dae.inmemory_storage package

Submodules

dae.inmemory_storage.inmemory_genotype_storage module

class dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage(storage_config: Dict[str, Any])

Bases: GenotypeStorage

A storage that uses the in-memory as its backend.

VALIDATION_SCHEMA = {'dir': {'check_with': <function validate_path>, 'required': True, 'type': 'string'}, 'id': {'type': 'string'}, 'read_only': {'default': False, 'type': 'boolean'}, 'storage_type': {'allowed': ['inmemory'], 'type': 'string'}}

build_backend(study_config: dict[str, Any], genome: ReferenceGenome, gene_models: GeneModels | None) → Any

Construct a query backend for this genotype storage.

get_data_dir(*path: str) → str

classmethod get_storage_types() → set[str]

Return the genotype storage type.

shutdown() → GenotypeStorage

No resources to close.

start() → GenotypeStorage

Allocate all resources needed for the genotype storage to work.

classmethod validate_and_normalize_config(config: Dict) → Dict

Normalize and validate the genotype storage configuration.

When validation passes returns the normalized and validated annotator configuration dict.

When validation fails, raises ValueError.

All genotype storage configurations are required to have:

• “storage_type” - which storage type this configuration is used for;

• “id” - the ID of the genotype storage instance that will be created.

dae.inmemory_storage.inmemory_import_storage module

class dae.inmemory_storage.inmemory_import_storage.InmemoryImportStorage

Bases: ImportStorage

Defines import storage for in-memory genotype storage.

generate_import_task_graph(project: ImportProject) → TaskGraph

Generate task grap for import of the project into this storage.

dae.inmemory_storage.raw_variants module

class dae.inmemory_storage.raw_variants.RawFamilyVariants(families: FamiliesData)

Bases: ABC

Base class that stores a reference to the families data.

build_family_variants_query_runner(regions: list[dae.utils.regions.Region] | None = None, genes: list[str] | None = None, effect_types: list[str] | None = None, family_ids: Sequence[str] | None = None, person_ids: Sequence[str] | None = None, inheritance: Sequence[str] | None = None, roles: str | None = None, sexes: str | None = None, variant_type: str | None = None, real_attr_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, **kwargs: Any) → RawVariantsQueryRunner

Return a query runner for the family variants.

static build_person_set_collection_query(person_set_collection: PersonSetCollection, person_set_collection_query: Tuple[str, List[str]]) → None

build_summary_variants_query_runner(**kwargs: Any) → RawVariantsQueryRunner

Return a query runner for the summary variants.

classmethod family_variant_filter_duplicate_function(**kwargs: Any) → Callable[[FamilyVariant], FamilyVariant | None]

Return a filter function that checks the conditions in kwargs.

classmethod family_variant_filter_function(**kwargs: Any) → Callable[[FamilyVariant], FamilyVariant | None]

Return a function that filters variants.

family_variants_iterator() → Iterator[FamilyVariant]

classmethod filter_allele(allele: FamilyAllele, genes: list[str] | None = None, effect_types: list[str] | None = None, person_ids: Sequence[str] | None = None, inheritance: Sequence[Matcher] | None = None, roles: Matcher | None = None, sexes: Matcher | None = None, variant_type: Matcher | None = None, real_attr_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]] | None = None, **kwargs: Any) → bool

Return True if a family allele meets the required conditions.

classmethod filter_family_variant(v: FamilyVariant, **kwargs: Any) → bool

Return true if variant meets conditions in kwargs.

static filter_gene_effects(v: SummaryAllele, effect_types: Sequence[str] | None, genes: Sequence[str] | None) → bool

Return True if variant’s effects are in effect types and genes.

static filter_real_attr(allele: SummaryAllele, real_attr_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]], is_frequency: bool = False) → bool

Return True if allele’s attrs are within bounds.

The bounds are specified in real_attr_filter.

static filter_regions(v: SummaryVariant, regions: list[dae.utils.regions.Region]) → bool

Return True if v is in regions.

classmethod filter_summary_allele(allele: SummaryAllele, genes: list[str] | None = None, effect_types: list[str] | None = None, variant_type: Matcher | None = None, real_attr_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[Optional[float], Optional[float]]]] | None = None, **kwargs: Any) → bool

Return True if a summary allele meets the required conditions.

classmethod filter_summary_variant(v: SummaryVariant, **kwargs: Any) → bool

Return true if variant meets conditions in kwargs.

abstract full_variants_iterator() → Iterator[Tuple[SummaryVariant, List[FamilyVariant]]]

query_summary_variants(**kwargs: Any) → Iterator[SummaryVariant]

Run a sammary variant query and yields the results.

query_variants(**kwargs: Any) → Iterator[FamilyVariant]

Query family variants and yield the results.

classmethod summary_variant_filter_duplicate_function(**kwargs: Any) → Callable[[SummaryVariant], SummaryVariant | None]

Return a filter function that checks the conditions in kwargs.

classmethod summary_variant_filter_function(**kwargs: Any) → Callable[[SummaryVariant], SummaryVariant | None]

Return a filter function that checks the conditions in kwargs.

summary_variants_iterator() → Iterator[SummaryVariant]

Create a generator to iterate over summary variants.

class dae.inmemory_storage.raw_variants.RawMemoryVariants(loaders: List[VariantsLoader], families: FamiliesData)

Bases: RawFamilyVariants

Store variants in memory.

property full_variants: List[Tuple[SummaryVariant, List[FamilyVariant]]]

Return the full list of variants.

full_variants_iterator() → Iterator[Tuple[SummaryVariant, List[FamilyVariant]]]

class dae.inmemory_storage.raw_variants.RawVariantsQueryRunner(variants_iterator: Iterator[Any], deserializer: Callable | None = None)

Bases: QueryRunner

Run a variant iterator as a query.

run() → None

Module contents