dae Interface
- Genomic Resources
- Classes and Functions
- dae.genomic_resources package
- Subpackages
- Submodules
- dae.genomic_resources.aggregators module
- dae.genomic_resources.cached_repository module
- dae.genomic_resources.cli module
- dae.genomic_resources.draw_score_histograms module
- dae.genomic_resources.fsspec_protocol module
- dae.genomic_resources.genomic_context module
- dae.genomic_resources.genomic_context_cli module
- dae.genomic_resources.genomic_scores module
- dae.genomic_resources.group_repository module
- dae.genomic_resources.histogram module
- dae.genomic_resources.liftover_chain module
- dae.genomic_resources.reference_genome module
- dae.genomic_resources.repository module
GenomicResource
GenomicResourceProtocolRepo
GenomicResourceRepo
Manifest
ManifestEntry
ManifestUpdate
Mode
ReadOnlyRepositoryProtocol
ReadWriteRepositoryProtocol
ResourceFileState
is_gr_id_token()
is_version_constraint_satisfied()
parse_gr_id_version_token()
parse_resource_id_version()
version_string_to_suffix()
version_tuple_to_string()
version_tuple_to_suffix()
- dae.genomic_resources.repository_factory module
- dae.genomic_resources.resource_implementation module
- dae.genomic_resources.testing module
build_filesystem_test_protocol()
build_filesystem_test_repository()
build_filesystem_test_resource()
build_http_test_protocol()
build_inmemory_test_protocol()
build_inmemory_test_repository()
build_inmemory_test_resource()
build_s3_test_bucket()
build_s3_test_filesystem()
build_s3_test_protocol()
convert_to_tab_separated()
copy_proto_genomic_resources()
proto_builder()
resource_builder()
s3_test_protocol()
s3_test_server_endpoint()
setup_bigwig()
setup_dae_transmitted()
setup_denovo()
setup_directories()
setup_empty_gene_models()
setup_gene_models()
setup_genome()
setup_gzip()
setup_pedigree()
setup_tabix()
setup_vcf()
- dae.genomic_resources.variant_utils module
- Module contents
- dae.genomic_resources package
- Classes and Functions
- Annotation
- Classes and Functions
- dae.annotation package
- Submodules
- dae.annotation.annotatable module
- dae.annotation.annotate_columns module
- dae.annotation.annotate_doc module
- dae.annotation.annotate_schema2_parquet module
- dae.annotation.annotate_utils module
- dae.annotation.annotate_vcf module
- dae.annotation.annotation_config module
- dae.annotation.annotation_factory module
build_annotation_pipeline()
check_for_repeated_attributes_in_annotator()
check_for_repeated_attributes_in_pipeline()
check_for_unused_parameters()
copy_annotation_pipeline()
copy_reannotation_pipeline()
get_annotator_factory()
get_available_annotator_types()
load_pipeline_from_file()
load_pipeline_from_yaml()
register_annotator_factory()
resolve_repeated_attributes()
- dae.annotation.annotation_pipeline module
- dae.annotation.annotator_base module
- dae.annotation.cnv_collection_annotator module
- dae.annotation.debug_annotator module
- dae.annotation.docker_annotator module
- dae.annotation.effect_annotator module
- dae.annotation.format_handlers module
- dae.annotation.gene_score_annotator module
- dae.annotation.gene_set_annotator module
- dae.annotation.genomic_context module
- dae.annotation.liftover_annotator module
- dae.annotation.normalize_allele_annotator module
- dae.annotation.parquet module
- dae.annotation.reannotate_instance module
- dae.annotation.record_to_annotatable module
- dae.annotation.score_annotator module
- dae.annotation.simple_effect_annotator module
- Module contents
- dae.annotation package
- Classes and Functions
- Effect Annotation
- Classes and Functions
- dae.effect_annotation package
- Subpackages
- Submodules
- dae.effect_annotation.annotation_effects module
- dae.effect_annotation.annotation_request module
- dae.effect_annotation.annotator module
- dae.effect_annotation.cli module
- dae.effect_annotation.effect module
- dae.effect_annotation.gene_codes module
- dae.effect_annotation.variant module
- Module contents
- dae.effect_annotation package
- Classes and Functions
- Genomic Variants
- Pedigrees Tools
- Classes and Functions
- dae.pedigrees package
- Submodules
- dae.pedigrees.drawing module
- dae.pedigrees.families_data module
- dae.pedigrees.family module
- dae.pedigrees.family_role_builder module
- dae.pedigrees.family_tag_builder module
FamilyTagsBuilder
check_affected_dad_family()
check_affected_mom_family()
check_affected_prb_family()
check_affected_sib_family()
check_control_family()
check_family_tags_query()
check_female_prb_family()
check_male_prb_family()
check_missing_dad_family()
check_missing_mom_family()
check_multiplex_family()
check_nuclear_family()
check_quad_family()
check_simplex_family()
check_tag()
check_trio_family()
check_unaffected_dad_family()
check_unaffected_mom_family()
check_unaffected_prb_family()
check_unaffected_sib_family()
set_attr()
set_tag()
tag_affected_dad_family()
tag_affected_mom_family()
tag_affected_prb_family()
tag_affected_sib_family()
tag_control_family()
tag_female_prb_family()
tag_male_prb_family()
tag_missing_dad_family()
tag_missing_mom_family()
tag_multiplex_family()
tag_nuclear_family()
tag_quad_family()
tag_simplex_family()
tag_trio_family()
tag_unaffected_dad_family()
tag_unaffected_mom_family()
tag_unaffected_prb_family()
tag_unaffected_sib_family()
unset_tag()
- dae.pedigrees.layout module
- dae.pedigrees.loader module
- dae.pedigrees.pedigrees module
- dae.pedigrees.testing module
- Module contents
- dae.pedigrees package
- Classes and Functions
- Variants Loaders
- dae.variants_loaders package
- dae.variants_loaders.raw package
- Submodules
- dae.variants_loaders.raw.flexible_variant_loader module
- dae.variants_loaders.raw.loader module
ArgumentType
CLIArgument
CLILoader
FamiliesGenotypes
VariantsGenotypesLoader
VariantsLoader
VariantsLoaderDecorator
VariantsLoaderDecorator.annotation_schema
VariantsLoaderDecorator.build_arguments_dict()
VariantsLoaderDecorator.build_cli_arguments()
VariantsLoaderDecorator.chromosomes
VariantsLoaderDecorator.cli_arguments()
VariantsLoaderDecorator.cli_defaults()
VariantsLoaderDecorator.close()
VariantsLoaderDecorator.get_attribute()
- Module contents
- dae.variants_loaders.dae package
- dae.variants_loaders.vcf package
- dae.variants_loaders.cnv package
- Import Tools
- What is Import Tools
- Import Tools config files
- Import Tools configuration format
- Working with the Import Tools CLI
- Running on a SGE cluster
- Running on a Kubernetes cluster
- Classes and Functions
- Genotype Data Parquet Writers
- dae.parquet package
- Subpackages
- Submodules
- dae.parquet.helpers module
- dae.parquet.parquet_writer module
- dae.parquet.partition_descriptor module
PartitionDescriptor
PartitionDescriptor.dataset_family_partition()
PartitionDescriptor.dataset_summary_partition()
PartitionDescriptor.family_partition()
PartitionDescriptor.get_variant_partitions()
PartitionDescriptor.has_coding_bins()
PartitionDescriptor.has_family_bins()
PartitionDescriptor.has_family_partitions()
PartitionDescriptor.has_frequency_bins()
PartitionDescriptor.has_partitions()
PartitionDescriptor.has_region_bins()
PartitionDescriptor.has_summary_partitions()
PartitionDescriptor.make_all_region_bins()
PartitionDescriptor.make_coding_bin()
PartitionDescriptor.make_family_bin()
PartitionDescriptor.make_frequency_bin()
PartitionDescriptor.make_region_bin()
PartitionDescriptor.make_region_bins_regions()
PartitionDescriptor.parse()
PartitionDescriptor.parse_dict()
PartitionDescriptor.parse_string()
PartitionDescriptor.partition_directory()
PartitionDescriptor.partition_filename()
PartitionDescriptor.path_to_partitions()
PartitionDescriptor.region_bins_count()
PartitionDescriptor.region_to_region_bins()
PartitionDescriptor.schema1_partition()
PartitionDescriptor.serialize()
PartitionDescriptor.summary_partition()
PartitionDescriptor.to_dict()
- Module contents
- dae.parquet.schema2 package
- Submodules
- dae.parquet.schema2.parquet_io module
ContinuousParquetFileWriter
ContinuousParquetFileWriter.BATCH_ROWS
ContinuousParquetFileWriter.DEFAULT_COMPRESSION
ContinuousParquetFileWriter.append_family_allele()
ContinuousParquetFileWriter.append_summary_allele()
ContinuousParquetFileWriter.build_batch()
ContinuousParquetFileWriter.build_table()
ContinuousParquetFileWriter.close()
ContinuousParquetFileWriter.data_reset()
ContinuousParquetFileWriter.size()
VariantsParquetWriter
- dae.parquet.schema2.serializers module
AlleleParquetSerializer
AlleleParquetSerializer.ENUM_PROPERTIES
AlleleParquetSerializer.FAMILY_ALLELE_BASE_SCHEMA
AlleleParquetSerializer.SUMMARY_ALLELE_BASE_SCHEMA
AlleleParquetSerializer.build_family_allele_batch_dict()
AlleleParquetSerializer.build_family_schema()
AlleleParquetSerializer.build_summary_allele_batch_dict()
AlleleParquetSerializer.build_summary_blob_schema()
AlleleParquetSerializer.build_summary_schema()
AlleleParquetSerializer.schema_family
AlleleParquetSerializer.schema_summary
JsonVariantsDataSerializer
VariantsDataAvroSerializer
VariantsDataSerializer
construct_avro_family_schema()
construct_avro_summary_schema()
- Module contents
- dae.parquet package
- Query Genomic Variants
- dae.query_variants package
- Subpackages
- Submodules
- dae.query_variants.attribute_queries module
AttributeQueryTransformer
AttributeQueryTransformerFunction
AttributeQueryTransformerSQL
AttributeQueryTransformerSQLLegacy
CompoundStripTransformer
Matcher
QueryCompoundAdditionTransformer
QueryCompoundAdditionTransformer.all()
QueryCompoundAdditionTransformer.and_()
QueryCompoundAdditionTransformer.any()
QueryCompoundAdditionTransformer.compound()
QueryCompoundAdditionTransformer.grouping()
QueryCompoundAdditionTransformer.literal()
QueryCompoundAdditionTransformer.neg()
QueryCompoundAdditionTransformer.or_()
SyntaxSugarTransformer
create_and_node()
create_or_node()
transform_attribute_query_to_function()
transform_attribute_query_to_sql_expression()
transform_attribute_query_to_sql_expression_schema1()
update_attribute_query_with_compounds()
- dae.query_variants.base_query_variants module
QueryVariants
QueryVariants.build_family_variants_query_runner()
QueryVariants.build_summary_variants_query_runner()
QueryVariants.has_affected_status_queries()
QueryVariants.query_summary_variants()
QueryVariants.query_variants()
QueryVariants.tags_to_family_ids()
QueryVariants.transform_roles_to_single_role_string()
QueryVariantsBase
- dae.query_variants.query_runners module
- Module contents
- dae.query_variants.sql package
- dae.query_variants.sql.schema2 package
- 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
Db2Layout
QueryBuilderBase
QueryBuilderBase.GENE_REGIONS_HEURISTIC_CUTOFF
QueryBuilderBase.GENE_REGIONS_HEURISTIC_EXTEND
QueryBuilderBase.REGION_BINS_HEURISTIC_CUTOFF
QueryBuilderBase.all_region_bins()
QueryBuilderBase.build_gene_regions()
QueryBuilderBase.build_schema()
QueryBuilderBase.build_variant_types_query()
QueryBuilderBase.calc_batched_heuristics()
QueryBuilderBase.calc_coding_bins()
QueryBuilderBase.calc_family_bins()
QueryBuilderBase.calc_frequency_bins()
QueryBuilderBase.calc_heuristics()
QueryBuilderBase.calc_region_bins()
QueryBuilderBase.check_inheritance_denovo_only()
QueryBuilderBase.check_inheritance_query_value()
QueryBuilderBase.check_roles_denovo_only()
QueryBuilderBase.check_roles_query_value()
QueryBuilderBase.check_variant_types_value()
QueryHeuristics
SqlQueryBuilder
SqlQueryBuilder.apply_family_heuristics()
SqlQueryBuilder.apply_summary_heuristics()
SqlQueryBuilder.build()
SqlQueryBuilder.build_family_variants_query()
SqlQueryBuilder.build_summary_variants_query()
SqlQueryBuilder.categorical_attr()
SqlQueryBuilder.coding_bins()
SqlQueryBuilder.effect_types()
SqlQueryBuilder.family_base()
SqlQueryBuilder.family_bins()
SqlQueryBuilder.family_ids()
SqlQueryBuilder.family_query()
SqlQueryBuilder.family_variants()
SqlQueryBuilder.frequency()
SqlQueryBuilder.frequency_bins()
SqlQueryBuilder.genes()
SqlQueryBuilder.inheritance()
SqlQueryBuilder.person_ids()
SqlQueryBuilder.real_attr()
SqlQueryBuilder.region_bins()
SqlQueryBuilder.regions()
SqlQueryBuilder.replace_tables()
SqlQueryBuilder.resolve_tags()
SqlQueryBuilder.roles()
SqlQueryBuilder.sexes()
SqlQueryBuilder.statuses()
SqlQueryBuilder.summary_base()
SqlQueryBuilder.summary_query()
SqlQueryBuilder.summary_variants()
SqlQueryBuilder.ultra_rare()
TagsQuery
ZygosityQuery
- dae.query_variants.sql.schema2.summary_builder module
- Module contents
- dae.query_variants package
- Genotype Storage
- dae.genotype_storage package
- Submodules
- dae.genotype_storage.genotype_storage module
- dae.genotype_storage.genotype_storage_registry module
GenotypeStorageRegistry
GenotypeStorageRegistry.get_all_genotype_storage_ids()
GenotypeStorageRegistry.get_all_genotype_storages()
GenotypeStorageRegistry.get_default_genotype_storage()
GenotypeStorageRegistry.get_genotype_storage()
GenotypeStorageRegistry.register_default_storage()
GenotypeStorageRegistry.register_genotype_storage()
GenotypeStorageRegistry.register_storage_config()
GenotypeStorageRegistry.register_storages_configs()
GenotypeStorageRegistry.shutdown()
- Module contents
- dae.genotype_storage package
- In-Memory Genotype Storage
- dae.inmemory_storage package
- Submodules
- dae.inmemory_storage.annotation_serialization module
- dae.inmemory_storage.inmemory_genotype_storage module
- dae.inmemory_storage.inmemory_import_storage module
- dae.inmemory_storage.raw_variants module
RawFamilyVariants
RawFamilyVariants.build_family_variants_query_runner()
RawFamilyVariants.build_summary_variants_query_runner()
RawFamilyVariants.family_variant_filter_function()
RawFamilyVariants.family_variants_iterator()
RawFamilyVariants.filter_allele()
RawFamilyVariants.filter_family_variant()
RawFamilyVariants.filter_gene_effects()
RawFamilyVariants.filter_real_attr()
RawFamilyVariants.filter_regions()
RawFamilyVariants.filter_summary_allele()
RawFamilyVariants.filter_summary_variant()
RawFamilyVariants.full_variants_iterator()
RawFamilyVariants.query_summary_variants()
RawFamilyVariants.query_variants()
RawFamilyVariants.summary_variant_filter_function()
RawFamilyVariants.summary_variants_iterator()
RawMemoryVariants
RawVariantsQueryRunner
- Module contents
- dae.inmemory_storage package
- Configuration
- Genotype Data
- Phenotype Data
- Pheno DB access
- Example usage of
PhenoDB
- Classes and Functions
- dae.pheno package
- Subpackages
- Submodules
- dae.pheno.browser module
- dae.pheno.build_pheno_browser module
- dae.pheno.common module
- dae.pheno.db module
- dae.pheno.graphs module
- dae.pheno.import_tools module
- dae.pheno.pheno_data module
- dae.pheno.pheno_import module
ImportInstrument
MeasureReport
add_pheno_common_inference()
collect_instruments()
create_import_tasks()
create_tables()
determine_destination()
generate_phenotype_data_config()
get_gpf_instance()
get_output_parquet_files_dir()
handle_measure_inference_tasks()
import_pheno_data()
infer_measures()
load_histogram_configs()
load_inference_configs()
load_instrument_description_file()
load_instrument_descriptions()
load_measure_description_file()
load_measure_descriptions()
main()
merge_histogram_configs()
merge_inference_configs()
open_file()
pheno_cli_parser()
read_and_classify_measure()
read_instrument_measure_names()
read_pedigree()
transform_cli_args()
write_descriptions()
write_reports_to_parquet()
write_results()
write_to_parquet()
- dae.pheno.prepare_data module
- dae.pheno.registry module
- dae.pheno.storage module
- dae.pheno.update_pheno_descriptions module
- Module contents
- dae.pheno package
- Phenotype tool
- Enrichment Tool
- dae
- dae package
- Subpackages
- dae.annotation package
- Submodules
- dae.annotation.annotatable module
- dae.annotation.annotate_columns module
- dae.annotation.annotate_doc module
- dae.annotation.annotate_schema2_parquet module
- dae.annotation.annotate_utils module
- dae.annotation.annotate_vcf module
- dae.annotation.annotation_config module
- dae.annotation.annotation_factory module
- dae.annotation.annotation_pipeline module
- dae.annotation.annotator_base module
- dae.annotation.cnv_collection_annotator module
- dae.annotation.debug_annotator module
- dae.annotation.docker_annotator module
- dae.annotation.effect_annotator module
- dae.annotation.format_handlers module
- dae.annotation.gene_score_annotator module
- dae.annotation.gene_set_annotator module
- dae.annotation.genomic_context module
- dae.annotation.liftover_annotator module
- dae.annotation.normalize_allele_annotator module
- dae.annotation.parquet module
- dae.annotation.reannotate_instance module
- dae.annotation.record_to_annotatable module
- dae.annotation.score_annotator module
- dae.annotation.simple_effect_annotator module
- Module contents
- dae.common_reports package
- dae.configuration package
- dae.dask package
- dae.duckdb_storage package
- Submodules
- dae.duckdb_storage.duckdb2_variants module
- dae.duckdb_storage.duckdb_connection_factory module
- dae.duckdb_storage.duckdb_genotype_storage module
- dae.duckdb_storage.duckdb_import_storage module
- dae.duckdb_storage.duckdb_legacy_genotype_storage module
- dae.duckdb_storage.duckdb_storage_config module
- dae.duckdb_storage.duckdb_storage_helpers module
- dae.duckdb_storage.duckdb_variants module
- Module contents
- dae.effect_annotation package
- Subpackages
- Submodules
- dae.effect_annotation.annotation_effects module
- dae.effect_annotation.annotation_request module
- dae.effect_annotation.annotator module
- dae.effect_annotation.cli module
- dae.effect_annotation.effect module
- dae.effect_annotation.gene_codes module
- dae.effect_annotation.variant module
- Module contents
- dae.enrichment_tool package
- Subpackages
- Submodules
- dae.enrichment_tool.base_enrichment_background module
- dae.enrichment_tool.build_coding_length_enrichment_background module
- dae.enrichment_tool.build_ur_synonymous_enrichment_background module
- dae.enrichment_tool.enrichment_builder module
- dae.enrichment_tool.enrichment_cache_builder module
- dae.enrichment_tool.enrichment_helper module
- dae.enrichment_tool.enrichment_serializer module
- dae.enrichment_tool.event_counters module
- dae.enrichment_tool.gene_weights_background module
- dae.enrichment_tool.genotype_helper module
- dae.enrichment_tool.samocha_background module
- Module contents
- dae.gene_profile package
- dae.gene_scores package
- dae.gene_sets package
- dae.genomic_resources package
- Subpackages
- Submodules
- dae.genomic_resources.aggregators module
- dae.genomic_resources.cached_repository module
- dae.genomic_resources.cli module
- dae.genomic_resources.draw_score_histograms module
- dae.genomic_resources.fsspec_protocol module
- dae.genomic_resources.genomic_context module
- dae.genomic_resources.genomic_context_cli module
- dae.genomic_resources.genomic_scores module
- dae.genomic_resources.group_repository module
- dae.genomic_resources.histogram module
- dae.genomic_resources.liftover_chain module
- dae.genomic_resources.reference_genome module
- dae.genomic_resources.repository module
- dae.genomic_resources.repository_factory module
- dae.genomic_resources.resource_implementation module
- dae.genomic_resources.testing module
- dae.genomic_resources.variant_utils module
- Module contents
- dae.genomic_scores package
- dae.genotype_storage package
- dae.gpf_instance package
- dae.gpf_instance_plugin package
- dae.import_tools package
- dae.inmemory_storage package
- dae.parquet package
- dae.parquet_storage package
- dae.pedigrees package
- Submodules
- dae.pedigrees.drawing module
- dae.pedigrees.families_data module
- dae.pedigrees.family module
- dae.pedigrees.family_role_builder module
- dae.pedigrees.family_tag_builder module
- dae.pedigrees.layout module
- dae.pedigrees.loader module
- dae.pedigrees.pedigrees module
- dae.pedigrees.testing module
- Module contents
- dae.person_filters package
- dae.person_sets package
- dae.pheno package
- Subpackages
- Submodules
- dae.pheno.browser module
- dae.pheno.build_pheno_browser module
- dae.pheno.common module
- dae.pheno.db module
- dae.pheno.graphs module
- dae.pheno.import_tools module
- dae.pheno.pheno_data module
- dae.pheno.pheno_import module
- dae.pheno.prepare_data module
- dae.pheno.registry module
- dae.pheno.storage module
- dae.pheno.update_pheno_descriptions module
- Module contents
- dae.pheno_tool package
- dae.query_variants package
- dae.schema2_storage package
- dae.studies package
- dae.task_graph package
- dae.testing package
- dae.tools package
- Submodules
- dae.tools.cnv_liftover module
- dae.tools.dae2vcf module
- dae.tools.dae_liftover module
- dae.tools.denovo2vcf module
- dae.tools.denovo_liftover module
- dae.tools.draw_pedigree module
- dae.tools.generate_common_report module
- dae.tools.generate_denovo_gene_sets module
- dae.tools.gpf_convert_study_config module
- dae.tools.gpf_validation_runner module
- dae.tools.grr_cache_repo module
- dae.tools.ped2ped module
- dae.tools.simple_study_import module
- dae.tools.to_gpf_gene_models_format module
- dae.tools.vcf2tsv module
- dae.tools.vcf_liftover module
- Module contents
- dae.utils package
- Submodules
- dae.utils.cnv_utils module
- dae.utils.dae_utils module
- dae.utils.debug_closing module
- dae.utils.dict_utils module
- dae.utils.filehash module
- dae.utils.fixtures module
- dae.utils.fs_utils module
- dae.utils.helpers module
- dae.utils.progress module
- dae.utils.regions module
- dae.utils.sql_utils module
- dae.utils.stats_collection module
- dae.utils.variant_utils module
- dae.utils.verbosity_configuration module
- Module contents
- dae.variants package
- dae.variants_loaders package
- dae.annotation package
- Module contents
- Subpackages
- dae package