dae.backends package

Subpackages

• dae.backends.cnv package
  • Submodules
  • dae.backends.cnv.flexible_cnv_loader module
  • dae.backends.cnv.loader module
    • Copy Number Variants (CNV) loader CNVLoader
      • Location of the CNVs
      • Genotype of the CNVs
      • Variant type for CNVs
      • Additional parameters
  • Module contents
• dae.backends.dae package
  • Submodules
  • dae.backends.dae.loader module
  • Module contents
• dae.backends.impala package
  • Submodules
  • dae.backends.impala.base_query_builder module
  • dae.backends.impala.family_variants_query_builder module
  • dae.backends.impala.hdfs_helpers module
  • dae.backends.impala.impala_helpers module
  • dae.backends.impala.impala_query_director module
  • dae.backends.impala.impala_variants module
  • dae.backends.impala.import_commons module
  • dae.backends.impala.parquet_io module
  • dae.backends.impala.rsync_helpers module
  • dae.backends.impala.serializers module
  • dae.backends.impala.summary_variants_query_builder module
  • Module contents
• dae.backends.raw package
  • Submodules
  • dae.backends.raw.flexible_variant_loader module
  • dae.backends.raw.loader module
  • dae.backends.raw.raw_variants module
  • Module contents
• dae.backends.schema2 package
  • Submodules
  • dae.backends.schema2.base_query_builder module
  • dae.backends.schema2.bigquery_variants module
  • dae.backends.schema2.family_builder module
  • dae.backends.schema2.impala_variants module
  • dae.backends.schema2.parquet_io module
  • dae.backends.schema2.serializers module
  • dae.backends.schema2.summary_builder module
  • dae.backends.schema2.vcf2schema2 module
  • Module contents
• dae.backends.storage package
  • Submodules
  • dae.backends.storage.filesystem_genotype_storage module
  • dae.backends.storage.genotype_storage module
  • dae.backends.storage.genotype_storage_factory module
  • dae.backends.storage.impala_genotype_storage module
  • dae.backends.storage.schema2_genotype_storage module
  • Module contents
• dae.backends.vcf package
  • Submodules
  • dae.backends.vcf.loader module
  • Module contents

Submodules

dae.backends.attributes_query module

class dae.backends.attributes_query.AndNode(children)

Bases: dae.backends.attributes_query.TreeNode

class dae.backends.attributes_query.BaseQueryTransformerMatcher(parser=Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter=None)

Bases: object

Base class for query transformer matchers.

parse(expression)

parse_and_transform(expression)

transform(tree)

transform_query_string_to_tree(expression)

transform_tree_to_matcher(tree)

class dae.backends.attributes_query.BaseTreeTransformer

Bases: object

transform(node)

class dae.backends.attributes_query.BitwiseTreeTransformer(token_converter)

Bases: lark.visitors.Interpreter

Transform bitwise expressions.

all(*args)

any(*args)

arg(*args)

eq(*args)

less_than(*args)

less_than_eq(*args)

logical_and(*args)

logical_or(*args)

more_than(*args)

more_than_eq(*args)

negation(*args)

simple_arg(*args)

start(*args)

class dae.backends.attributes_query.ContainsNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.ElementOfNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.EqualsNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.GreaterThanEqNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.GreaterThanNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.Leaf(op, value)

Bases: object

class dae.backends.attributes_query.LeafNode(arg)

Bases: object

class dae.backends.attributes_query.LessThanEqNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.LessThanNode(arg)

Bases: dae.backends.attributes_query.LeafNode

class dae.backends.attributes_query.Matcher(tree, parser, matcher)

Bases: object

No idea what this class is supposed to do. If you know please edit.

match(array)

pretty()

query_str()

class dae.backends.attributes_query.NotNode(children)

Bases: dae.backends.attributes_query.TreeNode

class dae.backends.attributes_query.OrNode(children)

Bases: dae.backends.attributes_query.TreeNode

class dae.backends.attributes_query.QueryTransformerMatcher(parser=Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter=None, transformer2=<dae.backends.attributes_query.QueryTreeToLambdaTransformer object>)

Bases: dae.backends.attributes_query.BaseQueryTransformerMatcher

No idea what this is supposed to do. Please edit.

transform_tree_to_matcher(tree)

class dae.backends.attributes_query.QueryTreeToBitwiseLambdaTransformer

Bases: dae.backends.attributes_query.BaseTreeTransformer

No idea what this is supposed to do. Please edit.

AndNode(children)

ContainsNode(arg)

ElementOfNode(arg)

EqualsNode(arg)

GreaterThanEqNode(arg)

GreaterThanNode(arg)

LessThanEqNode(arg)

LessThanNode(arg)

NotNode(children)

OrNode(children)

class dae.backends.attributes_query.QueryTreeToLambdaTransformer

Bases: dae.backends.attributes_query.BaseTreeTransformer

Transforma all nodes to python lambda functions.

AndNode(children)

ContainsNode(arg)

ElementOfNode(arg)

EqualsNode(arg)

GreaterThanEqNode(arg)

GreaterThanNode(arg)

LessThanEqNode(arg)

LessThanNode(arg)

NotNode(children)

OrNode(children)

class dae.backends.attributes_query.QueryTreeToSQLBitwiseTransformer(column_name, add_unnest=False)

Bases: dae.backends.attributes_query.QueryTreeToSQLTransformer

I don’t know what this class does. Please edit if you do.

static AndNode(children)

ContainsNode(arg)

ElementOfNode(arg)

EqualsNode(arg)

GreaterThanEqNode(arg)

GreaterThanNode(arg)

LessThanEqNode(arg)

LessThanNode(arg)

static NotNode(children)

static OrNode(children)

class dae.backends.attributes_query.QueryTreeToSQLListTransformer(column_name, add_unnest=False)

Bases: dae.backends.attributes_query.QueryTreeToSQLTransformer

I don’t know what this class does. Please edit if you do.

ContainsNode(arg)

ElementOfNode(arg)

EqualsNode(arg)

class dae.backends.attributes_query.QueryTreeToSQLTransformer(column_name, add_unnest=False)

Bases: dae.backends.attributes_query.BaseTreeTransformer

I don’t know what this class does. Please edit if you do.

static AndNode(children)

ContainsNode(arg)

ElementOfNode(arg)

EqualsNode(arg)

GreaterThanEqNode(arg)

GreaterThanNode(arg)

LessThanEqNode(arg)

LessThanNode(arg)

static NotNode(children)

static OrNode(children)

static token_converter(arg)

class dae.backends.attributes_query.StringListQueryToTreeTransformer

Bases: object

No idea what this is supposed to do. Please edit.

static parse_and_transform(expression)

class dae.backends.attributes_query.StringQueryToTreeTransformer(parser=Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter=None)

Bases: lark.visitors.InlineTransformer

Convert tokens using a token converter.

all(*args)

any(*args)

arg(*args)

eq(*args)

less_than(*args)

less_than_eq(*args)

logical_and(*args)

logical_or(*args)

more_than(*args)

more_than_eq(*args)

negation(*args)

simple_arg(*args)

start(*args)

class dae.backends.attributes_query.StringQueryToTreeTransformerWrapper(parser=Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter=None)

Bases: object

No idea what this is supposed to do. Please edit.

parse(expression)

parse_and_transform(expression)

transform(tree)

class dae.backends.attributes_query.TreeNode(children)

Bases: object

dae.backends.attributes_query.inheritance_converter(arg)

dae.backends.attributes_query.roles_converter(arg)

dae.backends.attributes_query.sex_converter(arg)

dae.backends.attributes_query.variant_type_converter(arg)

dae.backends.attributes_query_inheritance module

class dae.backends.attributes_query_inheritance.Expression(expression)

Bases: object

class dae.backends.attributes_query_inheritance.InheritanceTransformer(attr_name, *args, **kwargs)

Bases: lark.visitors.Transformer

No idea what this class is supposed to do. If you know please edit.

all(items)

any(items)

atom(items)

atomlist(items)

denovo(items)

expression(items)

Construct an Expression from items.

logical_and(items)

logical_or(items)

mendelian(items)

missing(items)

negative_primitive(items)

omission(items)

other(items)

possible_denovo(items)

possible_omission(items)

primitive(items)

reference(items)

unknown(items)

class dae.backends.attributes_query_inheritance.NegPrimitive(value)

Bases: object

class dae.backends.attributes_query_inheritance.Primitive(value)

Bases: object

dae.backends.query_runners module

class dae.backends.query_runners.QueryResult(runners: list[dae.backends.query_runners.QueryRunner], limit=- 1)

Bases: object

Run a list of queries in the background.

The result of the queries is enqueued on result_queue

close()

Gracefully close and dispose of resources.

done()

get(timeout=0)

Pop the next entry from the queue.

Return None if the queue is still empty after timeout seconds.

start()

class dae.backends.query_runners.QueryRunner(deserializer=None)

Bases: abc.ABC

Run a query in the backround using the provided executor.

adapt(adapter_func)

close()

closed()

done()

abstract run()

start(executor)

started()

Module contents