enrichment_api package

Subpackages

• enrichment_api.tests package
  • Submodules
  • enrichment_api.tests.conftest module
    • coding_len_background()
    • create_test_study()
    • enrichment_builder()
    • enrichment_helper()
    • enrichment_serializer()
    • f1_trio()
    • f1_trio_variants()
    • grr()
    • psc_config()
    • samocha_background()
    • study_data()
    • t4c8_fixture()
  • enrichment_api.tests.test_enrichment_api module
    • test_enrichment_api_permissions()
    • test_enrichment_models()
    • test_enrichment_models_missing_study()
    • test_enrichment_test_missing_dataset_id()
    • test_enrichment_test_missing_gene_symbols()
    • test_enrichment_test_missing_study()
    • test_enrichment_test_with_gene_score()
    • test_enrichment_test_with_gene_score_with_zero_range()
    • test_enrichment_test_with_gene_set()
    • test_enrichment_test_with_gene_symbols()
  • enrichment_api.tests.test_enrichment_builder module
    • test_build()
    • test_build_people_group_selector()
    • test_build_results()
  • enrichment_api.tests.test_enrichment_helper_simple module
    • test_get_default_background_model()
    • test_get_default_background_model_default()
    • test_get_selected_counting_models()
    • test_get_selected_counting_models_default()
    • test_get_selected_counting_models_default_with_counting()
    • test_get_selected_person_set_collections()
    • test_get_selected_person_set_collections_default()
    • test_get_study_background()
    • test_get_study_enrichment_config()
    • test_gpf_fixture()
  • enrichment_api.tests.test_enrichment_serializer module
    • test_serialize()
    • test_serialize_enrichment_result()
  • enrichment_api.tests.test_t4c8_enrichment module
    • denovo_1()
    • ped_1()
    • study_1()
    • test_build_study_1_enrichment_cache()
    • test_study_1()
    • test_study_1_enrichment()
    • test_study_1_enrichment_with_caching()
    • test_t4c8_coding_len_background()
    • test_t4c8_setup()
  • Module contents

Submodules

enrichment_api.enrichment_builder module

class enrichment_api.enrichment_builder.BaseEnrichmentBuilder(enrichment_helper: EnrichmentHelper, study: WDAEStudy)

Bases: object

Base class for enrichment builders.

abstract build(gene_syms: Iterable[str], background_id: str | None, counting_id: str | None) → list[dict[str, Any]]

class enrichment_api.enrichment_builder.EnrichmentBuilder(enrichment_helper: EnrichmentHelper, study: WDAEStudy)

Bases: BaseEnrichmentBuilder

Build enrichment tool test.

build(gene_syms: Iterable[str], background_id: str | None, counting_id: str | None) → list[dict[str, Any]]

build_results(gene_syms: Iterable[str], background_id: str | None, counting_id: str | None) → list[dict[str, Any]]

Build and return a list of enrichment results.

Returns:

A list of dictionaries representing the enrichment results.

enrichment_api.enrichment_helper module

class enrichment_api.enrichment_helper.EnrichmentHelper(grr: GenomicResourceRepo, study: WDAEStudy)

Bases: object

Helper class to create enrichment tool for a genotype data.

calc_enrichment_test(psc_id: str, gene_syms: Iterable[str], effect_groups: Iterable[str] | Iterable[Iterable[str]], background_id: str | None = None, counter_id: str | None = None) → dict[str, dict[str, EnrichmentResult]]

Perform enrichment test for a genotype data.

collect_genotype_data_backgrounds() → list[BaseEnrichmentBackground]

Collect enrichment backgrounds configured for a genotype data.

create_background(background_id: str) → BaseEnrichmentBackground

Construct and return an enrichment background.

create_counter(counter_id: str) → CounterBase

Create counter for a genotype data.

get_default_background_model() → str

Return default background model field from the enrichment config. If it is missing, default to the first selected background model.

get_default_counting_model() → str

get_selected_counting_models() → list[str]

Return selected counting models field from the enrichment config. If it is missing, default to the counting field.

get_selected_person_set_collections() → str

Return selected person set collections field from the enrichment config. If it is missing, default to the first available person set collection in the provided study.

enrichment_api.enrichment_serializer module

class enrichment_api.enrichment_serializer.EnrichmentSerializer(enrichment_config: dict[str, Any], results: list[dict[str, Any]])

Bases: EffectTypesMixin

Serializer for enrichment tool results.

serialize() → list[dict]

serialize_all(grouping_results: dict[str, Any], effect_type: str, result: EnrichmentSingleResult) → dict[str, Any]

serialize_common_filter(grouping_results: dict[str, dict[str, EnrichmentSingleResult]], effect_type: str, _result: EnrichmentSingleResult, gender: list[str] | None = None) → dict[str, Any]

Serialize common filter.

serialize_enrichment_result(result: EnrichmentSingleResult) → dict[str, Any]

Serialize enrichment result.

serialize_female(grouping_results: dict[str, Any], effect_type: str, result: EnrichmentSingleResult) → dict[str, Any]

serialize_male(grouping_results: dict[str, Any], effect_type: str, result: EnrichmentSingleResult) → dict[str, Any]

serialize_overlap_filter(grouping_results: dict[str, Any], effect_type: str, result: EnrichmentSingleResult, *, gender: list[str] | None = None, overlapped_genes: bool = False) → dict[str, Any]

Serialize overlapped events filter.

serialize_people_groups(grouping_results: dict[str, Any]) → dict[str, Any]

Serialize people group results.

serialize_rec(grouping_results: dict[str, Any], effect_type: str, result: EnrichmentSingleResult) → dict[str, Any]

Serialize recurrent events.

serialize_rec_filter(grouping_results: dict[str, Any], effect_type: str, result: EnrichmentSingleResult, gender: list[str] | None = None) → dict[str, Any]

Serialize recurrent events filter.

enrichment_api.urls module

enrichment_api.views module

class enrichment_api.views.EnrichmentModelsView

Bases: QueryBaseView

Select enrichment models view.

get(_request: Request, dataset_id: str) → Response

Return enrichment configuration prepared for choosing.

class enrichment_api.views.EnrichmentTestView

Bases: QueryBaseView

View for running enrichment testing.

enrichment_description(query: dict[str, Any]) → str

Build enrichment result description.

post(request: Request) → Response

Run the enrichment test and return the result.

Module contents