dae.query_variants package
Subpackages
- dae.query_variants.sql package
- Subpackages
- dae.query_variants.sql.schema2 package
- Subpackages
- Submodules
- dae.query_variants.sql.schema2.base_query_builder module
- dae.query_variants.sql.schema2.base_variants module
- dae.query_variants.sql.schema2.family_builder module
- dae.query_variants.sql.schema2.sql_query_builder module
- dae.query_variants.sql.schema2.summary_builder module
- Module contents
- dae.query_variants.sql.schema2 package
- Module contents
- Subpackages
- dae.query_variants.tests package
Submodules
dae.query_variants.attributes_query module
- class dae.query_variants.attributes_query.AndNode(children: Iterable[LeafNode | TreeNode])[source]
Bases:
TreeNode
- class dae.query_variants.attributes_query.BaseQueryTransformerMatcher(parser: ~lark.lark.Lark = Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter: ~typing.Callable[[~typing.Any], ~typing.Any] | None = None)[source]
Bases:
object
Base class for query transformer matchers.
- class dae.query_variants.attributes_query.BitwiseTreeTransformer(token_converter: Callable[[Any], LeafNode | TreeNode])[source]
Bases:
Interpreter
Transform bitwise expressions.
- class dae.query_variants.attributes_query.ContainsNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.ElementOfNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.EqualsNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.GreaterThanEqNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.GreaterThanNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.LessThanEqNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.LessThanNode(arg: LeafNode | TreeNode)[source]
Bases:
LeafNode
- class dae.query_variants.attributes_query.Matcher(tree: LeafNode | TreeNode, parser: Lark, matcher: Callable[[Any], bool])[source]
Bases:
object
No idea what this class is supposed to do. If you know please edit.
- class dae.query_variants.attributes_query.OrNode(children: Iterable[LeafNode | TreeNode])[source]
Bases:
TreeNode
- class dae.query_variants.attributes_query.QueryTransformerMatcher(parser: ~lark.lark.Lark = Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter: ~typing.Callable[[~typing.Any], ~typing.Any] | None = None, transformer2: ~dae.query_variants.attributes_query.BaseTreeTransformer = <dae.query_variants.attributes_query.QueryTreeToLambdaTransformer object>)[source]
Bases:
BaseQueryTransformerMatcher
No idea what this is supposed to do. Please edit.
- class dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer[source]
Bases:
BaseTreeTransformer
No idea what this is supposed to do. Please edit.
- class dae.query_variants.attributes_query.QueryTreeToLambdaTransformer[source]
Bases:
BaseTreeTransformer
Transforma all nodes to python lambda functions.
- class dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer(column_name: str, use_bit_and_function: bool = True)[source]
Bases:
QueryTreeToSQLTransformer
I don’t know what this class does. Please edit if you do.
- class dae.query_variants.attributes_query.QueryTreeToSQLTransformer(column_name: str)[source]
Bases:
BaseTreeTransformer
I don’t know what this class does. Please edit if you do.
- class dae.query_variants.attributes_query.StringQueryToTreeTransformer(_parser: ~lark.lark.Lark = Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter: ~typing.Callable[[~typing.Any], ~typing.Any] | None = None)[source]
Bases:
InlineTransformer
Convert tokens using a token converter.
- class dae.query_variants.attributes_query.TreeNode(children: Iterable[LeafNode | TreeNode])[source]
Bases:
object
- dae.query_variants.attributes_query.get_bit_and_str(arg1: Any, arg2: Any, use_bit_and_function: bool) str [source]
- dae.query_variants.attributes_query.inheritance_converter(arg: str | Inheritance) Inheritance | None [source]
dae.query_variants.attributes_query_inheritance module
- class dae.query_variants.attributes_query_inheritance.Expression(expression: str)[source]
Bases:
object
- class dae.query_variants.attributes_query_inheritance.InheritanceTransformer(attr_name: str, *args: Any, use_bit_and_function: bool = True, **kwargs: Any)[source]
Bases:
Transformer
No idea what this class is supposed to do. If you know please edit.
- all(items: list) Expression [source]
- any(items: list) Expression [source]
- atom(items: list) Primitive | NegPrimitive [source]
- expression(items: list) Expression [source]
Construct an Expression from items.
- logical_and(items: list) Expression [source]
- logical_or(items: list) Expression [source]
- negative_primitive(items: list) Primitive | NegPrimitive [source]
dae.query_variants.base_query_variants module
- class dae.query_variants.base_query_variants.QueryVariantsBase[source]
Bases:
ABC
Base class variants’ query interface.
- RUNNER_CLASS: type[QueryRunner]
- abstract 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]
Create a query runner for searching family variants.
- abstract 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]
Create query runner for searching summary variants.
- abstract 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]
Execute the summary variants query and yields summary variants.
- abstract 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]
Execute the family variants query and yields family variants.
dae.query_variants.query_runners module
- class dae.query_variants.query_runners.QueryResult(runners: list[QueryRunner], limit: int | None = -1)[source]
Bases:
object
Run a list of queries in the background.
The result of the queries is enqueued on result_queue
- CHECK_VERBOSITY = 20