AlphaGenome 1

Client, outputs and scorers for AlphaGenome 1.

DNA client

models.v1.dna_client.create(api_key, *[, ...])	Creates a model client for a given API key.
models.v1.dna_client.ModelVersion(value)	Enumeration of available model checkpoints.
models.v1.dna_client.Organism(value)	Enumeration of all the available organisms.
models.v1.dna_client.validate_sequence_length(length)	Validate that the input sequence length is supported by the model.
models.v1.dna_client.DnaClient(*, channel[, ...])	Client for interacting with a DNA model server.

Sequence lengths

Supported input sequence lengths, for use with sequence_length arguments and validate_sequence_length().

alphagenome.models.v1.dna_client.SEQUENCE_LENGTH_16KB = 16384

16,384 bp (2^14).

alphagenome.models.v1.dna_client.SEQUENCE_LENGTH_100KB = 131072

131,072 bp (2^17).

alphagenome.models.v1.dna_client.SEQUENCE_LENGTH_500KB = 524288

524,288 bp (2^19).

alphagenome.models.v1.dna_client.SEQUENCE_LENGTH_1MB = 1048576

1,048,576 bp (2^20).

DNA output

models.v1.dna_output.OutputType(value)	Enumeration of all the available types of outputs.
models.v1.dna_output.Output([atac, cage, ...])	Model outputs for a single prediction.
models.v1.dna_output.OutputMetadata(*[, ...])	Metadata detailing the content of model output.
models.v1.dna_output.VariantOutput(...)	Model outputs for a variant prediction.

Variant scorers

models.v1.variant_scorers.AggregationType(value)	Enum indicating the type of variant scorer aggregation.
models.v1.variant_scorers.BaseVariantScorer(value)	Enum indicating the type of variant scoring.
models.v1.variant_scorers.CenterMaskScorer(...)	Variant scorer for center mask scorers.
models.v1.variant_scorers.ContactMapScorer()	Variant scorer for contact map scorers.
models.v1.variant_scorers.GeneMaskLFCScorer(...)	Variant scorer for gene-mask log fold change scoring.
models.v1.variant_scorers.GeneMaskActiveScorer(...)	Variant scorer for gene-mask active allele scoring.
models.v1.variant_scorers.GeneMaskSplicingScorer(...)	Variant scorer for gene-mask scoring for splicing.
models.v1.variant_scorers.PolyadenylationScorer()	Variant scorer for polyadenylation QTLs (paQTLs).
models.v1.variant_scorers.SpliceJunctionScorer()	Variant scorer for splice junction scoring.
models.v1.variant_scorers.get_recommended_scorers(...)	Returns the recommended variant scorers for a given organism.
models.v1.variant_scorers.tidy_anndata(adata)	Formats an AnnData score as a tidy DataFrame.
models.v1.variant_scorers.tidy_scores(scores)	Formats scores into a tidy (long) pandas DataFrame.

alphagenome.models.v1.variant_scorers.RECOMMENDED_VARIANT_SCORERS

Immutable mapping from a short name (e.g. 'RNA_SEQ', 'ATAC') to a variant scorer configured with our recommended settings for that output type. Use get_recommended_scorers() to get the subset supported for a given organism.

alphagenome.models.v1.variant_scorers.VariantScorerTypes: TypeAlias

Union type alias of supported AlphaGenome1 variant scorer configurations.

Interval scorers

models.v1.interval_scorers.IntervalAggregationType(value)	Enum indicating the type of interval scorer aggregation.
models.v1.interval_scorers.BaseIntervalScorer(value)	Enum indicating the type of interval scoring.
models.v1.interval_scorers.GeneMaskScorer(...)	Interval scorer for gene-mask scoring.

alphagenome.models.v1.interval_scorers.IntervalScorerTypes

Union type alias of supported AlphaGenome 1 interval scorer configurations.