, max_workers=5, cell_conditioning=None, cell_condition_name=None)[source]#

Generate in silico mutagenesis (ISM) variant scores for a given interval.

Parameters:

  • interval (Interval) – DNA interval to make the prediction for.

  • ism_interval (Interval) – Interval to perform ISM.

  • condition (ModelCondition | str | None (default: None)) – The condition or composite curie to generate the prediction for.

  • variant_scorers (Sequence[CenterMaskScorer | ContactMapScorer | GeneMaskLFCScorer | GeneMaskActiveScorer | GeneMaskSplicingScorer | MethylationScorer | PolyadenylationScorer | SpliceJunctionScorer] (default: ())) – Sequence of variant scorers to use for scoring each variant. If no variant scorers are provided, the recommended variant scorers for the organism and conditioning type will be used.

  • interval_variant (Variant | None (default: None)) – Optional variant to apply to the sequence. If provided, the alternate allele is used for in silico mutagenesis, otherwise the unaltered reference sequence is used.

  • organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.

  • progress_bar (bool (default: True)) – If True, show a progress bar.

  • max_workers (int (default: 5)) – Number of parallel workers to use.

  • cell_conditioning (AnnData | None (default: None)) – Optional expression conditioning input (AnnData).

  • cell_condition_name (str | None (default: None)) – Optional label for expression conditioning. When provided, the output track names are suffixed with this name and the biosample_name column is set in the var metadata. Must be provided when cell_conditioning is used.

Return type:

list[list[AnnData]]

Returns:

List of variant scores for each variant in the ISM interval.