dae.pheno_tool package
Submodules
dae.pheno_tool.tool module
- class dae.pheno_tool.tool.PhenoResult[source]
Bases:
object
Represents a result of PhenoTool calculation.
- class dae.pheno_tool.tool.PhenoTool(phenotype_data: PhenotypeData, measure_id: str, person_ids: list[str] | None = None, family_ids: list[str] | None = None, normalize_by: list[dict[str, str]] | None = None)[source]
Bases:
object
Tool to estimate dependency between variants and phenotype measrues.
Arguments of the constructor are:
phenotype_data – an instance of PhenotypeData
measure_id – a phenotype measure ID
person_ids – an optional list of person IDs to filter the phenotype database with
normalize_by – list of continuous measure names. Default value is an empty list
- calc(variants: Counter, sex_split: bool = False) dict[str, dae.pheno_tool.tool.PhenoResult] | PhenoResult [source]
Perform calculation.
variants – an instance of Counter, matching personIds to an amount of variants
sex_split – should we split the result by sex or not. Default is False.
- class dae.pheno_tool.tool.PhenoToolHelper(genotype_data: GenotypeData, phenotype_data: PhenotypeData)[source]
Bases:
object
Helper class for PhenoTool.
Collects variants and person ids from genotype data.
Arguments of the constructor are:
genotype_data – an instance of StudyWrapper
- genotype_data_persons(family_ids: list[str] | None = None, roles: list[dae.variants.attributes.Role] | None = None) set[str] [source]
Collect person ids from genotype data.