pheno_tool_api package
Subpackages
- pheno_tool_api.tests package
- Submodules
- pheno_tool_api.tests.test_pheno_tool_api module
test_pheno_tool_api_permissions()test_pheno_tool_download_valid_request()test_pheno_tool_view_cnv_on_non_cnv_study()test_pheno_tool_view_family_ids_filter()test_pheno_tool_view_missense()test_pheno_tool_view_missing_dataset()test_pheno_tool_view_missing_measure()test_pheno_tool_view_na_values()test_pheno_tool_view_normalize()test_pheno_tool_view_pheno_filter()test_pheno_tool_view_query_no_limit()test_pheno_tool_view_valid_request()
- pheno_tool_api.tests.test_pheno_tool_view_class_static_methods module
- Module contents
Submodules
pheno_tool_api.adapter module
- class pheno_tool_api.adapter.PhenoToolAdapter(study: WDAEStudy)[source]
Bases:
PhenoToolAdapterBaseAdapter for PhenoTool class.
- build_report_description(measure_id: str, normalize_by: Any) str[source]
Build a description for a report.
- calc_by_effect(measure_id: str, effect: str, people_variants: Counter, *, person_ids: list[str] | None = None, family_ids: list[str] | None = None, normalize_by: list[dict[str, str]] | None = None) dict[str, Any][source]
Run the base pheno tool calc on given variant counts.
- get_result_by_sex(result: dict[str, PhenoResult], sex: str) dict[str, Any][source]
- static make_tool(study: WDAEAbstractStudy) GPFTool | None[source]
- produce_download(query_data: dict[str, Any], query_transformer: QueryTransformer) Generator[str, None, None][source]
Produce columns for download.
- class pheno_tool_api.adapter.PhenoToolAdapterBase[source]
Bases:
GPFToolBase class for pheno tool adapters.
- abstractmethod calc_variants(query_data: dict[str, Any]) dict[str, Any][source]
Return pheno tool result for given variants.
- abstractmethod produce_download(query_data: dict[str, Any], query_transformer: QueryTransformer) Generator[str, None, None][source]
Produce columns for download.