alphagenome.models.variant_scorers.GeneMaskSplicingScorer

class alphagenome.models.variant_scorers.GeneMaskSplicingScorer(requested_output, width)

Variant scorer for gene-mask scoring for splicing.

Variant scorer that quantifies changes in class assignment probabilties (dna_output.OutputType.SPLICE_SITES) or changes in the usage of splice sites (dna_output.OutputType.SPLICE_SITE_USAGE) between ALT and REF alleles using a gene exon mask.

requested_output

The requested output type (e.g. ATAC, DNASE, etc.)

width

The width of the mask around the variant.

base_variant_scorer

The base variant scorer.

name

The name of the scorer (a composite of the above attributes that uniquely identifies a scorer combination).

is_signed

Whether this variant scorer is directional (such that scores may be negative or positive) or non-directional (scores are always positive).

to_proto()

Converts the scorer to its corresponding proto message.

Raises:

ValueError – If the requested output or width is not supported.

Attributes

Table

base_variant_scorer
is_signed
name
requested_output
width

GeneMaskSplicingScorer.base_variant_scorer

GeneMaskSplicingScorer.is_signed

GeneMaskSplicingScorer.name

GeneMaskSplicingScorer.requested_output: OutputType

GeneMaskSplicingScorer.width: int | None

Methods

Table

to_proto()

GeneMaskSplicingScorer.to_proto()

Return type:

VariantScorer