dae.studies package
Submodules
dae.studies.study module
Classes to represent genotype data.
- class dae.studies.study.GenotypeData(config: Box, studies: list[dae.studies.study.GenotypeData])[source]
Bases:
ABC
Abstract base class for genotype data.
- property description: str | None
Load and return description of a genotype data.
- abstract property families: FamiliesData
- get_leaf_children() list[dae.studies.study.GenotypeDataStudy] [source]
Return list of genotype studies children of this group.
- get_person_set_collection(person_set_collection_id: str) PersonSetCollection | None [source]
- property has_cnv: bool
- property has_complex: bool
- property has_denovo: bool
- property has_transmitted: bool
- abstract property is_group: bool
- property name: str
- property parents: set[str]
- property person_set_collections: dict[str, dae.person_sets.PersonSetCollection]
- property phenotype: str | None
- property pub_med: str | None
- query_result_summary_variants(regions: list[dae.utils.regions.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, 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) QueryResult | None [source]
Build a query result for summary variants only.
- query_result_variants(regions: list[dae.utils.regions.Region] | None = None, genes: list[str] | None = None, effect_types: list[str] | None = None, family_ids: Iterable[str] | None = None, person_ids: Iterable[str] | None = None, person_set_collection: tuple[str, list[str]] | None = None, inheritance: str | list[str] | None = None, roles: str | None = None, sexes: str | None = None, variant_type: str | None = None, real_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: Iterable[str] | None = None, pedigree_fields: list[str] | None = None, **_kwargs: Any) QueryResult | None [source]
Build a query result.
- query_summary_variants(regions: list[dae.utils.regions.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, 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) Generator[SummaryVariant, None, None] [source]
Query and return generator containing summary variants.
- query_variants(regions: list[dae.utils.regions.Region] | None = None, genes: list[str] | None = None, effect_types: list[str] | None = None, family_ids: Iterable[str] | None = None, person_ids: Iterable[str] | None = None, person_set_collection: tuple[str, list[str]] | None = None, inheritance: str | list[str] | None = None, roles: str | None = None, sexes: str | None = None, variant_type: str | None = None, real_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: Iterable[str] | None = None, pedigree_fields: list[str] | None = None, unique_family_variants: bool = True, **kwargs: Any) Generator[FamilyVariant, None, None] [source]
Query and return generator containing variants.
- property study_id: str
- property study_type: str
- property year: str | None
- class dae.studies.study.GenotypeDataGroup(config: Box, studies: Iterable[GenotypeData])[source]
Bases:
GenotypeData
Represents a group of genotype data classes.
Queries to this object will be sent to all child data.
- property families: FamiliesData
- property is_group: bool
dae.studies.variants_db module
- class dae.studies.variants_db.VariantsDb(dae_config: Box, genome: ReferenceGenome, gene_models: GeneModels, genotype_storage_factory: GenotypeStorageRegistry)[source]
Bases:
object
Database responsible for keeping genotype data studies and groups.
- get(object_id: str) GenotypeData | None [source]
Deprecated since version start: using GPFInstance methods
- get_all_genotype_data() list[dae.studies.study.GenotypeData] [source]
- get_all_genotype_groups() list[dae.studies.study.GenotypeData] [source]
- get_all_genotype_studies() List[GenotypeDataStudy | Any] [source]
- get_config(config_id: str) Box | None [source]
Deprecated since version start: using GPFInstance methods
- get_genotype_group(group_id: str) GenotypeData | None [source]
- get_genotype_study(study_id: str) GenotypeData | None [source]
- register_genotype_data(genotype_data: GenotypeData | GenotypeDataGroup) None [source]
Add GenotypeData to DB.
- unregister_genotype_data(genotype_data: GenotypeData) None [source]
Remove GenotypeData from DB.