alphagenome.models.dna_client.DnaClient

alphagenome.models.dna_client.DnaClient#

class alphagenome.models.dna_client.DnaClient(*, channel, model_version=None, metadata=())[source]#

Client for interacting with a DNA model server.

channel#: gRPC channel to the DNA model server.

metadata#: Metadata to send with each request.

model_version#: Optional model version to use for the DNA model server.

Methods#

Table

`output_metadata`([organism])	Get the metadata for a given organism.
`predict_interval`(interval, *[, organism])	Generate predictions for a given DNA interval.
`predict_intervals`(intervals, *[, organism, ...])	Generate predictions for a sequence of DNA intervals.
`predict_sequence`(sequence, *[, organism])	Generate predictions for a given DNA sequence.
`predict_sequences`(sequences, *[, organism, ...])	Generate predictions for a given DNA sequence.
`predict_variant`(interval, variant, *[, organism])	Generate predictions for a given DNA variant.
`predict_variants`(intervals, variants, *[, ...])	Generate predictions for a given DNA variant.
`score_interval`(interval[, interval_scorers, ...])	Generate interval scores for a single given interval.
`score_intervals`(intervals[, ...])	Generate interval scores for a sequence of intervals.
`score_ism_variants`(interval, ism_interval[, ...])	Generate in-silico mutagenesis (ISM) variant scores for a given interval.
`score_variant`(interval, variant[, ...])	Generate variant scores for a single given DNA variant.
`score_variants`(intervals, variants[, ...])	Generate variant scores for a sequence of variants.

DnaClient.output_metadata(organism=Organism.HOMO_SAPIENS)[source]#

Get the metadata for a given organism.

Parameters:: organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to get metadata for.
Return type:: OutputMetadata
Returns:: OutputMetadata for the provided organism.

DnaClient.predict_interval(interval, *, organism=Organism.HOMO_SAPIENS, requested_outputs, ontology_terms)[source]#

Generate predictions for a given DNA interval.

Parameters:

interval (Interval) – DNA interval to make prediction for.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.
requested_outputs (Iterable[OutputType]) – Iterable of OutputTypes indicating which subsets of predictions to return.
ontology_terms (Iterable[OntologyTerm | str] | None) – Iterable of ontology terms or curies to generate predictions for. If None returns all ontologies.

Return type:

Output

Returns:

Output for the provided DNA interval.

DnaClient.predict_intervals(intervals, *, organism=Organism.HOMO_SAPIENS, requested_outputs, ontology_terms, progress_bar=True, max_workers=5)[source]#

Generate predictions for a sequence of DNA intervals.

Parameters:

intervals (Sequence[Interval]) – DNA intervals to make predictions for.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the predictions.
requested_outputs (Iterable[OutputType]) – Iterable of OutputTypes indicating which subsets of predictions to return.
ontology_terms (Iterable[OntologyTerm | str] | None) – Iterable of ontology terms or curies to generate predictions for. If None returns all ontologies.
progress_bar (bool (default: True)) – If True, show a progress bar.
max_workers (int (default: 5)) – Number of parallel workers to use.

Return type:

list[Output]

Returns:

Outputs for the provided DNA intervals.

DnaClient.predict_sequence(sequence, *, organism=Organism.HOMO_SAPIENS, requested_outputs, ontology_terms)[source]#

Generate predictions for a given DNA sequence.

Parameters:

sequence (str) – DNA sequence to make prediction for.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.
requested_outputs (Iterable[OutputType]) – Iterable of OutputTypes indicating which subsets of predictions to return.
ontology_terms (Iterable[OntologyTerm | str] | None) – Iterable of ontology terms or curies to generate predictions for. If None returns all ontologies.

Return type:

Output

Returns:

Output for the provided DNA sequence.

DnaClient.predict_sequences(sequences, *, organism=Organism.HOMO_SAPIENS, requested_outputs, ontology_terms, progress_bar=True, max_workers=5)[source]#

Generate predictions for a given DNA sequence.

Parameters:

sequences (Sequence[str]) – DNA sequences to make predictions for.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.
requested_outputs (Iterable[OutputType]) – Iterable of OutputTypes indicating which subsets of predictions to return.
ontology_terms (Iterable[OntologyTerm | str] | None) – Iterable of ontology terms or curies to generate predictions for. If None returns all ontologies.
progress_bar (bool (default: True)) – If True, show a progress bar.
max_workers (int (default: 5)) – Number of parallel workers to use.

Return type:

list[Output]

Returns:

Outputs for the provided DNA sequences.

DnaClient.predict_variant(interval, variant, *, organism=Organism.HOMO_SAPIENS, requested_outputs, ontology_terms)[source]#

Generate predictions for a given DNA variant.

Parameters:

interval (Interval) – DNA interval to make prediction for.
variant (Variant) – DNA variant to make prediction for.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.
requested_outputs (Iterable[OutputType]) – Iterable of OutputTypes indicating which subsets of predictions to return.
ontology_terms (Iterable[OntologyTerm | str] | None) – Iterable of ontology terms or curies to generate predictions for. If None returns all ontologies.

Return type:

VariantOutput

Returns:

Variant output for the provided DNA interval and variant.

DnaClient.predict_variants(intervals, variants, *, organism=Organism.HOMO_SAPIENS, requested_outputs, ontology_terms, progress_bar=True, max_workers=5)[source]#

Generate predictions for a given DNA variant.

Parameters:

intervals (Interval | Sequence[Interval]) – DNA interval(s) to make predictions for.
variants (Sequence[Variant]) – DNA variants to make prediction for.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.
requested_outputs (Iterable[OutputType]) – Iterable of OutputTypes indicating which subsets of predictions to return.
ontology_terms (Iterable[OntologyTerm | str] | None) – Iterable of ontology terms or curies to generate predictions for. If None returns all ontologies.
progress_bar (bool (default: True)) – If True, show a progress bar.
max_workers (int (default: 5)) – Number of parallel workers to use.

Return type:

list[VariantOutput]

Returns:

Variant outputs for each DNA interval and variant pair.

DnaClient.score_interval(interval, interval_scorers=(), *, organism=Organism.HOMO_SAPIENS)[source]#

Generate interval scores for a single given interval.

Parameters:

interval (Interval) – Interval to make prediction for.
interval_scorers (Sequence[TypeVar(IntervalScorerTypes, bound= GeneMaskScorer)] (default: ())) – Sequence of interval scorers to use for scoring. If no interval scorers are provided, the recommended interval scorers for the organism will be used.
organism (Organism (default: <Organism.HOMO_SAPIENS: 9606>)) – Organism to use for the prediction.

Return type:

list[AnnData]

Returns:

List of AnnData interval scores.

DnaClient.score_intervals(intervals, interval_scorers=(), *, organism=Organism.HOMO_SAPIENS, progress_bar=True, max_workers=5)[source]#

Generate interval scores for a sequence of intervals.

Parameters:

intervals (Sequence[Interval]) – Sequence of DNA intervals to make prediction for.
interval_scorers (Sequence[TypeVar(IntervalScorerTypes, bound= GeneMaskScorer)] (default: ())) – Sequence of interval scorers to use for scoring. If no interval scorers are provided, the recommended interval scorers for the organism will be 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.

Return type:

list[list[AnnData]]

Returns:

List of AnnData lists corresponding to score_interval outputs for each interval.

DnaClient.score_ism_variants(interval, ism_interval, variant_scorers=(), *, organism=Organism.HOMO_SAPIENS, progress_bar=True, max_workers=5)[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[TypeVar(VariantScorerTypes, 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.
progress_bar (bool (default: True)) – If True, show a progress bar.
max_workers (int (default: 5)) – Number of parallel workers to use.

Return type:

list[list[AnnData]]

Returns:

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

DnaClient.score_variant(interval, variant, variant_scorers=(), *, organism=Organism.HOMO_SAPIENS)[source]#

Generate variant scores for a single given DNA variant.

Parameters:

interval (Interval) – DNA interval to make prediction for.
variant (Variant) – DNA variant to make prediction for.
variant_scorers (Sequence[TypeVar(VariantScorerTypes, CenterMaskScorer, ContactMapScorer, GeneMaskLFCScorer, GeneMaskActiveScorer, GeneMaskSplicingScorer, PolyadenylationScorer, SpliceJunctionScorer)] (default: ())) – Sequence of variant scorers to use for scoring. 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.

Return type:

list[AnnData]

Returns:

List of AnnData variant scores.

DnaClient.score_variants(intervals, variants, variant_scorers=(), *, organism=Organism.HOMO_SAPIENS, progress_bar=True, max_workers=5)[source]#

Generate variant scores for a sequence of variants.

Parameters:

intervals (Interval | Sequence[Interval]) – DNA interval(s) to make prediction for. If a single interval is provided, then the same interval will be used for all variants.
variants (Sequence[Variant]) – Sequence of DNA variants to make prediction for.
variant_scorers (Sequence[TypeVar(VariantScorerTypes, CenterMaskScorer, ContactMapScorer, GeneMaskLFCScorer, GeneMaskActiveScorer, GeneMaskSplicingScorer, PolyadenylationScorer, SpliceJunctionScorer)] (default: ())) – Sequence of variant scorers to use for scoring. 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.
progress_bar (bool (default: True)) – If True, show a progress bar.
max_workers (int (default: 5)) – Number of parallel workers to use.

Return type:

list[list[AnnData]]

Returns:

List of AnnData lists corresponding to score_variant outputs for each variant.

alphagenome.models.dna_client.DnaClient

Contents

alphagenome.models.dna_client.DnaClient#

Methods#