gpf.studies package

Submodules

gpf.studies.study module

Classes to represent genotype data.

class gpf.studies.study.CommonStudyMixin(config: Box)

Bases: object

Mixin class for common study functionality to be reused.

property description: str | None

Load and return description of a genotype data.

class gpf.studies.study.GenotypeData(registry: GenotypeStorageRegistry, config: Box, studies: list[GenotypeData])

Bases: CommonStudyMixin, ABC

Abstract base class for genotype data.

add_parent(genotype_data_id: str) → None

build_and_save(*, force: bool = False) → CommonReport | None

Build a common report for a study, saves it and returns the report.

If the common reports are disabled for the study, the function skips building the report and returns None.

If the report already exists the default behavior is to skip building the report. You can force building the report by passing force=True to the function.

build_report() → CommonReport

Generate common report JSON from genotpye data study.

close() → None

abstract property families: FamiliesData

abstractmethod get_children_ids(*, leaves: bool = True) → list[str]

get_common_report() → CommonReport | None

Return a study’s common report.

get_leaf_children() → list[GenotypeDataStudy]

Return list of genotype studies children of this group.

get_person_set_collection(person_set_collection_id: str | None) → PersonSetCollection | None

get_query_leaf_studies(study_filters: Iterable[str] | None) → list[GenotypeDataStudy]

Collect studies contained in local hierarchy.

abstractmethod get_studies_ids(*, leaves: bool = True) → list[str]

property has_cnv: bool

property has_complex: bool

property has_denovo: bool

property has_transmitted: bool

property has_zygosity: bool

abstract property is_group: bool

property name: str

property parents: set[str]

property person_set_collections: dict[str, PersonSetCollection]

property phenotype: str | None

property pub_med: str | None

query_summary_variants(*, regions: list[Region] | None = None, genes: list[str] | None = None, effect_types: list[str] | None = None, variant_type: str | None = None, real_attr_filter: list[tuple] | None = None, category_attr_filter: list[tuple] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, study_filters: list[str] | None = None, **kwargs: Any) → Iterable[SummaryVariant]

Query and return generator containing summary variants.

query_variants(*, regions: list[Region] | None = None, genes: list[str] | None = None, effect_types: list[str] | None = None, family_ids: list[str] | None = None, person_ids: list[str] | None = None, person_set_collection: PSCQuery | None = None, inheritance: str | list[str] | None = None, roles: str | None = None, sexes: str | None = None, affected_statuses: str | None = None, variant_type: str | None = None, real_attr_filter: list[tuple] | None = None, categorical_attr_filter: list[tuple] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, summary_variant_ids: list[str] | None = None, study_filters: list[str] | None = None, unique_family_variants: bool = True, tags_query: TagsQuery | None = None, zygosity_in_status: str | None = None) → Iterable[FamilyVariant]

Query and return generator containing variants.

property study_id: str

property study_type: str

property year: str | None

class gpf.studies.study.GenotypeDataGroup(registry: GenotypeStorageRegistry, config: Box, studies: Iterable[GenotypeData])

Bases: GenotypeData

Represents a group of genotype data classes.

Queries to this object will be sent to all child data.

property families: FamiliesData

get_children_ids(*, leaves: bool = True) → list[str]

get_studies_ids(*, leaves: bool = True) → list[str]

property has_denovo: bool

property has_transmitted: bool

property is_group: bool

rebuild_families() → None

Construct genotype group families data from child studies.

class gpf.studies.study.GenotypeDataStudy(registry: GenotypeStorageRegistry, config: Box)

Bases: GenotypeData

Represents a singular genotype data study.

property backend: QueryVariantsBase

property families: FamiliesData

get_children_ids(*, leaves: bool = True) → list[str]

get_studies_ids(*, leaves: bool = True) → list[str]

property is_group: bool

property study_phenotype: str

class gpf.studies.study.PSCQueryAdjustments(affected_statues: str | None, sexes: str | None, roles: str | None, person_ids: list[str] | None)

Bases: object

Query adjustments from person set collection query.

affected_statues: str | None

person_ids: list[str] | None

roles: str | None

sexes: str | None

gpf.studies.variants_db module

class gpf.studies.variants_db.VariantsDb(dae_config: Box, genome: ReferenceGenome, gene_models: GeneModels, annotation: list[AttributeInfo], storage_registry: GenotypeStorageRegistry)

Bases: object

Database responsible for keeping genotype data studies and groups.

get(object_id: str) → GenotypeData | None

Deprecated since version start: using GPFInstance methods

get_all_genotype_data() → list[GenotypeData]

get_all_genotype_group_ids() → list[str]

get_all_genotype_groups() → list[GenotypeData]

get_all_genotype_studies() → list[GenotypeDataStudy]

get_all_genotype_study_ids() → list[str | Any]

get_genotype_group(group_id: str) → GenotypeData | None

get_genotype_group_config(group_id: str) → Box | None

get_genotype_study(study_id: str) → GenotypeData | None

get_genotype_study_config(study_id: str) → Box | None

register_genotype_data(genotype_data: GenotypeData | GenotypeDataGroup) → None

Add GenotypeData to DB.

reload() → None

Load all studies and groups again.

unregister_genotype_data(genotype_data: GenotypeData) → None

Remove GenotypeData from DB.

Module contents