Index

_

__init__() (anyvar.anyvar.AnyVar method) (anyvar.mapping.projection_models.ProjectedVariation method) (anyvar.mapping.projection_models.ProjectionFailure method) (anyvar.mapping.projection_models.ProjectionNotApplicable method) (anyvar.mapping.projection_models.ProjectionResults method) (anyvar.mapping.protocols.VariantProjectorProtocol method) (anyvar.storage.base.AlleleSearchPage method) (anyvar.storage.base.Storage method) (anyvar.storage.duckdb.DuckDbObjectStore method) (anyvar.storage.mapper_registry.MapperRegistry method) (anyvar.storage.mappers.AlleleMapper method) (anyvar.storage.mappers.CanonicalAlleleMapper method) (anyvar.storage.mappers.ProteinSequenceConsequenceMapper method) (anyvar.storage.mappers.SequenceLocationMapper method) (anyvar.storage.no_db.NoObjectStore method) (anyvar.storage.orm.Allele method) (anyvar.storage.orm.Base method) (anyvar.storage.orm.CanonicalAllele method) (anyvar.storage.orm.Extension method) (anyvar.storage.orm.Location method) (anyvar.storage.orm.ProteinSequenceConsequence method) (anyvar.storage.orm.SequenceReference method) (anyvar.storage.orm.VariationMapping method) (anyvar.storage.orm.VrsObject method) (anyvar.storage.postgres.PostgresObjectStore method) (anyvar.translate.vrs_python.VrsPythonTranslator method) (anyvar.translate.vrs_python.WindowedSeqRepoDataProxy method) (anyvar.vcf.ingest.VcfRegistrar method) (anyvar.vcf.ingest.VrsObjectRegistrationBatcher method)

A

AccessionConversionError add() (anyvar.mapping.projection_models.ProjectionResults method) add_ca_catvar() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) add_extension() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) add_mapping() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) add_objects() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) add_projection_mappings() (in module anyvar.translate.register) add_psq_catvar() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) add_to_batch() (anyvar.vcf.ingest.VrsObjectRegistrationBatcher method) allele (anyvar.storage.orm.CanonicalAllele attribute) (anyvar.storage.orm.ProteinSequenceConsequence attribute) Allele (class in anyvar.storage.orm) allele_id (anyvar.storage.orm.CanonicalAllele attribute) (anyvar.storage.orm.ProteinSequenceConsequence attribute) AlleleMapper (class in anyvar.storage.mappers) AlleleSearchPage (class in anyvar.storage.base) AmbiguousCoordinateConversionError annotate() (anyvar.vcf.ingest.VcfRegistrar method) AnyVar (class in anyvar.anyvar) anyvar.anyvar module anyvar.core.categorical_variants module anyvar.core.metadata module

anyvar.core.objects module anyvar.mapping.liftover module anyvar.mapping.projection_models module anyvar.mapping.protocols module anyvar.storage.base module anyvar.storage.duckdb module anyvar.storage.mapper_registry module anyvar.storage.mappers module anyvar.storage.no_db module anyvar.storage.orm module anyvar.storage.postgres module anyvar.translate.base module anyvar.translate.register module anyvar.translate.vrs_python module anyvar.vcf.ingest module anyvar_instance (anyvar.vcf.ingest.VrsObjectRegistrationBatcher attribute)

B

Base (class in anyvar.storage.orm) base_error_message (anyvar.mapping.liftover.LiftoverError attribute)

BaseMapper (class in anyvar.storage.mappers) batch_collection (anyvar.vcf.ingest.VrsObjectRegistrationBatcher attribute) BATCH_SIZE (anyvar.vcf.ingest.VrsObjectRegistrationBatcher attribute)

C

CanonicalAllele (class in anyvar.core.categorical_variants) (class in anyvar.storage.orm) CanonicalAlleleMapper (class in anyvar.storage.mappers) close() (anyvar.storage.base.Storage method) (anyvar.storage.duckdb.DuckDbObjectStore method) (anyvar.storage.no_db.NoObjectStore method) (anyvar.storage.postgres.PostgresObjectStore method)

convert_position() (in module anyvar.mapping.liftover) CoordinateConversionFailureError create_projector() (in module anyvar.anyvar) create_storage() (in module anyvar.anyvar) create_tables() (in module anyvar.storage.orm) create_timestamp_if_missing() (anyvar.anyvar.AnyVar method) create_translator() (in module anyvar.anyvar) CREATION_TIMESTAMP (anyvar.core.metadata.ExtensionName attribute)

D

DataIntegrityError delete_extensions() (anyvar.storage.base.Storage method) (anyvar.storage.duckdb.DuckDbObjectStore method) (anyvar.storage.no_db.NoObjectStore method) (anyvar.storage.postgres.PostgresObjectStore method) delete_mapping() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) delete_object() (anyvar.anyvar.AnyVar method) delete_object_extensions() (anyvar.anyvar.AnyVar method) delete_objects() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method)

description (anyvar.mapping.projection_models.ProjectionFailure attribute) dest_id (anyvar.core.metadata.VariationMapping attribute) (anyvar.storage.orm.VariationMapping attribute) destination_molecule_type (anyvar.mapping.projection_models.ProjectionFailure attribute) (anyvar.mapping.projection_models.ProjectionNotApplicable attribute) destination_variation (anyvar.mapping.projection_models.ProjectedVariation attribute) disassemble() (anyvar.storage.orm.Base method) dp (anyvar.translate.base.Translator attribute) DuckDbObjectStore (class in anyvar.storage.duckdb)

E

end (anyvar.storage.orm.Location attribute) end_inner (anyvar.storage.orm.Location attribute) end_outer (anyvar.storage.orm.Location attribute) error_details (anyvar.mapping.liftover.AccessionConversionError attribute) (anyvar.mapping.liftover.AmbiguousCoordinateConversionError attribute) (anyvar.mapping.liftover.CoordinateConversionFailureError attribute) (anyvar.mapping.liftover.LiftoverError attribute) (anyvar.mapping.liftover.RoundtripError attribute) (anyvar.mapping.liftover.UnsupportedReferenceAssemblyError attribute) (anyvar.mapping.liftover.UnsupportedVariantLocationTypeError attribute)

Extension (class in anyvar.core.metadata) (class in anyvar.storage.orm) ExtensionMapper (class in anyvar.storage.mappers) ExtensionName (class in anyvar.core.metadata)

F

failures (anyvar.mapping.projection_models.ProjectionResults attribute) from_db_entity() (anyvar.storage.mapper_registry.MapperRegistry method) (anyvar.storage.mappers.AlleleMapper method) (anyvar.storage.mappers.BaseMapper method) (anyvar.storage.mappers.CanonicalAlleleMapper method) (anyvar.storage.mappers.ExtensionMapper method) (anyvar.storage.mappers.ProteinSequenceConsequenceMapper method) (anyvar.storage.mappers.SequenceLocationMapper method) (anyvar.storage.mappers.SequenceReferenceMapper method) (anyvar.storage.mappers.VariationMappingMapper method)

from_error() (anyvar.mapping.projection_models.ProjectionFailure class method) fully_succeeded (anyvar.mapping.projection_models.ProjectionResults property)

G

get_ca_catvar() (anyvar.anyvar.AnyVar method) (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) get_catvars_by_allele_ids() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) get_disassembler() (anyvar.storage.orm.Allele method) (anyvar.storage.orm.Base method) (anyvar.storage.orm.Location method) get_error_message() (anyvar.mapping.liftover.LiftoverError class method) get_extensions() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) get_mapper() (anyvar.storage.mapper_registry.MapperRegistry method) get_mappings() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method)

get_molecule_type() (in module anyvar.core.categorical_variants) get_object() (anyvar.anyvar.AnyVar method) get_object_extensions() (anyvar.anyvar.AnyVar method) get_object_mappings() (anyvar.anyvar.AnyVar method) get_objects() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) get_psq_catvar() (anyvar.anyvar.AnyVar method) (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) get_sequence_id() (anyvar.translate.base.Translator method) (anyvar.translate.vrs_python.VrsPythonTranslator method) GRCH37 (anyvar.mapping.liftover.ReferenceAssembly attribute) GRCH38 (anyvar.mapping.liftover.ReferenceAssembly attribute)

H

has_queueing_enabled() (in module anyvar.anyvar)

has_variations_queueing_enabled() (in module anyvar.anyvar)

I

id (anyvar.storage.orm.Allele attribute) (anyvar.storage.orm.CanonicalAllele attribute) (anyvar.storage.orm.Extension attribute) (anyvar.storage.orm.Location attribute) (anyvar.storage.orm.ProteinSequenceConsequence attribute) (anyvar.storage.orm.SequenceReference attribute) (anyvar.storage.orm.VrsObject attribute)

IncompleteVrsObjectError InvalidCategoricalVariantError InvalidSearchParamsError is_expected_molecule_type() (in module anyvar.core.categorical_variants) items (anyvar.storage.base.AlleleSearchPage attribute)

L

liftover_and_register_variant() (in module anyvar.mapping.liftover) LIFTOVER_TO (anyvar.core.metadata.VariationMappingType attribute) liftover_variant() (in module anyvar.mapping.liftover)

LiftoverError location (anyvar.storage.orm.Allele attribute) Location (class in anyvar.storage.orm) location_id (anyvar.storage.orm.Allele attribute)

M

MapperRegistry (class in anyvar.storage.mapper_registry) mapping (anyvar.mapping.projection_models.ProjectedVariation attribute) mapping_type (anyvar.core.metadata.VariationMapping attribute) (anyvar.storage.orm.VariationMapping attribute) MissingVariationReferenceError module anyvar.anyvar anyvar.core.categorical_variants anyvar.core.metadata anyvar.core.objects anyvar.mapping.liftover anyvar.mapping.projection_models anyvar.mapping.protocols anyvar.storage.base anyvar.storage.duckdb anyvar.storage.mapper_registry anyvar.storage.mappers anyvar.storage.no_db anyvar.storage.orm anyvar.storage.postgres anyvar.translate.base anyvar.translate.register anyvar.translate.vrs_python anyvar.vcf.ingest

molecule_type (anyvar.storage.orm.SequenceReference attribute)

N

name (anyvar.core.metadata.Extension attribute) (anyvar.storage.orm.CanonicalAllele attribute) (anyvar.storage.orm.Extension attribute) (anyvar.storage.orm.ProteinSequenceConsequence attribute)

next_cursor (anyvar.storage.base.AlleleSearchPage attribute) NoObjectStore (class in anyvar.storage.no_db) not_applicable (anyvar.mapping.projection_models.ProjectionResults attribute)

O

object_id (anyvar.core.metadata.Extension attribute) (anyvar.storage.orm.Extension attribute)

ObjectNotFoundError on_vrs_object() (anyvar.vcf.ingest.VcfRegistrar method) on_vrs_object_collection() (anyvar.vcf.ingest.VcfRegistrar method)

P

PostgresObjectStore (class in anyvar.storage.postgres) project_and_register_variations() (in module anyvar.mapping.protocols) project_variations() (anyvar.mapping.protocols.VariantProjectorProtocol method) ProjectedVariation (class in anyvar.mapping.projection_models) ProjectionError ProjectionFailure (class in anyvar.mapping.projection_models) ProjectionNotApplicable (class in anyvar.mapping.projection_models)

ProjectionResults (class in anyvar.mapping.projection_models) projections (anyvar.mapping.projection_models.ProjectionResults attribute) ProteinSequenceConsequence (class in anyvar.core.categorical_variants) (class in anyvar.storage.orm) ProteinSequenceConsequenceMapper (class in anyvar.storage.mappers) put_extension() (anyvar.anyvar.AnyVar method) put_mapping() (anyvar.anyvar.AnyVar method) put_objects() (anyvar.anyvar.AnyVar method)

R

raise_for_output_args() (anyvar.vcf.ingest.VcfRegistrar method) reason (anyvar.mapping.projection_models.ProjectionNotApplicable attribute) recursive_identify() (in module anyvar.core.objects) ReferenceAssembly (class in anyvar.mapping.liftover) register_batch() (anyvar.vcf.ingest.VrsObjectRegistrationBatcher method) register_ca_catvar() (anyvar.anyvar.AnyVar method)

register_existing_annotations() (in module anyvar.vcf.ingest) register_psq_catvar() (anyvar.anyvar.AnyVar method) register_variations() (in module anyvar.translate.register) registry (anyvar.storage.orm.Base attribute) RequiredAnnotationsError RoundtripError

S

search_alleles() (anyvar.storage.base.Storage method) (anyvar.storage.no_db.NoObjectStore method) sequence_reference (anyvar.storage.orm.Location attribute) sequence_reference_id (anyvar.storage.orm.Location attribute) SequenceLocationMapper (class in anyvar.storage.mappers) SequenceReference (class in anyvar.storage.orm) SequenceReferenceMapper (class in anyvar.storage.mappers) session_factory() (in module anyvar.storage.orm) source_id (anyvar.core.metadata.VariationMapping attribute) (anyvar.mapping.projection_models.ProjectionFailure attribute) (anyvar.mapping.projection_models.ProjectionNotApplicable attribute) (anyvar.storage.orm.VariationMapping attribute)

start (anyvar.storage.orm.Location attribute) start_inner (anyvar.storage.orm.Location attribute) start_outer (anyvar.storage.orm.Location attribute) state (anyvar.storage.orm.Allele attribute) Storage (class in anyvar.storage.base) StorageError SupportedVrsObject (in module anyvar.core.objects) SupportedVrsVariation (in module anyvar.core.objects)

T

to_db_entity() (anyvar.storage.mapper_registry.MapperRegistry method) (anyvar.storage.mappers.AlleleMapper method) (anyvar.storage.mappers.BaseMapper method) (anyvar.storage.mappers.CanonicalAlleleMapper method) (anyvar.storage.mappers.ExtensionMapper method) (anyvar.storage.mappers.ProteinSequenceConsequenceMapper method) (anyvar.storage.mappers.SequenceLocationMapper method) (anyvar.storage.mappers.SequenceReferenceMapper method) (anyvar.storage.mappers.VariationMappingMapper method) to_dict() (anyvar.storage.orm.Base method)

TRANSCRIBE_TO (anyvar.core.metadata.VariationMappingType attribute) translate_allele() (anyvar.translate.base.Translator method) (anyvar.translate.vrs_python.VrsPythonTranslator method) TRANSLATE_TO (anyvar.core.metadata.VariationMappingType attribute) translate_variation() (anyvar.translate.base.Translator method) (anyvar.translate.vrs_python.VrsPythonTranslator method) (in module anyvar.translate.register) TranslationError Translator (class in anyvar.translate.base) TranslatorConnectionError TranslatorSetupError

U

UnsupportedReferenceAssemblyError

UnsupportedVariantLocationTypeError

V

value (anyvar.core.metadata.Extension attribute) (anyvar.storage.orm.Extension attribute) VariantProjectorProtocol (class in anyvar.mapping.protocols) VariationMapping (class in anyvar.core.metadata) (class in anyvar.storage.orm) VariationMappingMapper (class in anyvar.storage.mappers)

VariationMappingType (class in anyvar.core.metadata) VcfRegistrar (class in anyvar.vcf.ingest) vrs_object (anyvar.storage.orm.VrsObject attribute) vrs_object_registration_batcher (anyvar.vcf.ingest.VcfRegistrar attribute) VrsObject (class in anyvar.storage.orm) VrsObjectRegistrationBatcher (class in anyvar.vcf.ingest) VrsPythonTranslator (class in anyvar.translate.vrs_python)

W

wait_for_writes() (anyvar.storage.base.Storage method) (anyvar.storage.duckdb.DuckDbObjectStore method) (anyvar.storage.no_db.NoObjectStore method) (anyvar.storage.postgres.PostgresObjectStore method)

WindowedSeqRepoDataProxy (class in anyvar.translate.vrs_python) wipe_db() (anyvar.storage.base.Storage method) (anyvar.storage.duckdb.DuckDbObjectStore method) (anyvar.storage.no_db.NoObjectStore method)