dae.person_filters package

Submodules

dae.person_filters.person_filters module

class dae.person_filters.person_filters.CriteriaFilter(criteria: str, values: Collection)[source]

Bases: PersonFilter

Filter individuals based on given criteria and their values.

apply(families: FamiliesData, roles: list[str] | None = None) → set[str][source]: Return a set of person ids for individuals matching the filter.

class dae.person_filters.person_filters.FamilyFilter(person_filter: PersonFilter)[source]

Bases: PersonFilter

Apply a given PersonFilter, but collect a set of family ids instead.

apply(families: FamiliesData, *args: Any, **kwargs: Any) → set[str][source]

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.person_filters.PersonFilter[source]

Bases: object

Generic interface for a filter working on FamiliesData objects.

apply(families: FamiliesData, roles: list[str] | None = None) → set[str][source]

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.person_filters.PersonFilterRange(criteria: str, values: Collection)[source]

Bases: CriteriaFilter

Filter based on a range of values.

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.person_filters.PersonFilterSet(criteria: str, values: Collection)[source]

Bases: CriteriaFilter

Filter based on a specific set of values.

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.person_filters.PhenoFilter(criteria: str, values: Collection, phenotype_data: PhenotypeData)[source]

Bases: CriteriaFilter

Filter using a phenotype measure as criteria.

apply(families: FamiliesData, roles: list[str] | None = None) → set[str][source]: Return a set of person ids for individuals matching the filter.

class dae.person_filters.person_filters.PhenoFilterRange(measure: Measure, values: Collection, phenotype_data: PhenotypeData)[source]

Bases: PhenoFilter, PersonFilterRange

Filter based on a range of phenotype measure values.

class dae.person_filters.person_filters.PhenoFilterSet(measure: Measure, values: Collection, phenotype_data: PhenotypeData)[source]

Bases: PhenoFilter, PersonFilterSet

Filter based on a specific set of phenotype measure values.

dae.person_filters.person_filters.make_pedigree_filter(pedigree_filter: dict) → PersonFilter[source]: Create a PersonFilter based on a dict config.

dae.person_filters.person_filters.make_pheno_filter(pheno_filter: dict, phenotype_data: PhenotypeData) → PersonFilter[source]: Create a PhenoFilter based on a dict config.

dae.person_filters.person_filters.make_pheno_filter_beta(pheno_filter: dict, phenotype_data: PhenotypeData) → PersonFilter[source]: Create a PhenoFilter based on a dict config.

Module contents

class dae.person_filters.FamilyFilter(person_filter: PersonFilter)[source]

Bases: PersonFilter

Apply a given PersonFilter, but collect a set of family ids instead.

apply(families: FamiliesData, *args: Any, **kwargs: Any) → set[str][source]

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.PersonFilter[source]

Bases: object

Generic interface for a filter working on FamiliesData objects.

apply(families: FamiliesData, roles: list[str] | None = None) → set[str][source]

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.PersonFilterRange(criteria: str, values: Collection)[source]

Bases: CriteriaFilter

Filter based on a range of values.

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.PersonFilterSet(criteria: str, values: Collection)[source]

Bases: CriteriaFilter

Filter based on a specific set of values.

apply_to_df(df: DataFrame) → DataFrame[source]

class dae.person_filters.PhenoFilter(criteria: str, values: Collection, phenotype_data: PhenotypeData)[source]

Bases: CriteriaFilter

Filter using a phenotype measure as criteria.

apply(families: FamiliesData, roles: list[str] | None = None) → set[str][source]: Return a set of person ids for individuals matching the filter.

class dae.person_filters.PhenoFilterRange(measure: Measure, values: Collection, phenotype_data: PhenotypeData)[source]

Bases: PhenoFilter, PersonFilterRange

Filter based on a range of phenotype measure values.

class dae.person_filters.PhenoFilterSet(measure: Measure, values: Collection, phenotype_data: PhenotypeData)[source]

Bases: PhenoFilter, PersonFilterSet

Filter based on a specific set of phenotype measure values.

dae.person_filters.make_pedigree_filter(pedigree_filter: dict) → PersonFilter[source]: Create a PersonFilter based on a dict config.

dae.person_filters.make_pheno_filter(pheno_filter: dict, phenotype_data: PhenotypeData) → PersonFilter[source]: Create a PhenoFilter based on a dict config.

dae.person_filters.make_pheno_filter_beta(pheno_filter: dict, phenotype_data: PhenotypeData) → PersonFilter[source]: Create a PhenoFilter based on a dict config.