dae.studies package

Subpackages

Submodules

dae.studies.dataset_helpers module

class dae.studies.dataset_helpers.DatasetHelpers(gpf_instance=None)[source]

Bases: object

Helper class for work with studies in impala genotype storage.

disable_study_config(dataset_id, dry_run=None)[source]

Disable dataset.

find_genotype_data_config(dataset_id)[source]

Find and return configuration of a dataset.

find_genotype_data_config_file(dataset_id)[source]

Find and return config filename for a dataset.

get_genotype_storage(dataset_id)[source]

Find the genotype storage that stores a dataset.

remove_study_config(dataset_id)[source]
rename_study_config(dataset_id, new_id, config_content, dry_run=None)[source]

Rename study config for a dataset.

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.

add_parent(genotype_data_id: str) None[source]
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.

close() None[source]
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]
abstract get_studies_ids(*, leaves: bool = True) list[str][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
get_studies_ids(*, leaves: bool = True) list[str][source]
property is_group: bool
rebuild_families() None[source]

Construct genotype group families data from child studies.

class dae.studies.study.GenotypeDataStudy(config: Box, backend: QueryVariantsBase)[source]

Bases: GenotypeData

Represents a singular genotype data study.

property backend: QueryVariantsBase
property families: FamiliesData
get_studies_ids(*, leaves: bool = True) list[str][source]
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_group_configs() list[Box][source]
get_all_genotype_group_ids() list[str][source]
get_all_genotype_groups() list[GenotypeData][source]
get_all_genotype_studies() list[GenotypeDataStudy][source]
get_all_genotype_study_configs() list[Box][source]
get_all_genotype_study_ids() list[str | Any][source]
get_all_ids() list[str][source]

Deprecated since version start: using GPFInstance methods

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_group_config(group_id: str) Box | None[source]
get_genotype_study(study_id: str) GenotypeData | None[source]
get_genotype_study_config(study_id: str) Box | None[source]
register_genotype_data(genotype_data: GenotypeData | GenotypeDataGroup) None[source]

Add GenotypeData to DB.

reload() None[source]

Load all studies and groups again.

unregister_genotype_data(genotype_data: GenotypeData) None[source]

Remove GenotypeData from DB.

Module contents