studies package

Subpackages

• studies.tests package
  • Submodules
  • studies.tests.test_pheno_measures_columns module
    • test_pheno_measure_genotype_browser_columns()
    • test_study_with_phenotype_data()
  • studies.tests.test_query_transformer_family_tags module
    • test_transform_and_mode_family_tags_kwargs()
    • test_transform_complex_family_tags_kwargs()
    • test_transform_deselected_family_tags_kwargs()
    • test_transform_or_mode_family_tags_kwargs()
    • test_transform_selected_family_tags_kwargs()
  • studies.tests.test_query_transformer_present_in_child_and_parent module
    • test_attributes_query_roles()
    • test_transform_present_in_child_and_present_in_parent()
    • test_transform_present_in_child_and_present_in_parent_inheritance()
    • test_transform_present_in_child_and_present_in_parent_roles()
  • studies.tests.test_response_transformer_columns module
    • fv1()
    • fv2()
    • phenotype_person_sets()
    • test_inheritance_type_column()
    • test_is_denovo()
    • test_phenotype_attr_columns()
    • test_special_attr_columns()
    • test_special_attrs_formatting()
  • studies.tests.test_study_config_genotype_browser_columns module
    • gpf_fixture()
    • test_genotype_browser_download_columns_default()
    • test_genotype_browser_download_columns_ext()
    • test_genotype_browser_preview_columns_default()
    • test_genotype_browser_preview_columns_ext()
    • test_study_wrapper_download_columns_ext()
    • test_study_wrapper_preview_columns_ext()
    • trio_study()
  • studies.tests.test_study_group_person_sets_queries module
    • dataset()
    • gpf_fixture()
    • query_transformer()
    • response_transformer()
    • study_1()
    • study_2()
    • test_dataset_person_sets_queries()
    • test_dataset_simple()
    • wgpf_fixture()
  • studies.tests.test_study_query_request module
    • test_query_request_simple()
  • studies.tests.test_study_wrapper module
    • test_is_group_dataset()
    • test_is_group_study()
    • test_t4c8_dataset()
    • test_t4c8_study_1()
    • test_t4c8_study_2()
  • studies.tests.test_study_wrapper_queries module
    • test_query_all_variants()
    • test_query_complex_query()
    • test_query_effect_types_variants()
    • test_query_family_filters()
    • test_query_family_variants()
    • test_query_gene_scores()
    • test_query_gene_scores_formatting()
    • test_query_inheritance_types()
    • test_query_limit_variants()
    • test_query_person_filters()
    • test_query_present_in_child()
    • test_query_present_in_parent()
    • test_query_present_in_parent_and_present_in_child()
    • test_query_present_in_parent_and_present_in_child_and_phenotypes()
    • test_query_regions_variants()
    • test_query_sexes_variants()
    • test_query_study_filters()
    • test_query_unique_family_variants()
    • test_query_variant_type_variants()
    • test_study_2_query_inheritance_variants()
  • Module contents

Submodules

studies.query_transformer module

class studies.query_transformer.QueryTransformer(gene_scores_db: GeneScoresDb, chromosomes: list[str], chr_prefix: str)

Bases: QueryTransformerProtocol

Transform genotype data query WEB parameters into query variants.

FILTER_RENAMES_MAP: ClassVar[dict[str, str]] = {'effectTypes': 'effect_types', 'familyIds': 'family_ids', 'genders': 'sexes', 'geneSymbols': 'genes', 'personIds': 'person_ids', 'regionS': 'regions', 'variantTypes': 'variant_type'}

extract_person_set_collection_query(study: WDAEStudy, kwargs: dict[str, Any]) → PSCQuery

get_unique_family_variants(kwargs: dict[str, Any]) → bool

transform_kwargs(study: WDAEStudy, **kwargs: Any) → dict[str, Any]

Transform WEB query variants params into genotype data params.

Requires a study wrapper to handle study context specific arguments, such as person set collections and phenotype filters.

Returns None if the query is deemed empty.

studies.query_transformer.get_or_create_query_transformer(gpf_instance: GPFInstance) → QueryTransformer

Get or create query transformer singleton instance.

studies.query_transformer.make_query_transformer(gpf_instance: GPFInstance) → QueryTransformer

studies.response_transformer module

class studies.response_transformer.ResponseTransformer(gene_scores_db: GeneScoresDb | None)

Bases: ResponseTransformerProtocol

Helper class to transform genotype browser response.

PHENOTYPE_ATTRS: ClassVar[dict[str, Callable]] = {'carrier_phenotypes': <function ResponseTransformer.<lambda>>, 'family_phenotypes': <function ResponseTransformer.<lambda>>}

SPECIAL_ATTRS: ClassVar[dict[str, Callable]] = {'alternative': <function ResponseTransformer.<lambda>>, 'best_st': <function ResponseTransformer.<lambda>>, 'carrier_person_attributes': <function ResponseTransformer.<lambda>>, 'carrier_person_ids': <function ResponseTransformer.<lambda>>, 'effect_details': <function ResponseTransformer.<lambda>>, 'effects': <function ResponseTransformer.<lambda>>, 'family': <function ResponseTransformer.<lambda>>, 'family_person_attributes': <function ResponseTransformer.<lambda>>, 'family_person_ids': <function ResponseTransformer.<lambda>>, 'family_structure': <function ResponseTransformer.<lambda>>, 'full_effect_details': <function ResponseTransformer.<lambda>>, 'genes': <function ResponseTransformer.<lambda>>, 'genotype': <function ResponseTransformer.<lambda>>, 'inheritance_type': <function ResponseTransformer.<lambda>>, 'is_denovo': <function ResponseTransformer.<lambda>>, 'location': <function ResponseTransformer.<lambda>>, 'position': <function ResponseTransformer.<lambda>>, 'raw_effects': <function ResponseTransformer.<lambda>>, 'reference': <function ResponseTransformer.<lambda>>, 'seen_in_affected': <function ResponseTransformer.<lambda>>, 'seen_in_unaffected': <function ResponseTransformer.<lambda>>, 'variant': <function ResponseTransformer.<lambda>>, 'worst_effect': <function ResponseTransformer.<lambda>>}

STREAMING_CHUNK_SIZE = 20

build_variant_row(study: WDAEStudy, v: SummaryVariant | FamilyVariant, column_descs: list[dict], **kwargs: str | None) → list

Construct response row for a variant.

transform_gene_view_summary_variant(variant: SummaryVariant, frequency_column: str) → Generator[dict[str, Any], None, None]

Transform gene view summary response into dicts.

transform_gene_view_summary_variant_download(variants: Iterable[SummaryVariant], frequency_column: str, summary_variant_ids: set[str]) → Iterator[str]

Transform gene view summary response into rows.

variant_transformer(study: WDAEStudy, pheno_values: dict[str, Any] | None) → Callable[[FamilyVariant], FamilyVariant]

Build and return a variant transformer function.

studies.response_transformer.get_or_create_response_transformer(gpf_instance: GPFInstance) → ResponseTransformer

Get or create response transformer singleton instance.

studies.response_transformer.make_response_transformer(gpf_instance: GPFInstance) → ResponseTransformer

studies.response_transformer.members_in_order_get_family_structure(mio: list[Person]) → str

studies.study_wrapper module

class studies.study_wrapper.QueryTransformerProtocol(*args, **kwargs)

Bases: Protocol

Protocol for query transformer interface.

abstract extract_person_set_collection_query(study: WDAEStudy, kwargs: dict[str, Any]) → PSCQuery

abstract get_unique_family_variants(kwargs: dict[str, Any]) → bool

abstract transform_kwargs(study: WDAEStudy, **kwargs: Any) → dict[str, Any]

class studies.study_wrapper.ResponseTransformerProtocol(*args, **kwargs)

Bases: Protocol

Protocol for response transformer interface.

abstract build_variant_row(study: WDAEStudy, v: SummaryVariant | FamilyVariant, column_descs: list[dict], **kwargs: str | None) → list

abstract transform_gene_view_summary_variant(variant: SummaryVariant, frequency_column: str) → Generator[dict[str, Any], None, None]

abstract transform_gene_view_summary_variant_download(variants: Iterable[SummaryVariant], frequency_column: str, summary_variant_ids: set[str]) → Iterator[str]

Produce an iterator for a download file response.

abstract variant_transformer(study: WDAEStudy, pheno_values: dict[str, Any] | None) → Callable[[FamilyVariant], FamilyVariant]

class studies.study_wrapper.WDAEAbstractStudy(genotype_data: GenotypeData | None = None, phenotype_data: PhenotypeData | None = None)

Bases: object

A genotype and phenotype data wrapper for use in the wdae module.

property config: dict[str, Any]

property config_columns: dict[str, Any] | None

property description: str | None

property families: FamiliesData

property genotype_data: GenotypeData

get_children_ids(*, leaves: bool = True) → list[str]

Return the list of children ids.

property has_pheno_data: bool

property is_genotype: bool

property is_group: bool

property is_phenotype: bool

make_config(genotype_data: GenotypeData | None, phenotype_data: PhenotypeData | None) → dict[str, Any]

Create a configuration for the WDAEStudy.

property name: str

property parents: set[str]

property person_set_collections: dict[str, PersonSetCollection]

property phenotype_data: PhenotypeData

abstract query_variants_wdae_streaming(kwargs: dict[str, Any], sources: list[dict[str, Any]], query_transformer: QueryTransformerProtocol, response_transformer: ResponseTransformerProtocol, max_variants_count: int | None = 10000, *, max_variants_message: bool = False) → Generator[list | None, None, None]

Wrap query variants method for WDAE streaming.

property study_id: str

class studies.study_wrapper.WDAEStudy(genotype_data: GenotypeData | None, phenotype_data: PhenotypeData | None)

Bases: WDAEAbstractStudy

A genotype and phenotype data wrapper for use in the wdae module.

static build_genotype_data_all_datasets(genotype_data: GenotypeData) → dict[str, Any]

Prepare response for all genotype datasets.

static build_genotype_data_description(gpf_instance: Any, genotype_data: GenotypeData, person_set_collection_configs: dict[str, Any] | None) → dict[str, Any]

Build and return genotype data group description.

static get_columns_as_sources(config: dict[str, Any], column_ids: list[str]) → list[dict[str, Any]]

Return the list of column sources.

get_gene_view_summary_variants(frequency_column: str, query_transformer: QueryTransformerProtocol, response_transformer: ResponseTransformerProtocol, **kwargs: Any) → Generator[dict[str, Any], None, None]

Return gene browser summary variants.

get_gene_view_summary_variants_download(frequency_column: str, query_transformer: QueryTransformerProtocol, response_transformer: ResponseTransformerProtocol, **kwargs: Any) → Iterable

Return gene browser summary variants for downloading.

query_variants_wdae(kwargs: dict[str, Any], sources: list[dict[str, Any]], query_transformer: QueryTransformerProtocol, response_transformer: ResponseTransformerProtocol, max_variants_count: int | None = 10000, *, max_variants_message: bool = False) → Iterable[list]

Wrap query variants method for WDAE streaming.

query_variants_wdae_streaming(kwargs: dict[str, Any], sources: list[dict[str, Any]], query_transformer: QueryTransformerProtocol, response_transformer: ResponseTransformerProtocol, max_variants_count: int | None = 10000, *, max_variants_message: bool = False) → Generator[list | None, None, None]

Wrap query variants method for WDAE streaming of variants.

class studies.study_wrapper.WDAEStudyGroup(genotype_data: GenotypeData | None, pheno_data: PhenotypeData | None, children: list[WDAEStudy])

Bases: WDAEStudy

Genotype data study wrapper class for WDAE.

get_studies_ids(*, leaves: bool = True) → list[str]

studies.study_wrapper.get_clean_config(config: dict[str, Any]) → dict[str, Any]

studies.study_wrapper.remove_none_values(config: dict[str, Any]) → dict[str, Any]

Remove None values from config

Module contents