genos.api.variant_predictor

Functions

check_chromosome(chrom)	Check if the chromosome is valid.
check_position(assembly, chrom, pos)	Check if the position is valid.

Classes

VariantPredictorAPI(session, base_url[, timeout])

Wrapper class for the Variant Prediction API endpoint.

check_chromosome(chrom: str) → bool

Check if the chromosome is valid.

check_position(assembly: str, chrom: str, pos: int) → bool

Check if the position is valid.

class VariantPredictorAPI(session: Session, base_url: str, timeout: int = 30)

Bases: BaseAPI

Wrapper class for the Variant Prediction API endpoint.

This class handles requests to the /predict endpoint for variant pathogenicity prediction. It validates input and raises structured SDK exceptions on errors.

predict(assembly: str, chrom: str, pos: int, ref: str, alt: str) → dict

Predict the pathogenicity of a genetic variant.

Parameters:

• assembly (str) – Reference genome version, allowed values: ‘hg38’ or ‘hg19’.

• chrom (str) – Chromosome, e.g., ‘chr6’.

• pos (int) – Position, 1-based coordinate.

• ref (str) – Reference allele, single letter or sequence.

• alt (str) – Alternate allele, single letter or sequence.

Returns:

Prediction result, typically containing:

• ”variant”: input variant

• ”prediction”: “Pathogenic” or “Benign”

• ”score_Benign”: float

• ”score_Pathogenic”: float

Return type:

dict

Raises:

• ValueError – If any argument is invalid.

• APIRequestError – If the API request fails or the server returns an error.