dae.studies package
Subpackages
- dae.studies.tests package
- Submodules
- dae.studies.tests.conftest module
- dae.studies.tests.test_dataset module
- dae.studies.tests.test_dataset_config module
- dae.studies.tests.test_dataset_families module
- dae.studies.tests.test_study module
- dae.studies.tests.test_study_config module
- dae.studies.tests.test_study_config_parser module
- dae.studies.tests.test_study_group_person_sets_queries module
- dae.studies.tests.test_study_without_variants module
- dae.studies.tests.test_variants_db module
- Module contents
Submodules
dae.studies.dataset_helpers module
dae.studies.study module
Classes to represent genotype data.
- class dae.studies.study.GenotypeData(config: Box, studies: list[GenotypeData])[source]
Bases:
ABC
Abstract base class for genotype data.
- build_and_save(*, force: bool = False) CommonReport | None [source]
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 [source]
Generate common report JSON from genotpye data study.
- property description: str | None
Load and return description of a genotype data.
- abstract property families: FamiliesData
- get_common_report() CommonReport | None [source]
Return a study’s common report.
- get_leaf_children() list[GenotypeDataStudy] [source]
Return list of genotype studies children of this group.
- get_person_set_collection(person_set_collection_id: str | None) 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, PersonSetCollection]
- property phenotype: str | None
- property pub_med: str | None
- query_result_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) QueryResult | None [source]
Build a query result for summary variants only.
- query_result_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, study_filters: list[str] | None = None, **kwargs: Any) QueryResult | None [source]
Build a query result.
- 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) Generator[SummaryVariant, None, None] [source]
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, study_filters: 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
- class dae.studies.study.GenotypeDataStudy(config: Box, backend: QueryVariantsBase)[source]
Bases:
GenotypeData
Represents a singular genotype data study.
- property backend: QueryVariantsBase
- property families: FamiliesData
- property is_group: bool
- property study_phenotype: str
- class dae.studies.study.PSCQueryAdjustments(affected_statues: str | None, sexes: str | None, roles: str | None, person_ids: list[str] | None)[source]
Bases:
object
Query adjustments from person set collection query.
- affected_statues: str | None
- person_ids: list[str] | None
- roles: str | None
- sexes: str | None
dae.studies.variants_db module
- class dae.studies.variants_db.VariantsDb(dae_config: Box, genome: ReferenceGenome, gene_models: GeneModels, storage_registry: 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[GenotypeData] [source]
- get_all_genotype_groups() list[GenotypeData] [source]
- get_all_genotype_studies() list[GenotypeDataStudy] [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.