score_ism_variants

score_ism_variants#

DnaClient.score_ism_variants(interval, ism_interval, variant_scorers=(), *, organism=Organism.HOMO_SAPIENS, interval_variant=None, progress_bar=True, max_workers=5, merge_stranded_gene_tracks=True)[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.

  • variant_scorers (Sequence[CenterMaskScorer | ContactMapScorer | GeneMaskLFCScorer | GeneMaskActiveScorer | GeneMaskSplicingScorer | 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 will be used.

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

  • 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.

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

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

  • merge_stranded_gene_tracks (bool (default: True)) – If True, merges gene-centric scores from stranded tracks into a single, unstranded track.

Return type:

list[list[AnnData]]

Returns:

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