dae.query_variants.sql.schema2 package

Subpackages

dae.query_variants.sql.schema2.tests package

Submodules

dae.query_variants.sql.schema2.base_query_builder module

class dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder(dialect: Dialect, db: str | None, family_variant_table: str | None, summary_allele_table: str, pedigree_table: str, family_variant_schema: dict[str, str] | None, summary_allele_schema: dict[str, str], partition_descriptor: dict | None, pedigree_schema: dict[str, str], families: FamiliesData, gene_models: GeneModels | None = None)[source]

Bases: ABC

Class that abstracts away the process of building a query.

GENE_REGIONS_HEURISTIC_CUTOFF = 20

GENE_REGIONS_HEURISTIC_EXTEND = 20000

MAX_CHILD_NUMBER = 9999

QUOTE = "'"

WHERE = '\n WHERE\n {where}\n '

build_query(regions: list[Region] | None = None, genes: list[str] | None = None, effect_types: list[str] | None = None, family_ids: Iterable[str] | None = None, person_ids: Iterable[str] | None = None, inheritance: str | list[str] | None = None, roles: str | None = None, sexes: str | None = None, variant_type: str | None = None, real_attr_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, pedigree_fields: tuple | None = None) → str[source]: Build an SQL query in the correct order.

class dae.query_variants.sql.schema2.base_query_builder.Dialect(namespace: str | None = None)[source]

Bases: ABC

Caries info about a SQL dialect.

static add_unnest_in_join() → bool[source]

static array_item_suffix() → str[source]

build_array_join(column: str, allias: str) → str[source]

build_table_name(table: str, db: str | None) → str[source]

static escape_char() → str[source]

static escape_quote_char() → str[source]

static float_type() → str[source]

static int_type() → str[source]

static use_bit_and_function() → bool[source]

dae.query_variants.sql.schema2.base_variants module

class dae.query_variants.sql.schema2.base_variants.SqlSchema2Variants(dialect: Dialect, db: str | None, family_variant_table: str | None, summary_allele_table: str | None, pedigree_table: str, meta_table: str, gene_models: GeneModels | None = None)[source]

Bases: QueryVariantsBase

Base class for Schema2 SQL like variants’ query interface.

RUNNER_CLASS: type[QueryRunner]

build_family_variants_query_runner(*, 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, inheritance: list[str] | None = None, roles: str | None = None, sexes: str | None = None, variant_type: str | None = None, real_attr_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, study_filters: list[str] | None = None, pedigree_fields: tuple | None = None, **kwargs: Any) → QueryRunner[source]: Build a query selecting the appropriate family variants.

static build_person_set_collection_query(person_set_collection: PersonSetCollection, person_set_collection_query: tuple[str, set[str]]) → tuple | tuple[list[str], list[str]] | None[source]: No idea what it does. If you know please edit.

build_summary_variants_query_runner(*, 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[str, tuple[float | None, float | None]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, **kwargs: Any) → QueryRunner[source]: Build a query selecting the appropriate summary variants.

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[str, tuple[float | None, float | None]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, **kwargs: Any) → Generator[SummaryVariant, None, None][source]: Query 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, inheritance: list[str] | None = None, roles: str | None = None, sexes: str | None = None, variant_type: str | None = None, real_attr_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, ultra_rare: bool | None = None, frequency_filter: list[tuple[str, tuple[float | None, float | None]]] | None = None, return_reference: bool | None = None, return_unknown: bool | None = None, limit: int | None = None, pedigree_fields: tuple | None = None, **kwargs: Any) → Generator[FamilyVariant, None, None][source]: Query family variants.

dae.query_variants.sql.schema2.family_builder module

class dae.query_variants.sql.schema2.family_builder.FamilyQueryBuilder(dialect: Dialect, db: str, family_variant_table: str, summary_allele_table: str, pedigree_table: str, family_variant_schema: dict[str, str], summary_allele_schema: dict[str, str], table_properties: dict | None, pedigree_schema: dict[str, str], families: FamiliesData, gene_models: GeneModels | None = None, do_join_pedigree: bool = False, do_join_allele_in_members: bool = False)[source]

Bases: BaseQueryBuilder

Build queries related to family variants.

dae.query_variants.sql.schema2.sql_query_builder module

class dae.query_variants.sql.schema2.sql_query_builder.Db2Layout(db: str | None, study: str, pedigree: str, summary: str | None, family: str | None, meta: str)[source]

Bases: object

Genotype data layout in the database.

db: str | None

family: str | None

meta: str

pedigree: str

study: str

summary: str | None

class dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder(db_layout: Db2Layout, pedigree_schema: dict[str, str], summary_schema: dict[str, str], family_schema: dict[str, str], partition_descriptor: PartitionDescriptor | None, families: FamiliesData, gene_models: GeneModels, reference_genome: ReferenceGenome | None = None)[source]