dae package

Subpackages

• dae.annotation package
  • Submodules
  • dae.annotation.annotatable module
    • Annotatable
      • Annotatable.Type
      • Annotatable.chrom
      • Annotatable.chromosome
      • Annotatable.end_position
      • Annotatable.from_string()
      • Annotatable.pos
      • Annotatable.pos_end
      • Annotatable.position
      • Annotatable.tokenize()
    • CNVAllele
      • CNVAllele.from_string()
    • Position
      • Position.from_string()
    • Region
      • Region.from_string()
    • VCFAllele
      • VCFAllele.alt
      • VCFAllele.alternative
      • VCFAllele.from_string()
      • VCFAllele.ref
      • VCFAllele.reference
  • dae.annotation.annotate_columns module
    • AnnotateColumnsTool
      • AnnotateColumnsTool.add_tasks_to_graph()
      • AnnotateColumnsTool.get_argument_parser()
      • AnnotateColumnsTool.prepare_for_annotation()
    • cli()
    • combine()
  • dae.annotation.annotate_doc module
    • cli()
    • configure_argument_parser()
  • dae.annotation.annotate_schema2_parquet module
    • AnnotateSchema2ParquetTool
      • AnnotateSchema2ParquetTool.add_tasks_to_graph()
      • AnnotateSchema2ParquetTool.dry_run()
      • AnnotateSchema2ParquetTool.get_argument_parser()
      • AnnotateSchema2ParquetTool.prepare_for_annotation()
      • AnnotateSchema2ParquetTool.print_meta()
    • cli()
  • dae.annotation.annotate_utils module
    • AnnotationTool
      • AnnotationTool.add_tasks_to_graph()
      • AnnotationTool.annotate()
      • AnnotationTool.get_argument_parser()
      • AnnotationTool.get_task_dir()
      • AnnotationTool.prepare_for_annotation()
      • AnnotationTool.produce_annotation_pipeline()
      • AnnotationTool.run()
      • AnnotationTool.setup_work_dir()
    • produce_partfile_paths()
    • produce_regions()
    • produce_tabix_index()
  • dae.annotation.annotate_vcf module
    • AnnotateVCFTool
      • AnnotateVCFTool.add_tasks_to_graph()
      • AnnotateVCFTool.get_argument_parser()
      • AnnotateVCFTool.prepare_for_annotation()
    • cli()
    • combine()
  • dae.annotation.annotation_config module
    • AnnotationConfigParser
      • AnnotationConfigParser.has_wildcard()
      • AnnotationConfigParser.match_labels_query()
      • AnnotationConfigParser.parse_complete()
      • AnnotationConfigParser.parse_minimal()
      • AnnotationConfigParser.parse_raw()
      • AnnotationConfigParser.parse_raw_attribute_config()
      • AnnotationConfigParser.parse_raw_attributes()
      • AnnotationConfigParser.parse_short()
      • AnnotationConfigParser.parse_str()
      • AnnotationConfigParser.query_resources()
    • AnnotationConfigurationError
    • AnnotationPreamble
      • AnnotationPreamble.description
      • AnnotationPreamble.input_reference_genome
      • AnnotationPreamble.input_reference_genome_res
      • AnnotationPreamble.metadata
      • AnnotationPreamble.summary
    • AnnotatorInfo
      • AnnotatorInfo.annotator_id
      • AnnotatorInfo.attributes
      • AnnotatorInfo.documentation
      • AnnotatorInfo.parameters
      • AnnotatorInfo.resources
      • AnnotatorInfo.type
    • AttributeInfo
      • AttributeInfo.description
      • AttributeInfo.documentation
      • AttributeInfo.internal
      • AttributeInfo.name
      • AttributeInfo.parameters
      • AttributeInfo.source
      • AttributeInfo.type
    • ParamsUsageMonitor
      • ParamsUsageMonitor.get_unused_keys()
      • ParamsUsageMonitor.get_used_keys()
    • RawFullConfig
      • RawFullConfig.annotators
      • RawFullConfig.preamble
    • RawPreamble
      • RawPreamble.description
      • RawPreamble.input_reference_genome
      • RawPreamble.metadata
      • RawPreamble.summary
  • 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
    • AnnotationPipeline
      • AnnotationPipeline.add_annotator()
      • AnnotationPipeline.annotate()
      • AnnotationPipeline.batch_annotate()
      • AnnotationPipeline.build_pipeline_genomic_context()
      • AnnotationPipeline.close()
      • AnnotationPipeline.get_annotator_by_attribute_info()
      • AnnotationPipeline.get_attribute_info()
      • AnnotationPipeline.get_attributes()
      • AnnotationPipeline.get_info()
      • AnnotationPipeline.get_resource_ids()
      • AnnotationPipeline.open()
      • AnnotationPipeline.print()
    • Annotator
      • Annotator.annotate()
      • Annotator.attributes
      • Annotator.batch_annotate()
      • Annotator.close()
      • Annotator.get_info()
      • Annotator.is_open()
      • Annotator.open()
      • Annotator.resource_ids
      • Annotator.resources
      • Annotator.used_context_attributes
    • AnnotatorDecorator
      • AnnotatorDecorator.close()
      • AnnotatorDecorator.is_open()
      • AnnotatorDecorator.open()
    • FullReannotationPipeline
    • InputAnnotableAnnotatorDecorator
      • InputAnnotableAnnotatorDecorator.annotate()
      • InputAnnotableAnnotatorDecorator.decorate()
      • InputAnnotableAnnotatorDecorator.used_context_attributes
    • ReannotationPipeline
      • ReannotationPipeline.AnnotationDependencyGraph
      • ReannotationPipeline.annotate()
      • ReannotationPipeline.build_dependency_graph()
      • ReannotationPipeline.get_attributes()
      • ReannotationPipeline.get_dependencies_for()
      • ReannotationPipeline.get_dependents_for()
      • ReannotationPipeline.print()
    • ValueTransformAnnotatorDecorator
      • ValueTransformAnnotatorDecorator.annotate()
      • ValueTransformAnnotatorDecorator.decorate()
  • dae.annotation.annotator_base module
    • AnnotatorBase
      • AnnotatorBase.annotate()
      • AnnotatorBase.batch_annotate()
      • AnnotatorBase.open()
  • dae.annotation.cnv_collection_annotator module
    • CnvCollectionAnnotator
      • CnvCollectionAnnotator.annotate()
      • CnvCollectionAnnotator.close()
      • CnvCollectionAnnotator.open()
    • build_cnv_collection_annotator()
  • dae.annotation.debug_annotator module
    • HelloWorldAnnotator
      • HelloWorldAnnotator.annotate()
    • build_annotator()
  • dae.annotation.docker_annotator module
    • DockerAnnotator
      • DockerAnnotator.open()
      • DockerAnnotator.run()
  • dae.annotation.effect_annotator module
    • EffectAnnotatorAdapter
      • EffectAnnotatorAdapter.close()
      • EffectAnnotatorAdapter.open()
    • build_effect_annotator()
  • dae.annotation.format_handlers module
    • AbstractFormat
      • AbstractFormat.close()
      • AbstractFormat.get_task_dir()
      • AbstractFormat.open()
      • AbstractFormat.process()
      • AbstractFormat.process_batched()
    • ColumnsFormat
      • ColumnsFormat.close()
      • ColumnsFormat.open()
    • ParquetFormat
      • ParquetFormat.close()
      • ParquetFormat.open()
    • VCFFormat
      • VCFFormat.close()
      • VCFFormat.open()
    • stringify()
  • dae.annotation.gene_score_annotator module
    • GeneScoreAnnotator
      • GeneScoreAnnotator.DEFAULT_AGGREGATOR_TYPE
      • GeneScoreAnnotator.aggregate_gene_values()
      • GeneScoreAnnotator.annotate()
      • GeneScoreAnnotator.used_context_attributes
    • build_gene_score_annotator()
  • dae.annotation.gene_set_annotator module
    • GeneSetAnnotator
      • GeneSetAnnotator.used_context_attributes
    • build_gene_set_annotator()
  • dae.annotation.genomic_context module
    • CLIAnnotationContextProvider
      • CLIAnnotationContextProvider.add_argparser_arguments()
      • CLIAnnotationContextProvider.init()
    • get_context_pipeline()
  • dae.annotation.liftover_annotator module
    • AbstractLiftoverAnnotator
      • AbstractLiftoverAnnotator.close()
      • AbstractLiftoverAnnotator.liftover_allele()
      • AbstractLiftoverAnnotator.liftover_cnv()
      • AbstractLiftoverAnnotator.liftover_position()
      • AbstractLiftoverAnnotator.liftover_region()
      • AbstractLiftoverAnnotator.open()
    • BasicLiftoverAnnotator
    • BcfLiftoverAnnotator
    • basic_liftover_allele()
    • basic_liftover_variant()
    • bcf_liftover_allele()
    • bcf_liftover_variant()
    • build_liftover_annotator()
  • dae.annotation.normalize_allele_annotator module
    • NormalizeAlleleAnnotator
      • NormalizeAlleleAnnotator.close()
      • NormalizeAlleleAnnotator.open()
    • build_normalize_allele_annotator()
    • normalize_allele()
  • dae.annotation.parquet module
    • annotate_parquet()
    • backup_schema2_study()
    • merge_non_partitioned()
    • merge_partitioned()
    • produce_regions()
    • produce_schema2_annotation_tasks()
    • produce_schema2_merging_tasks()
    • symlink_pedigree_and_family_variants()
    • write_new_meta()
  • dae.annotation.reannotate_instance module
    • ReannotateInstanceTool
      • ReannotateInstanceTool.get_argument_parser()
      • ReannotateInstanceTool.run()
    • cli()
  • dae.annotation.record_to_annotatable module
    • CSHLAlleleRecordToAnnotatable
      • CSHLAlleleRecordToAnnotatable.build()
    • DaeAlleleRecordToAnnotatable
      • DaeAlleleRecordToAnnotatable.build()
    • RecordToAnnotable
      • RecordToAnnotable.build()
    • RecordToCNVAllele
      • RecordToCNVAllele.build()
    • RecordToPosition
      • RecordToPosition.build()
    • RecordToRegion
      • RecordToRegion.build()
    • RecordToVcfAllele
      • RecordToVcfAllele.build()
    • VcfLikeRecordToVcfAllele
      • VcfLikeRecordToVcfAllele.build()
    • add_record_to_annotable_arguments()
    • build_record_to_annotatable()
  • dae.annotation.score_annotator module
    • AlleleScoreAnnotator
      • AlleleScoreAnnotator.annotate()
      • AlleleScoreAnnotator.build_score_aggregator_documentation()
    • GenomicScoreAnnotatorBase
      • GenomicScoreAnnotatorBase.add_score_aggregator_documentation()
      • GenomicScoreAnnotatorBase.build_score_aggregator_documentation()
      • GenomicScoreAnnotatorBase.close()
      • GenomicScoreAnnotatorBase.is_open()
      • GenomicScoreAnnotatorBase.open()
    • PositionScoreAnnotator
      • PositionScoreAnnotator.annotate()
      • PositionScoreAnnotator.build_score_aggregator_documentation()
    • build_allele_score_annotator()
    • build_np_score_annotator()
    • build_position_score_annotator()
    • get_genomic_resource()
  • dae.annotation.simple_effect_annotator module
    • SimpleEffectAnnotator
      • SimpleEffectAnnotator.call_region()
      • SimpleEffectAnnotator.cds_intron_regions()
      • SimpleEffectAnnotator.noncoding_regions()
      • SimpleEffectAnnotator.open()
      • SimpleEffectAnnotator.peripheral_regions()
      • SimpleEffectAnnotator.run_annotate()
      • SimpleEffectAnnotator.utr_regions()
    • build_simple_effect_annotator()
  • Module contents
• dae.common_reports package
  • Submodules
  • dae.common_reports.common_report module
    • CommonReport
      • CommonReport.load()
      • CommonReport.save()
      • CommonReport.to_dict()
  • dae.common_reports.denovo_report module
    • DenovoReport
      • DenovoReport.from_genotype_study()
      • DenovoReport.is_empty()
      • DenovoReport.to_dict()
    • DenovoReportTable
      • DenovoReportTable.from_variants()
      • DenovoReportTable.is_empty()
      • DenovoReportTable.to_dict()
    • EffectCell
      • EffectCell.column_name
      • EffectCell.count_variant()
      • EffectCell.is_empty()
      • EffectCell.number_of_children_with_event
      • EffectCell.number_of_observed_events
      • EffectCell.observed_rate_per_child
      • EffectCell.percent_of_children_with_events
      • EffectCell.to_dict()
    • EffectRow
      • EffectRow.count_variant()
      • EffectRow.get_empty()
      • EffectRow.is_row_empty()
      • EffectRow.remove_elements()
      • EffectRow.to_dict()
  • dae.common_reports.family_counter module
    • FamiliesGroupCounters
      • FamiliesGroupCounters.from_families()
      • FamiliesGroupCounters.to_dict()
    • FamilyCounter
      • FamilyCounter.family
      • FamilyCounter.from_family()
      • FamilyCounter.to_dict()
    • get_family_pedigree()
    • get_family_type()
  • dae.common_reports.family_report module
    • FamiliesReport
      • FamiliesReport.from_families_data()
      • FamiliesReport.from_study()
      • FamiliesReport.to_dict()
  • dae.common_reports.people_counter module
    • PeopleCounter
      • PeopleCounter.from_person_set()
      • PeopleCounter.is_empty()
      • PeopleCounter.is_empty_field()
      • PeopleCounter.to_dict()
    • PeopleCounters
      • PeopleCounters.from_person_set_collection()
      • PeopleCounters.to_dict()
    • PeopleReport
      • PeopleReport.from_person_set_collections()
      • PeopleReport.to_dict()
  • Module contents
• dae.configuration package
  • Subpackages
    • dae.configuration.schemas package
      • Submodules
      • dae.configuration.schemas.dae_conf module
      • dae.configuration.schemas.gene_profile module
      • dae.configuration.schemas.gene_weights_db module
      • dae.configuration.schemas.person_sets module
      • dae.configuration.schemas.phenotype_data module
      • dae.configuration.schemas.study_config module
      • dae.configuration.schemas.wdae_study_config module
      • Module contents
  • Submodules
  • dae.configuration.gpf_config_parser module
    • DefaultBox
    • FrozenBox
    • GPFConfigParser
      • GPFConfigParser.collect_directory_configs()
      • GPFConfigParser.filetype_parsers
      • GPFConfigParser.load_config()
      • GPFConfigParser.load_config_dict()
      • GPFConfigParser.load_config_raw()
      • GPFConfigParser.load_directory_configs()
      • GPFConfigParser.merge_config()
      • GPFConfigParser.modify_tuple()
      • GPFConfigParser.parse_and_interpolate()
      • GPFConfigParser.parse_and_interpolate_file()
      • GPFConfigParser.process_config()
      • GPFConfigParser.process_config_raw()
      • GPFConfigParser.validate_config()
    • GPFConfigValidator
      • GPFConfigValidator.checkers
      • GPFConfigValidator.coercers
      • GPFConfigValidator.default_setters
      • GPFConfigValidator.normalization_rules
      • GPFConfigValidator.rules
      • GPFConfigValidator.validation_rules
  • dae.configuration.study_config_builder module
    • ConfigDumper
      • ConfigDumper.increase_indent()
    • StudyConfigBuilder
      • StudyConfigBuilder.build_config()
    • TOMLDict
      • TOMLDict.from_dict()
    • TOMLList
      • TOMLList.from_list()
  • dae.configuration.utils module
    • validate_existing_path()
    • validate_path()
  • Module contents
• dae.dask package
  • Submodules
  • dae.dask.config module
    • reconfigure()
  • dae.dask.named_cluster module
    • set_up_kubernetes_cluster()
    • set_up_local_cluster()
    • set_up_sge_cluster()
    • set_up_slurm_cluster()
    • setup_client()
    • setup_client_from_config()
  • Module contents
• dae.duckdb_storage package
  • Submodules
  • dae.duckdb_storage.duckdb2_variants module
    • DuckDb2Runner
      • DuckDb2Runner.run()
    • DuckDb2Variants
      • DuckDb2Variants.build_family_variants_query_runner()
      • DuckDb2Variants.build_summary_variants_query_runner()
      • DuckDb2Variants.fetch_annotation()
      • DuckDb2Variants.query_summary_variants()
      • DuckDb2Variants.query_variants()
  • dae.duckdb_storage.duckdb_connection_factory module
    • DuckDbConnectionFactory
      • DuckDbConnectionFactory.connect()
  • dae.duckdb_storage.duckdb_genotype_storage module
    • AbstractDuckDbStorage
      • AbstractDuckDbStorage.build_backend()
      • AbstractDuckDbStorage.build_study_layout()
      • AbstractDuckDbStorage.connect()
      • AbstractDuckDbStorage.is_read_only()
      • AbstractDuckDbStorage.shutdown()
    • DuckDbParquetStorage
      • DuckDbParquetStorage.build_study_layout()
      • DuckDbParquetStorage.get_storage_types()
      • DuckDbParquetStorage.start()
    • DuckDbS3ParquetStorage
      • DuckDbS3ParquetStorage.build_study_layout()
      • DuckDbS3ParquetStorage.get_storage_types()
      • DuckDbS3ParquetStorage.start()
    • DuckDbS3Storage
      • DuckDbS3Storage.build_study_layout()
      • DuckDbS3Storage.get_db_filename()
      • DuckDbS3Storage.get_storage_types()
      • DuckDbS3Storage.start()
    • DuckDbStorage
      • DuckDbStorage.build_study_layout()
      • DuckDbStorage.get_db_filename()
      • DuckDbStorage.get_storage_types()
      • DuckDbStorage.start()
    • duckdb_parquet_storage_factory()
    • duckdb_s3_parquet_storage_factory()
    • duckdb_s3_storage_factory()
    • duckdb_storage_factory()
  • dae.duckdb_storage.duckdb_import_storage module
    • AbstractDuckDbImportStorage
      • AbstractDuckDbImportStorage.do_study_config()
      • AbstractDuckDbImportStorage.generate_import_task_graph()
    • DuckDbImportStorage
    • DuckDbLegacyImportStorage
    • DuckDbParquetImportStorage
    • DuckDbS3ImportStorage
    • DuckDbS3ParquetImportStorage
  • dae.duckdb_storage.duckdb_legacy_genotype_storage module
    • DuckDbLegacyStorage
      • DuckDbLegacyStorage.VALIDATION_SCHEMA
      • DuckDbLegacyStorage.build_backend()
      • DuckDbLegacyStorage.close()
      • DuckDbLegacyStorage.connect()
      • DuckDbLegacyStorage.create_database_connection()
      • DuckDbLegacyStorage.create_parquet_scans_layout_from_layout()
      • DuckDbLegacyStorage.create_parquet_scans_layout_relative()
      • DuckDbLegacyStorage.create_table()
      • DuckDbLegacyStorage.create_table_layout()
      • DuckDbLegacyStorage.create_table_partitioned()
      • DuckDbLegacyStorage.get_base_dir()
      • DuckDbLegacyStorage.get_db()
      • DuckDbLegacyStorage.get_db_filename()
      • DuckDbLegacyStorage.get_memory_limit()
      • DuckDbLegacyStorage.get_storage_types()
      • DuckDbLegacyStorage.get_work_dir()
      • DuckDbLegacyStorage.import_dataset()
      • DuckDbLegacyStorage.shutdown()
      • DuckDbLegacyStorage.start()
      • DuckDbLegacyStorage.validate_and_normalize_config()
    • duckdb_connect()
  • dae.duckdb_storage.duckdb_storage_config module
    • DuckDbBaseConf
      • DuckDbBaseConf.id
      • DuckDbBaseConf.memory_limit
      • DuckDbBaseConf.model_computed_fields
      • DuckDbBaseConf.model_config
      • DuckDbBaseConf.model_fields
    • DuckDbConf
      • DuckDbConf.base_dir
      • DuckDbConf.db
      • DuckDbConf.model_computed_fields
      • DuckDbConf.model_config
      • DuckDbConf.model_fields
      • DuckDbConf.read_only
      • DuckDbConf.storage_type
    • DuckDbParquetConf
      • DuckDbParquetConf.base_dir
      • DuckDbParquetConf.model_computed_fields
      • DuckDbParquetConf.model_config
      • DuckDbParquetConf.model_fields
      • DuckDbParquetConf.storage_type
    • DuckDbS3Conf
      • DuckDbS3Conf.bucket_url
      • DuckDbS3Conf.db
      • DuckDbS3Conf.endpoint_url
      • DuckDbS3Conf.model_computed_fields
      • DuckDbS3Conf.model_config
      • DuckDbS3Conf.model_fields
      • DuckDbS3Conf.storage_type
    • DuckDbS3ParquetConf
      • DuckDbS3ParquetConf.bucket_url
      • DuckDbS3ParquetConf.endpoint_url
      • DuckDbS3ParquetConf.model_computed_fields
      • DuckDbS3ParquetConf.model_config
      • DuckDbS3ParquetConf.model_fields
      • DuckDbS3ParquetConf.storage_type
    • parse_duckdb_config()
  • dae.duckdb_storage.duckdb_storage_helpers module
    • create_database_connection()
    • create_duckdb_tables()
    • create_memory_connection()
    • create_relative_parquet_scans_layout()
    • create_s3_attach_db_clause()
    • create_s3_filesystem()
    • create_s3_secret_clause()
    • create_study_parquet_tables_layout()
    • create_table_layout()
    • get_study_config_tables()
    • join_base_url_and_parquet_scan()
  • dae.duckdb_storage.duckdb_variants module
    • DuckDbQueryDialect
      • DuckDbQueryDialect.add_unnest_in_join()
      • DuckDbQueryDialect.array_item_suffix()
      • DuckDbQueryDialect.build_array_join()
      • DuckDbQueryDialect.build_table_name()
      • DuckDbQueryDialect.escape_char()
      • DuckDbQueryDialect.escape_quote_char()
      • DuckDbQueryDialect.float_type()
      • DuckDbQueryDialect.int_type()
      • DuckDbQueryDialect.use_bit_and_function()
    • DuckDbRunner
      • DuckDbRunner.run()
    • DuckDbVariants
      • DuckDbVariants.RUNNER_CLASS
  • Module contents
• dae.effect_annotation package
  • Subpackages
    • dae.effect_annotation.effect_checkers package
      • Submodules
      • dae.effect_annotation.effect_checkers.coding module
      • dae.effect_annotation.effect_checkers.effect_checker module
      • dae.effect_annotation.effect_checkers.frame_shift module
      • dae.effect_annotation.effect_checkers.intron module
      • dae.effect_annotation.effect_checkers.promoter module
      • dae.effect_annotation.effect_checkers.protein_change module
      • dae.effect_annotation.effect_checkers.splice_site module
      • dae.effect_annotation.effect_checkers.start_loss module
      • dae.effect_annotation.effect_checkers.stop_loss module
      • dae.effect_annotation.effect_checkers.utr module
      • Module contents
  • Submodules
  • dae.effect_annotation.annotation_effects module
    • get_effect_types()
    • get_effect_types_set()
  • dae.effect_annotation.annotation_request module
    • BaseAnnotationRequest
      • BaseAnnotationRequest.cds_regions()
      • BaseAnnotationRequest.cod2aa()
      • BaseAnnotationRequest.get_coding_left()
      • BaseAnnotationRequest.get_coding_region_for_pos()
      • BaseAnnotationRequest.get_coding_right()
      • BaseAnnotationRequest.get_codons_left()
      • BaseAnnotationRequest.get_codons_right()
      • BaseAnnotationRequest.get_exonic_distance()
      • BaseAnnotationRequest.get_exonic_length()
      • BaseAnnotationRequest.get_exonic_position()
      • BaseAnnotationRequest.get_nucleotides_count_to_full_codon()
      • BaseAnnotationRequest.get_protein_position()
      • BaseAnnotationRequest.get_protein_position_for_pos()
      • BaseAnnotationRequest.has_utr3_region()
      • BaseAnnotationRequest.has_utr5_region()
      • BaseAnnotationRequest.is_start_codon_affected()
      • BaseAnnotationRequest.is_stop_codon_affected()
    • NegativeStrandAnnotationRequest
      • NegativeStrandAnnotationRequest.cod2aa()
      • NegativeStrandAnnotationRequest.complement()
      • NegativeStrandAnnotationRequest.get_amino_acids()
      • NegativeStrandAnnotationRequest.get_codons()
      • NegativeStrandAnnotationRequest.get_frame()
      • NegativeStrandAnnotationRequest.get_protein_length()
      • NegativeStrandAnnotationRequest.get_protein_position()
      • NegativeStrandAnnotationRequest.has_utr3_region()
      • NegativeStrandAnnotationRequest.has_utr5_region()
      • NegativeStrandAnnotationRequest.in_start_codons()
      • NegativeStrandAnnotationRequest.is_start_codon_affected()
      • NegativeStrandAnnotationRequest.is_stop_codon_affected()
    • PositiveStrandAnnotationRequest
      • PositiveStrandAnnotationRequest.get_amino_acids()
      • PositiveStrandAnnotationRequest.get_codons()
      • PositiveStrandAnnotationRequest.get_frame()
      • PositiveStrandAnnotationRequest.get_protein_length()
      • PositiveStrandAnnotationRequest.get_protein_position()
      • PositiveStrandAnnotationRequest.in_start_codons()
  • dae.effect_annotation.annotator module
    • AnnotationRequestFactory
      • AnnotationRequestFactory.create_annotation_request()
    • EffectAnnotator
      • EffectAnnotator.annotate()
      • EffectAnnotator.annotate_allele()
      • EffectAnnotator.annotate_cnv()
      • EffectAnnotator.annotate_region()
      • EffectAnnotator.annotate_variant()
      • EffectAnnotator.do_annotate_variant()
      • EffectAnnotator.get_effect_for_transcript()
  • dae.effect_annotation.cli module
    • AnnotationAttributes
      • AnnotationAttributes.ALL_ATTRIBUTE_IDXS
      • AnnotationAttributes.get_out_attributes()
      • AnnotationAttributes.get_source_attributes()
      • AnnotationAttributes.get_values()
      • AnnotationAttributes.set_argument()
    • EffectAnnotatorBuilder
      • EffectAnnotatorBuilder.build_effect_annotator()
      • EffectAnnotatorBuilder.get_gene_models()
      • EffectAnnotatorBuilder.get_genomic_context()
      • EffectAnnotatorBuilder.get_grr()
      • EffectAnnotatorBuilder.get_refernce_genome()
      • EffectAnnotatorBuilder.set_arguments()
    • VariantColumnInputFile
      • VariantColumnInputFile.close()
      • VariantColumnInputFile.get_header()
      • VariantColumnInputFile.get_lines()
      • VariantColumnInputFile.set_argument()
      • VariantColumnInputFile.variant_columns
    • VariantColumnOutputFile
      • VariantColumnOutputFile.close()
      • VariantColumnOutputFile.set_argument()
      • VariantColumnOutputFile.write_columns()
    • cli_columns()
    • cli_vcf()
  • dae.effect_annotation.effect module
    • AlleleEffects
      • AlleleEffects.from_effects()
      • AlleleEffects.from_simplified_effects()
      • AlleleEffects.from_string()
      • AlleleEffects.types
      • AlleleEffects.worst
    • AnnotationEffect
      • AnnotationEffect.SEVERITY
      • AnnotationEffect.create_effect_details()
      • AnnotationEffect.effect_severity()
      • AnnotationEffect.effects_description()
      • AnnotationEffect.filter_gene_effects()
      • AnnotationEffect.gene_effects()
      • AnnotationEffect.simplify_effects()
      • AnnotationEffect.sort_effects()
      • AnnotationEffect.transcript_effects()
      • AnnotationEffect.worst_effect()
    • EffectFactory
      • EffectFactory.create_effect()
      • EffectFactory.create_effect_with_aa_change()
      • EffectFactory.create_effect_with_prot_length()
      • EffectFactory.create_effect_with_prot_pos()
      • EffectFactory.create_effect_with_request()
      • EffectFactory.create_effect_with_tm()
      • EffectFactory.create_intronic_effect()
      • EffectFactory.create_intronic_non_coding_effect()
    • EffectGene
      • EffectGene.from_gene_effects()
      • EffectGene.from_string()
      • EffectGene.from_tuple()
    • EffectTranscript
      • EffectTranscript.from_effect_transcripts()
      • EffectTranscript.from_string()
      • EffectTranscript.from_tuple()
    • EffectTypesMixin
      • EffectTypesMixin.EFFECT_GROUPS
      • EffectTypesMixin.EFFECT_TYPES
      • EffectTypesMixin.EFFECT_TYPES_MAPPING
      • EffectTypesMixin.EFFECT_TYPES_UI_NAMING
      • EffectTypesMixin.build_effect_types()
      • EffectTypesMixin.build_effect_types_groups()
      • EffectTypesMixin.build_effect_types_list()
      • EffectTypesMixin.build_effect_types_naming()
      • EffectTypesMixin.get_effect_types()
    • expand_effect_types()
    • gd2str()
    • ge2str()
    • gene_effect_get_genes()
    • gene_effect_get_genes_worst()
    • gene_effect_get_worst_effect()
  • dae.effect_annotation.gene_codes module
    • NuclearCode
      • NuclearCode.CodonsAa
      • NuclearCode.CodonsAaKeys
      • NuclearCode.startCodons
      • NuclearCode.stopCodons
  • dae.effect_annotation.variant module
    • Variant
      • Variant.set_position()
      • Variant.set_ref_alt()
      • Variant.set_ref_alt_from_variant()
      • Variant.trim_equal_ref_alt_parts()
  • Module contents
• dae.enrichment_tool package
  • Subpackages
    • dae.enrichment_tool.resource_implementations package
      • Submodules
      • dae.enrichment_tool.resource_implementations.enrichment_resource_impl module
      • Module contents
  • Submodules
  • dae.enrichment_tool.base_enrichment_background module
    • BaseEnrichmentBackground
      • BaseEnrichmentBackground.background_id
      • BaseEnrichmentBackground.background_type
      • BaseEnrichmentBackground.calc_enrichment_test()
      • BaseEnrichmentBackground.is_loaded()
      • BaseEnrichmentBackground.load()
      • BaseEnrichmentBackground.name
      • BaseEnrichmentBackground.resource_id
    • BaseEnrichmentResourceBackground
      • BaseEnrichmentResourceBackground.filename
      • BaseEnrichmentResourceBackground.get_schema()
      • BaseEnrichmentResourceBackground.name
  • dae.enrichment_tool.build_coding_length_enrichment_background module
    • build_coding_length_background()
    • cli()
  • dae.enrichment_tool.build_ur_synonymous_enrichment_background module
    • cli()
  • dae.enrichment_tool.enrichment_builder module
    • BaseEnrichmentBuilder
      • BaseEnrichmentBuilder.build()
    • EnrichmentBuilder
      • EnrichmentBuilder.build()
      • EnrichmentBuilder.build_results()
  • dae.enrichment_tool.enrichment_cache_builder module
    • cli()
  • dae.enrichment_tool.enrichment_helper module
    • EnrichmentHelper
      • EnrichmentHelper.build_enrichment_event_counts_cache()
      • EnrichmentHelper.calc_enrichment_test()
      • EnrichmentHelper.collect_genotype_data_backgrounds()
      • EnrichmentHelper.create_background()
      • EnrichmentHelper.create_counter()
      • EnrichmentHelper.get_default_background_model()
      • EnrichmentHelper.get_default_counting_model()
      • EnrichmentHelper.get_enrichment_config()
      • EnrichmentHelper.get_selected_counting_models()
      • EnrichmentHelper.get_selected_person_set_collections()
      • EnrichmentHelper.has_enrichment_config()
  • dae.enrichment_tool.enrichment_serializer module
    • EnrichmentSerializer
      • EnrichmentSerializer.serialize()
      • EnrichmentSerializer.serialize_all()
      • EnrichmentSerializer.serialize_common_filter()
      • EnrichmentSerializer.serialize_enrichment_result()
      • EnrichmentSerializer.serialize_female()
      • EnrichmentSerializer.serialize_male()
      • EnrichmentSerializer.serialize_overlap_filter()
      • EnrichmentSerializer.serialize_people_groups()
      • EnrichmentSerializer.serialize_rec()
      • EnrichmentSerializer.serialize_rec_filter()
  • dae.enrichment_tool.event_counters module
    • CounterBase
      • CounterBase.event_counts()
      • CounterBase.events()
      • CounterBase.select_events_in_person_set()
      • CounterBase.split_events()
    • EnrichmentResult
      • EnrichmentResult.all
      • EnrichmentResult.female
      • EnrichmentResult.male
      • EnrichmentResult.rec
      • EnrichmentResult.rec_genes
      • EnrichmentResult.unspecified
    • EnrichmentSingleResult
    • EventCountersResult
      • EventCountersResult.all
      • EventCountersResult.female
      • EventCountersResult.from_events_result()
      • EventCountersResult.male
      • EventCountersResult.rec
      • EventCountersResult.rec_genes
      • EventCountersResult.unspecified
    • EventsCounter
      • EventsCounter.events()
    • EventsResult
      • EventsResult.all
      • EventsResult.female
      • EventsResult.male
      • EventsResult.rec
      • EventsResult.unspecified
    • GeneEventsCounter
      • GeneEventsCounter.events()
    • VariantEventsResult
      • VariantEventsResult.all
      • VariantEventsResult.female
      • VariantEventsResult.male
      • VariantEventsResult.rec
      • VariantEventsResult.unspecified
    • filter_denovo_one_event_per_family()
    • filter_denovo_one_gene_per_events()
    • filter_denovo_one_gene_per_recurrent_events()
    • filter_overlapping_events()
    • get_sym_2_fn()
    • overlap_enrichment_result_dict()
    • overlap_event_counts()
  • dae.enrichment_tool.gene_weights_background module
    • GeneScoreEnrichmentBackground
      • GeneScoreEnrichmentBackground.background_id
      • GeneScoreEnrichmentBackground.background_type
      • GeneScoreEnrichmentBackground.calc_enrichment_test()
      • GeneScoreEnrichmentBackground.calc_expected_observed_pvalue()
      • GeneScoreEnrichmentBackground.filename
      • GeneScoreEnrichmentBackground.genes_prob()
      • GeneScoreEnrichmentBackground.genes_weight()
      • GeneScoreEnrichmentBackground.is_loaded()
      • GeneScoreEnrichmentBackground.load()
      • GeneScoreEnrichmentBackground.name
      • GeneScoreEnrichmentBackground.resource_id
      • GeneScoreEnrichmentBackground.score_id
    • GeneWeightsEnrichmentBackground
      • GeneWeightsEnrichmentBackground.calc_enrichment_test()
      • GeneWeightsEnrichmentBackground.calc_expected_observed_pvalue()
      • GeneWeightsEnrichmentBackground.genes_prob()
      • GeneWeightsEnrichmentBackground.genes_weight()
      • GeneWeightsEnrichmentBackground.is_loaded()
      • GeneWeightsEnrichmentBackground.load()
  • dae.enrichment_tool.genotype_helper module
    • AlleleEvent
      • AlleleEvent.effect_genes
      • AlleleEvent.persons
    • GeneEffect
      • GeneEffect.effect
      • GeneEffect.gene
    • GenotypeHelper
      • GenotypeHelper.collect_denovo_events()
      • GenotypeHelper.get_denovo_events()
    • VariantEvent
      • VariantEvent.allele_events
      • VariantEvent.family_id
      • VariantEvent.fvuid
  • dae.enrichment_tool.samocha_background module
    • SamochaEnrichmentBackground
      • SamochaEnrichmentBackground.calc_enrichment_test()
      • SamochaEnrichmentBackground.get_schema()
      • SamochaEnrichmentBackground.is_loaded()
      • SamochaEnrichmentBackground.load()
      • SamochaEnrichmentBackground.name
    • poisson_test()
  • Module contents
• dae.gene_profile package
  • Submodules
  • dae.gene_profile.convert_gene_profile_to_duckdb module
    • main()
  • dae.gene_profile.db module
    • GeneProfileDB
      • GeneProfileDB.PAGE_SIZE
      • GeneProfileDB.get_gp()
      • GeneProfileDB.gp_from_table_row()
      • GeneProfileDB.gp_from_table_row_single_view()
      • GeneProfileDB.list_symbols()
      • GeneProfileDB.query_gps()
    • GeneProfileDBWriter
      • GeneProfileDBWriter.build_configuration()
      • GeneProfileDBWriter.drop_gp_table()
      • GeneProfileDBWriter.gp_table_exists()
      • GeneProfileDBWriter.insert_gp()
      • GeneProfileDBWriter.insert_gps()
      • GeneProfileDBWriter.update_gps_with_values()
  • dae.gene_profile.exporter module
    • cli_export()
  • dae.gene_profile.generate_gene_profile module
    • add_variant_count()
    • calculate_table_values()
    • collect_variant_counts()
    • count_variant()
    • generate_gp()
    • main()
  • dae.gene_profile.statistic module
    • GPStatistic
      • GPStatistic.to_json()
  • Module contents
• dae.gene_scores package
  • Subpackages
    • dae.gene_scores.implementations package
      • Submodules
      • dae.gene_scores.implementations.gene_scores_impl module
      • Module contents
  • Submodules
  • dae.gene_scores.gene_scores module
    • GeneScore
      • GeneScore.files
      • GeneScore.get_all_scores()
      • GeneScore.get_gene_value()
      • GeneScore.get_genes()
      • GeneScore.get_histogram_filename()
      • GeneScore.get_histogram_image_filename()
      • GeneScore.get_histogram_image_url()
      • GeneScore.get_max()
      • GeneScore.get_min()
      • GeneScore.get_number_range()
      • GeneScore.get_schema()
      • GeneScore.get_score_df()
      • GeneScore.get_score_histogram()
      • GeneScore.get_scores()
      • GeneScore.get_values()
      • GeneScore.get_x_scale()
      • GeneScore.get_y_scale()
      • GeneScore.to_tsv()
    • GeneScoresDb
      • GeneScoresDb.build_descs_from_score()
      • GeneScoresDb.get_gene_score()
      • GeneScoresDb.get_gene_score_ids()
      • GeneScoresDb.get_gene_scores()
      • GeneScoresDb.get_score_desc()
      • GeneScoresDb.get_score_ids()
      • GeneScoresDb.get_scores()
    • ScoreDef
      • ScoreDef.desc
      • ScoreDef.hist_conf
      • ScoreDef.large_values_desc
      • ScoreDef.name
      • ScoreDef.score_id
      • ScoreDef.small_values_desc
    • ScoreDesc
      • ScoreDesc.description
      • ScoreDesc.help
      • ScoreDesc.hist
      • ScoreDesc.large_values_desc
      • ScoreDesc.name
      • ScoreDesc.resource_id
      • ScoreDesc.score_id
      • ScoreDesc.small_values_desc
    • build_gene_score_from_resource()
    • build_gene_score_from_resource_id()
  • Module contents
• dae.gene_sets package
  • Subpackages
    • dae.gene_sets.implementations package
      • Submodules
      • dae.gene_sets.implementations.gene_sets_impl module
      • Module contents
  • Submodules
  • dae.gene_sets.denovo_gene_set_collection module
    • DenovoGeneSetCollection
      • DenovoGeneSetCollection.add_gene()
      • DenovoGeneSetCollection.build_collection()
      • DenovoGeneSetCollection.create_empty_collection()
      • DenovoGeneSetCollection.get_all_gene_sets()
      • DenovoGeneSetCollection.get_gene_set()
      • DenovoGeneSetCollection.get_gene_set_from_collections()
      • DenovoGeneSetCollection.get_gene_sets_types_legend()
      • DenovoGeneSetCollection.get_person_set_collection_legend()
      • DenovoGeneSetCollection.is_cached()
      • DenovoGeneSetCollection.load()
      • DenovoGeneSetCollection.save()
  • dae.gene_sets.denovo_gene_set_helpers module
    • DenovoGeneSetHelpers
      • DenovoGeneSetHelpers.build_collection()
      • DenovoGeneSetHelpers.load_collection()
      • DenovoGeneSetHelpers.load_collection_from_dict()
  • dae.gene_sets.denovo_gene_sets_config module
    • DGSCQuery
      • DGSCQuery.effects
      • DGSCQuery.gene_set_id
      • DGSCQuery.model_computed_fields
      • DGSCQuery.model_config
      • DGSCQuery.model_fields
      • DGSCQuery.psc_id
      • DGSCQuery.recurrency
      • DGSCQuery.selected_person_sets
      • DGSCQuery.sex
    • DGSSpec
      • DGSSpec.criterias
      • DGSSpec.gene_set_id
      • DGSSpec.model_computed_fields
      • DGSSpec.model_config
      • DGSSpec.model_fields
    • DenovoGeneSetsConfig
      • DenovoGeneSetsConfig.effect_types
      • DenovoGeneSetsConfig.enabled
      • DenovoGeneSetsConfig.gene_sets_ids
      • DenovoGeneSetsConfig.model_computed_fields
      • DenovoGeneSetsConfig.model_config
      • DenovoGeneSetsConfig.model_fields
      • DenovoGeneSetsConfig.recurrency
      • DenovoGeneSetsConfig.selected_person_set_collections
      • DenovoGeneSetsConfig.sexes
    • EffectsCriteria
      • EffectsCriteria.effects
      • EffectsCriteria.model_computed_fields
      • EffectsCriteria.model_config
      • EffectsCriteria.model_fields
      • EffectsCriteria.name
    • RecurrentCriteria
      • RecurrentCriteria.end
      • RecurrentCriteria.model_computed_fields
      • RecurrentCriteria.model_config
      • RecurrentCriteria.model_fields
      • RecurrentCriteria.name
      • RecurrentCriteria.start
    • SexesCriteria
      • SexesCriteria.model_computed_fields
      • SexesCriteria.model_config
      • SexesCriteria.model_fields
      • SexesCriteria.name
      • SexesCriteria.sexes
    • SingleCriteria
      • SingleCriteria.end
      • SingleCriteria.model_computed_fields
      • SingleCriteria.model_config
      • SingleCriteria.model_fields
      • SingleCriteria.name
      • SingleCriteria.start
    • TripleCriteria
      • TripleCriteria.end
      • TripleCriteria.model_computed_fields
      • TripleCriteria.model_config
      • TripleCriteria.model_fields
      • TripleCriteria.name
      • TripleCriteria.start
    • create_denovo_gene_set_spec()
    • parse_denovo_gene_sets_config()
    • parse_denovo_gene_sets_study_config()
    • parse_dgsc_query()
    • parse_recurrency_criteria()
  • dae.gene_sets.denovo_gene_sets_db module
    • DenovoGeneSetsDb
      • DenovoGeneSetsDb.build_cache()
      • DenovoGeneSetsDb.collections_descriptions
      • DenovoGeneSetsDb.denovo_gene_sets_types
      • DenovoGeneSetsDb.get_all_gene_sets()
      • DenovoGeneSetsDb.get_collection_types_legend()
      • DenovoGeneSetsDb.get_gene_set()
      • DenovoGeneSetsDb.get_gene_set_ids()
      • DenovoGeneSetsDb.get_genotype_data_ids()
      • DenovoGeneSetsDb.has_gene_sets()
      • DenovoGeneSetsDb.reload()
      • DenovoGeneSetsDb.update_cache()
  • dae.gene_sets.gene_sets_db module
    • BaseGeneSetCollection
      • BaseGeneSetCollection.get_all_gene_sets()
      • BaseGeneSetCollection.get_gene_set()
    • BaseResourceSchema
      • BaseResourceSchema.meta
      • BaseResourceSchema.model_computed_fields
      • BaseResourceSchema.model_config
      • BaseResourceSchema.model_fields
      • BaseResourceSchema.type
    • CategoricalHistogramSchema
      • CategoricalHistogramSchema.displayed_values_count
      • CategoricalHistogramSchema.displayed_values_percent
      • CategoricalHistogramSchema.enforce_type
      • CategoricalHistogramSchema.label_rotation
      • CategoricalHistogramSchema.model_computed_fields
      • CategoricalHistogramSchema.model_config
      • CategoricalHistogramSchema.model_fields
      • CategoricalHistogramSchema.natural_order
      • CategoricalHistogramSchema.plot_function
      • CategoricalHistogramSchema.type
      • CategoricalHistogramSchema.value_order
      • CategoricalHistogramSchema.y_log_scale
    • GeneSet
      • GeneSet.count
      • GeneSet.desc
      • GeneSet.name
      • GeneSet.syms
    • GeneSetCollection
      • GeneSetCollection.add_statistics_build_tasks()
      • GeneSetCollection.calc_info_hash()
      • GeneSetCollection.calc_statistics_hash()
      • GeneSetCollection.files
      • GeneSetCollection.get_all_gene_sets()
      • GeneSetCollection.get_gene_set()
      • GeneSetCollection.get_gene_sets_per_gene_hist_filename()
      • GeneSetCollection.get_genes_per_gene_set_hist_filename()
      • GeneSetCollection.load_gene_sets()
    • GeneSetResourceSchema
      • GeneSetResourceSchema.directory
      • GeneSetResourceSchema.filename
      • GeneSetResourceSchema.histograms
      • GeneSetResourceSchema.model_computed_fields
      • GeneSetResourceSchema.model_config
      • GeneSetResourceSchema.model_fields
      • GeneSetResourceSchema.resource_format
      • GeneSetResourceSchema.resource_id
      • GeneSetResourceSchema.web_format_str
      • GeneSetResourceSchema.web_label
    • GeneSetsDb
      • GeneSetsDb.collections_descriptions
      • GeneSetsDb.get_all_gene_sets()
      • GeneSetsDb.get_gene_set()
      • GeneSetsDb.get_gene_set_collection_ids()
      • GeneSetsDb.get_gene_set_ids()
      • GeneSetsDb.has_gene_set_collection()
    • MetaSchema
      • MetaSchema.description
      • MetaSchema.labels
      • MetaSchema.model_computed_fields
      • MetaSchema.model_config
      • MetaSchema.model_fields
    • NumericHistogramSchema
      • NumericHistogramSchema.displayed_values_count
      • NumericHistogramSchema.model_computed_fields
      • NumericHistogramSchema.model_config
      • NumericHistogramSchema.model_fields
      • NumericHistogramSchema.number_of_bins
      • NumericHistogramSchema.plot_function
      • NumericHistogramSchema.type
      • NumericHistogramSchema.value_order
      • NumericHistogramSchema.view_range
      • NumericHistogramSchema.x_log_scale
      • NumericHistogramSchema.x_min_log
      • NumericHistogramSchema.y_log_scale
    • ViewRangeSchema
      • ViewRangeSchema.max
      • ViewRangeSchema.min
      • ViewRangeSchema.model_computed_fields
      • ViewRangeSchema.model_config
      • ViewRangeSchema.model_fields
    • build_gene_set_collection_from_file()
    • build_gene_set_collection_from_resource()
    • build_gene_set_collection_from_resource_id()
  • dae.gene_sets.gene_term module
    • GeneInfo
      • GeneInfo.description
      • GeneInfo.gene_id
      • GeneInfo.gene_sym
      • GeneInfo.synonyms
    • GeneTerms
      • GeneTerms.filter_genes()
      • GeneTerms.rename_genes()
      • GeneTerms.save()
    • NCBIGeneInfo
      • NCBIGeneInfo.genes
      • NCBIGeneInfo.ns_tokens
    • dd()
    • get_clean_gene_id()
    • load_gene_terms()
    • load_ncbi_gene_info()
    • read_ewa_set_file()
    • read_gmt_file()
    • read_mapping_file()
    • rename_gene_terms()
  • Module contents
• dae.genomic_resources package
  • Subpackages
    • dae.genomic_resources.gene_models package
      • Submodules
      • dae.genomic_resources.gene_models.gene_models module
      • dae.genomic_resources.gene_models.parsing module
      • dae.genomic_resources.gene_models.serialization module
      • Module contents
    • dae.genomic_resources.genomic_position_table package
      • Submodules
      • dae.genomic_resources.genomic_position_table.line module
      • dae.genomic_resources.genomic_position_table.table module
      • dae.genomic_resources.genomic_position_table.table_bigwig module
      • dae.genomic_resources.genomic_position_table.table_inmemory module
      • dae.genomic_resources.genomic_position_table.table_tabix module
      • dae.genomic_resources.genomic_position_table.table_vcf module
      • dae.genomic_resources.genomic_position_table.utils module
      • Module contents
    • dae.genomic_resources.implementations package
      • Submodules
      • dae.genomic_resources.implementations.annotation_pipeline_impl module
      • dae.genomic_resources.implementations.gene_models_impl module
      • dae.genomic_resources.implementations.genomic_scores_impl module
      • dae.genomic_resources.implementations.liftover_chain_impl module
      • dae.genomic_resources.implementations.reference_genome_impl module
      • Module contents
    • dae.genomic_resources.statistics package
      • Submodules
      • dae.genomic_resources.statistics.base_statistic module
      • dae.genomic_resources.statistics.min_max module
      • Module contents
  • Submodules
  • dae.genomic_resources.aggregators module
    • Aggregator
      • Aggregator.add()
      • Aggregator.aggregate()
      • Aggregator.clear()
      • Aggregator.get_final()
      • Aggregator.get_total_count()
      • Aggregator.get_used_count()
    • ConcatAggregator
      • ConcatAggregator.get_final()
    • CountAggregator
      • CountAggregator.get_final()
    • DictAggregator
      • DictAggregator.get_final()
    • JoinAggregator
      • JoinAggregator.get_final()
    • ListAggregator
      • ListAggregator.get_final()
    • MaxAggregator
      • MaxAggregator.get_final()
    • MeanAggregator
      • MeanAggregator.get_final()
    • MedianAggregator
      • MedianAggregator.get_final()
    • MinAggregator
      • MinAggregator.get_final()
    • ModeAggregator
      • ModeAggregator.get_final()
    • build_aggregator()
    • create_aggregator()
    • create_aggregator_definition()
    • get_aggregator_class()
    • validate_aggregator()
  • dae.genomic_resources.cached_repository module
    • CacheResource
    • CachingProtocol
      • CachingProtocol.file_exists()
      • CachingProtocol.get_all_resources()
      • CachingProtocol.get_resource_file_url()
      • CachingProtocol.get_resource_url()
      • CachingProtocol.get_url()
      • CachingProtocol.invalidate()
      • CachingProtocol.load_manifest()
      • CachingProtocol.open_bigwig_file()
      • CachingProtocol.open_raw_file()
      • CachingProtocol.open_tabix_file()
      • CachingProtocol.open_vcf_file()
      • CachingProtocol.refresh_cached_resource()
      • CachingProtocol.refresh_cached_resource_file()
    • GenomicResourceCachedRepo
      • GenomicResourceCachedRepo.find_resource()
      • GenomicResourceCachedRepo.get_all_resources()
      • GenomicResourceCachedRepo.get_resource()
      • GenomicResourceCachedRepo.get_resource_cached_files()
      • GenomicResourceCachedRepo.invalidate()
    • cache_resources()
  • dae.genomic_resources.cli module
    • cli_browse()
    • cli_manage()
    • collect_dvc_entries()
  • dae.genomic_resources.draw_score_histograms module
    • main()
    • parse_cli_arguments()
  • dae.genomic_resources.fsspec_protocol module
    • FsspecReadOnlyProtocol
      • FsspecReadOnlyProtocol.file_exists()
      • FsspecReadOnlyProtocol.get_all_resources()
      • FsspecReadOnlyProtocol.get_url()
      • FsspecReadOnlyProtocol.invalidate()
      • FsspecReadOnlyProtocol.load_manifest()
      • FsspecReadOnlyProtocol.open_bigwig_file()
      • FsspecReadOnlyProtocol.open_raw_file()
      • FsspecReadOnlyProtocol.open_tabix_file()
      • FsspecReadOnlyProtocol.open_vcf_file()
    • FsspecReadWriteProtocol
      • FsspecReadWriteProtocol.build_content_file()
      • FsspecReadWriteProtocol.build_index_info()
      • FsspecReadWriteProtocol.collect_all_resources()
      • FsspecReadWriteProtocol.collect_resource_entries()
      • FsspecReadWriteProtocol.copy_resource_file()
      • FsspecReadWriteProtocol.delete_resource_file()
      • FsspecReadWriteProtocol.get_all_resources()
      • FsspecReadWriteProtocol.get_resource_file_size()
      • FsspecReadWriteProtocol.get_resource_file_timestamp()
      • FsspecReadWriteProtocol.load_resource_file_state()
      • FsspecReadWriteProtocol.obtain_resource_file_lock()
      • FsspecReadWriteProtocol.save_resource_file_state()
      • FsspecReadWriteProtocol.update_resource_file()
    • build_fsspec_protocol()
    • build_inmemory_protocol()
    • build_local_resource()
  • dae.genomic_resources.genomic_context module
    • DefaultRepositoryContextProvider
      • DefaultRepositoryContextProvider.add_argparser_arguments()
      • DefaultRepositoryContextProvider.init()
    • GenomicContext
      • GenomicContext.get_context_keys()
      • GenomicContext.get_context_object()
      • GenomicContext.get_gene_models()
      • GenomicContext.get_genomic_resources_repository()
      • GenomicContext.get_reference_genome()
      • GenomicContext.get_source()
    • GenomicContextProvider
      • GenomicContextProvider.add_argparser_arguments()
      • GenomicContextProvider.get_context_provider_priority()
      • GenomicContextProvider.get_context_provider_type()
      • GenomicContextProvider.init()
    • PriorityGenomicContext
      • PriorityGenomicContext.get_context_keys()
      • PriorityGenomicContext.get_context_object()
      • PriorityGenomicContext.get_source()
    • SimpleGenomicContext
      • SimpleGenomicContext.get_all_context_objects()
      • SimpleGenomicContext.get_context_keys()
      • SimpleGenomicContext.get_context_object()
      • SimpleGenomicContext.get_source()
    • context_providers_add_argparser_arguments()
    • context_providers_init()
    • get_genomic_context()
    • register_context()
    • register_context_provider()
  • dae.genomic_resources.genomic_context_cli module
    • CLIGenomicContextProvider
      • CLIGenomicContextProvider.add_argparser_arguments()
      • CLIGenomicContextProvider.init()
  • dae.genomic_resources.genomic_scores module
    • AlleleScore
      • AlleleScore.Mode
      • AlleleScore.alleles_mode()
      • AlleleScore.fetch_region()
      • AlleleScore.fetch_scores()
      • AlleleScore.fetch_scores_agg()
      • AlleleScore.get_schema()
      • AlleleScore.open()
      • AlleleScore.substitutions_mode()
    • AlleleScoreAggr
      • AlleleScoreAggr.allele_aggregator
      • AlleleScoreAggr.position_aggregator
      • AlleleScoreAggr.score
    • AlleleScoreQuery
      • AlleleScoreQuery.allele_aggregator
      • AlleleScoreQuery.position_aggregator
      • AlleleScoreQuery.score
    • CNV
      • CNV.attributes
      • CNV.chrom
      • CNV.pos_begin
      • CNV.pos_end
      • CNV.size
    • CnvCollection
      • CnvCollection.fetch_cnvs()
      • CnvCollection.get_schema()
      • CnvCollection.open()
    • GenomicScore
      • GenomicScore.close()
      • GenomicScore.get_all_chromosomes()
      • GenomicScore.get_all_scores()
      • GenomicScore.get_config()
      • GenomicScore.get_default_annotation_attribute()
      • GenomicScore.get_default_annotation_attributes()
      • GenomicScore.get_histogram_filename()
      • GenomicScore.get_histogram_image_filename()
      • GenomicScore.get_histogram_image_url()
      • GenomicScore.get_number_range()
      • GenomicScore.get_schema()
      • GenomicScore.get_score_definition()
      • GenomicScore.get_score_histogram()
      • GenomicScore.is_open()
      • GenomicScore.open()
    • PositionScore
      • PositionScore.fetch_region()
      • PositionScore.fetch_scores()
      • PositionScore.fetch_scores_agg()
      • PositionScore.get_region_scores()
      • PositionScore.get_schema()
      • PositionScore.open()
    • PositionScoreAggr
      • PositionScoreAggr.position_aggregator
      • PositionScoreAggr.score
    • PositionScoreQuery
      • PositionScoreQuery.position_aggregator
      • PositionScoreQuery.score
    • ScoreDef
      • ScoreDef.allele_aggregator
      • ScoreDef.desc
      • ScoreDef.hist_conf
      • ScoreDef.large_values_desc
      • ScoreDef.pos_aggregator
      • ScoreDef.score_id
      • ScoreDef.small_values_desc
      • ScoreDef.value_type
    • ScoreLine
      • ScoreLine.alt
      • ScoreLine.chrom
      • ScoreLine.get_available_scores()
      • ScoreLine.get_score()
      • ScoreLine.pos_begin
      • ScoreLine.pos_end
      • ScoreLine.ref
    • build_score_from_resource()
    • build_score_from_resource_id()
  • dae.genomic_resources.group_repository module
    • GenomicResourceGroupRepo
      • GenomicResourceGroupRepo.find_resource()
      • GenomicResourceGroupRepo.get_all_resources()
      • GenomicResourceGroupRepo.get_resource()
      • GenomicResourceGroupRepo.invalidate()
  • dae.genomic_resources.histogram module
    • CategoricalHistogram
      • CategoricalHistogram.UNIQUE_VALUES_LIMIT
      • CategoricalHistogram.add_value()
      • CategoricalHistogram.deserialize()
      • CategoricalHistogram.display_values
      • CategoricalHistogram.from_dict()
      • CategoricalHistogram.merge()
      • CategoricalHistogram.plot()
      • CategoricalHistogram.raw_values
      • CategoricalHistogram.serialize()
      • CategoricalHistogram.to_dict()
      • CategoricalHistogram.type
      • CategoricalHistogram.values_domain()
    • CategoricalHistogramConfig
      • CategoricalHistogramConfig.allow_only_whole_values_y
      • CategoricalHistogramConfig.default_config()
      • CategoricalHistogramConfig.displayed_values_count
      • CategoricalHistogramConfig.displayed_values_percent
      • CategoricalHistogramConfig.enforce_type
      • CategoricalHistogramConfig.from_dict()
      • CategoricalHistogramConfig.label_rotation
      • CategoricalHistogramConfig.natural_order
      • CategoricalHistogramConfig.plot_function
      • CategoricalHistogramConfig.to_dict()
      • CategoricalHistogramConfig.value_order
      • CategoricalHistogramConfig.y_log_scale
    • HistogramError
    • HistogramStatisticMixin
      • HistogramStatisticMixin.get_histogram_file()
      • HistogramStatisticMixin.get_histogram_image_file()
    • NullHistogram
      • NullHistogram.add_value()
      • NullHistogram.deserialize()
      • NullHistogram.from_dict()
      • NullHistogram.merge()
      • NullHistogram.plot()
      • NullHistogram.serialize()
      • NullHistogram.to_dict()
      • NullHistogram.type
      • NullHistogram.values_domain()
    • NullHistogramConfig
      • NullHistogramConfig.default_config()
      • NullHistogramConfig.from_dict()
      • NullHistogramConfig.reason
      • NullHistogramConfig.to_dict()
    • NumberHistogram
      • NumberHistogram.add_value()
      • NumberHistogram.choose_bin_lin()
      • NumberHistogram.choose_bin_log()
      • NumberHistogram.deserialize()
      • NumberHistogram.from_dict()
      • NumberHistogram.merge()
      • NumberHistogram.plot()
      • NumberHistogram.serialize()
      • NumberHistogram.to_dict()
      • NumberHistogram.type
      • NumberHistogram.values_domain()
      • NumberHistogram.view_max()
      • NumberHistogram.view_min()
    • NumberHistogramConfig
      • NumberHistogramConfig.default_config()
      • NumberHistogramConfig.from_dict()
      • NumberHistogramConfig.has_view_range()
      • NumberHistogramConfig.number_of_bins
      • NumberHistogramConfig.plot_function
      • NumberHistogramConfig.to_dict()
      • NumberHistogramConfig.view_range
      • NumberHistogramConfig.x_log_scale
      • NumberHistogramConfig.x_min_log
      • NumberHistogramConfig.y_log_scale
    • build_default_histogram_conf()
    • build_empty_histogram()
    • build_histogram_config()
    • load_histogram()
    • plot_histogram()
    • save_histogram()
  • dae.genomic_resources.liftover_chain module
    • LiftoverChain
      • LiftoverChain.close()
      • LiftoverChain.convert_coordinate()
      • LiftoverChain.files
      • LiftoverChain.get_schema()
      • LiftoverChain.is_open()
      • LiftoverChain.map_chromosome()
      • LiftoverChain.open()
    • build_liftover_chain_from_resource()
    • build_liftover_chain_from_resource_id()
  • dae.genomic_resources.reference_genome module
    • ReferenceGenome
      • ReferenceGenome.chrom_prefix
      • ReferenceGenome.chromosomes
      • ReferenceGenome.close()
      • ReferenceGenome.fetch()
      • ReferenceGenome.get_all_chrom_lengths()
      • ReferenceGenome.get_chrom_length()
      • ReferenceGenome.get_schema()
      • ReferenceGenome.get_sequence()
      • ReferenceGenome.is_open()
      • ReferenceGenome.is_pseudoautosomal()
      • ReferenceGenome.open()
      • ReferenceGenome.resource_id
      • ReferenceGenome.split_into_regions()
    • build_reference_genome_from_file()
    • build_reference_genome_from_resource()
    • build_reference_genome_from_resource_id()
  • dae.genomic_resources.repository module
    • GenomicResource
      • GenomicResource.file_exists()
      • GenomicResource.get_config()
      • GenomicResource.get_description()
      • GenomicResource.get_file_content()
      • GenomicResource.get_file_url()
      • GenomicResource.get_full_id()
      • GenomicResource.get_genomic_resource_id_version()
      • GenomicResource.get_id()
      • GenomicResource.get_labels()
      • GenomicResource.get_manifest()
      • GenomicResource.get_repo_url()
      • GenomicResource.get_summary()
      • GenomicResource.get_type()
      • GenomicResource.get_url()
      • GenomicResource.get_version_str()
      • GenomicResource.invalidate()
      • GenomicResource.open_bigwig_file()
      • GenomicResource.open_raw_file()
      • GenomicResource.open_tabix_file()
      • GenomicResource.open_vcf_file()
    • GenomicResourceProtocolRepo
      • GenomicResourceProtocolRepo.find_resource()
      • GenomicResourceProtocolRepo.get_all_resources()
      • GenomicResourceProtocolRepo.get_resource()
      • GenomicResourceProtocolRepo.invalidate()
    • GenomicResourceRepo
      • GenomicResourceRepo.definition
      • GenomicResourceRepo.find_resource()
      • GenomicResourceRepo.get_all_resources()
      • GenomicResourceRepo.get_resource()
      • GenomicResourceRepo.invalidate()
      • GenomicResourceRepo.repo_id
    • Manifest
      • Manifest.add()
      • Manifest.from_file_content()
      • Manifest.from_manifest_entries()
      • Manifest.get_files()
      • Manifest.names()
      • Manifest.to_manifest_entries()
      • Manifest.update()
    • ManifestEntry
      • ManifestEntry.md5
      • ManifestEntry.name
      • ManifestEntry.size
    • ManifestUpdate
      • ManifestUpdate.entries_to_delete
      • ManifestUpdate.entries_to_update
      • ManifestUpdate.manifest
    • Mode
      • Mode.READONLY
      • Mode.READWRITE
    • ReadOnlyRepositoryProtocol
      • ReadOnlyRepositoryProtocol.CHUNK_SIZE
      • ReadOnlyRepositoryProtocol.build_genomic_resource()
      • ReadOnlyRepositoryProtocol.compute_md5_sum()
      • ReadOnlyRepositoryProtocol.file_exists()
      • ReadOnlyRepositoryProtocol.find_resource()
      • ReadOnlyRepositoryProtocol.get_all_resources()
      • ReadOnlyRepositoryProtocol.get_file_content()
      • ReadOnlyRepositoryProtocol.get_id()
      • ReadOnlyRepositoryProtocol.get_manifest()
      • ReadOnlyRepositoryProtocol.get_resource()
      • ReadOnlyRepositoryProtocol.get_resource_file_url()
      • ReadOnlyRepositoryProtocol.get_resource_url()
      • ReadOnlyRepositoryProtocol.get_url()
      • ReadOnlyRepositoryProtocol.invalidate()
      • ReadOnlyRepositoryProtocol.load_manifest()
      • ReadOnlyRepositoryProtocol.load_yaml()
      • ReadOnlyRepositoryProtocol.mode()
      • ReadOnlyRepositoryProtocol.open_bigwig_file()
      • ReadOnlyRepositoryProtocol.open_raw_file()
      • ReadOnlyRepositoryProtocol.open_tabix_file()
      • ReadOnlyRepositoryProtocol.open_vcf_file()
    • ReadWriteRepositoryProtocol
      • ReadWriteRepositoryProtocol.build_content_file()
      • ReadWriteRepositoryProtocol.build_manifest()
      • ReadWriteRepositoryProtocol.build_resource_file_state()
      • ReadWriteRepositoryProtocol.check_update_manifest()
      • ReadWriteRepositoryProtocol.collect_all_resources()
      • ReadWriteRepositoryProtocol.collect_resource_entries()
      • ReadWriteRepositoryProtocol.copy_resource()
      • ReadWriteRepositoryProtocol.copy_resource_file()
      • ReadWriteRepositoryProtocol.delete_resource_file()
      • ReadWriteRepositoryProtocol.get_manifest()
      • ReadWriteRepositoryProtocol.get_or_create_resource()
      • ReadWriteRepositoryProtocol.get_resource_file_size()
      • ReadWriteRepositoryProtocol.get_resource_file_timestamp()
      • ReadWriteRepositoryProtocol.load_resource_file_state()
      • ReadWriteRepositoryProtocol.mode()
      • ReadWriteRepositoryProtocol.save_index()
      • ReadWriteRepositoryProtocol.save_manifest()
      • ReadWriteRepositoryProtocol.save_resource_file_state()
      • ReadWriteRepositoryProtocol.update_manifest()
      • ReadWriteRepositoryProtocol.update_resource()
      • ReadWriteRepositoryProtocol.update_resource_file()
    • ResourceFileState
      • ResourceFileState.filename
      • ResourceFileState.md5
      • ResourceFileState.size
      • ResourceFileState.timestamp
    • 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
    • build_genomic_resource_group_repository()
    • build_genomic_resource_repository()
    • build_resource_implementation()
    • get_default_grr_definition()
    • get_default_grr_definition_path()
    • load_definition_file()
  • dae.genomic_resources.resource_implementation module
    • GenomicResourceImplementation
      • GenomicResourceImplementation.add_statistics_build_tasks()
      • GenomicResourceImplementation.calc_info_hash()
      • GenomicResourceImplementation.calc_statistics_hash()
      • GenomicResourceImplementation.files
      • GenomicResourceImplementation.get_config()
      • GenomicResourceImplementation.get_info()
      • GenomicResourceImplementation.get_statistics()
      • GenomicResourceImplementation.get_statistics_info()
      • GenomicResourceImplementation.reload_statistics()
      • GenomicResourceImplementation.resource_id
    • InfoImplementationMixin
      • InfoImplementationMixin.FileEntry
      • InfoImplementationMixin.get_info()
      • InfoImplementationMixin.get_statistics_info()
      • InfoImplementationMixin.get_statistics_template_data()
      • InfoImplementationMixin.get_template()
      • InfoImplementationMixin.get_template_data()
      • InfoImplementationMixin.resource
    • ResourceConfigValidationMixin
      • ResourceConfigValidationMixin.get_schema()
      • ResourceConfigValidationMixin.validate_and_normalize_schema()
    • ResourceStatistics
      • ResourceStatistics.get_statistics_folder()
    • get_base_resource_schema()
  • 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
    • maximally_extend_variant()
    • normalize_variant()
  • Module contents
    • GenomicResource
      • GenomicResource.file_exists()
      • GenomicResource.get_config()
      • GenomicResource.get_description()
      • GenomicResource.get_file_content()
      • GenomicResource.get_file_url()
      • GenomicResource.get_full_id()
      • GenomicResource.get_genomic_resource_id_version()
      • GenomicResource.get_id()
      • GenomicResource.get_labels()
      • GenomicResource.get_manifest()
      • GenomicResource.get_repo_url()
      • GenomicResource.get_summary()
      • GenomicResource.get_type()
      • GenomicResource.get_url()
      • GenomicResource.get_version_str()
      • GenomicResource.invalidate()
      • GenomicResource.open_bigwig_file()
      • GenomicResource.open_raw_file()
      • GenomicResource.open_tabix_file()
      • GenomicResource.open_vcf_file()
    • build_genomic_resource_repository()
    • get_resource_implementation_builder()
• dae.genomic_scores package
  • Submodules
  • dae.genomic_scores.scores module
    • GenomicScoresRegistry
      • GenomicScoresRegistry.build_genomic_scores_registry()
      • GenomicScoresRegistry.get_scores()
    • ScoreDesc
      • ScoreDesc.description
      • ScoreDesc.from_json()
      • ScoreDesc.help
      • ScoreDesc.hist
      • ScoreDesc.large_values_desc
      • ScoreDesc.name
      • ScoreDesc.resource_id
      • ScoreDesc.small_values_desc
      • ScoreDesc.source
      • ScoreDesc.to_json()
  • Module contents
• dae.genotype_storage package
  • Submodules
  • dae.genotype_storage.genotype_storage module
    • GenotypeStorage
      • GenotypeStorage.build_backend()
      • GenotypeStorage.get_storage_types()
      • GenotypeStorage.is_read_only()
      • GenotypeStorage.read_only
      • GenotypeStorage.shutdown()
      • GenotypeStorage.start()
      • GenotypeStorage.validate_and_normalize_config()
  • 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
    • get_genotype_storage_factory()
    • get_genotype_storage_types()
    • register_genotype_storage_factory()
• dae.gpf_instance package
  • Subpackages
    • dae.gpf_instance.adjustments package
      • Submodules
      • dae.gpf_instance.adjustments.adjust_command module
      • dae.gpf_instance.adjustments.adjust_duckdb_storage module
      • dae.gpf_instance.adjustments.adjust_impala_storage module
      • dae.gpf_instance.adjustments.gpf_instance_adjustments module
      • Module contents
  • Submodules
  • dae.gpf_instance.gpf_instance module
    • GPFInstance
      • GPFInstance.build()
      • GPFInstance.denovo_gene_sets_db
      • GPFInstance.gene_models
      • GPFInstance.gene_scores_db
      • GPFInstance.gene_sets_db
      • GPFInstance.genomic_scores
      • GPFInstance.genotype_storages
      • GPFInstance.get_all_common_report_configs()
      • GPFInstance.get_all_gene_score_descs()
      • GPFInstance.get_all_gene_scores()
      • GPFInstance.get_all_genotype_data()
      • GPFInstance.get_all_phenotype_data()
      • GPFInstance.get_annotation_pipeline()
      • GPFInstance.get_annotation_pipeline_config()
      • GPFInstance.get_cache_path()
      • GPFInstance.get_common_report()
      • GPFInstance.get_dataset()
      • GPFInstance.get_enrichment_builder()
      • GPFInstance.get_gene_score()
      • GPFInstance.get_gene_score_desc()
      • GPFInstance.get_genotype_data()
      • GPFInstance.get_genotype_data_config()
      • GPFInstance.get_genotype_data_ids()
      • GPFInstance.get_gp_configuration()
      • GPFInstance.get_gp_statistic()
      • GPFInstance.get_pheno_cache_path()
      • GPFInstance.get_pheno_tool_adapter()
      • GPFInstance.get_phenotype_data()
      • GPFInstance.get_phenotype_data_config()
      • GPFInstance.get_phenotype_data_ids()
      • GPFInstance.get_transcript_models()
      • GPFInstance.grr
      • GPFInstance.has_gene_score()
      • GPFInstance.has_phenotype_data()
      • GPFInstance.list_gp_gene_symbols()
      • GPFInstance.load()
      • GPFInstance.make_enrichment_builder()
      • GPFInstance.make_pheno_tool_adapter()
      • GPFInstance.phenotype_storages
      • GPFInstance.query_gp_statistics()
      • GPFInstance.reference_genome
      • GPFInstance.register_enrichment_builder()
      • GPFInstance.register_pheno_tool_adapter()
      • GPFInstance.reload()
  • Module contents
    • GPFInstance
      • GPFInstance.build()
      • GPFInstance.denovo_gene_sets_db
      • GPFInstance.gene_models
      • GPFInstance.gene_scores_db
      • GPFInstance.gene_sets_db
      • GPFInstance.genomic_scores
      • GPFInstance.genotype_storages
      • GPFInstance.get_all_common_report_configs()
      • GPFInstance.get_all_gene_score_descs()
      • GPFInstance.get_all_gene_scores()
      • GPFInstance.get_all_genotype_data()
      • GPFInstance.get_all_phenotype_data()
      • GPFInstance.get_annotation_pipeline()
      • GPFInstance.get_annotation_pipeline_config()
      • GPFInstance.get_cache_path()
      • GPFInstance.get_common_report()
      • GPFInstance.get_dataset()
      • GPFInstance.get_enrichment_builder()
      • GPFInstance.get_gene_score()
      • GPFInstance.get_gene_score_desc()
      • GPFInstance.get_genotype_data()
      • GPFInstance.get_genotype_data_config()
      • GPFInstance.get_genotype_data_ids()
      • GPFInstance.get_gp_configuration()
      • GPFInstance.get_gp_statistic()
      • GPFInstance.get_pheno_cache_path()
      • GPFInstance.get_pheno_tool_adapter()
      • GPFInstance.get_phenotype_data()
      • GPFInstance.get_phenotype_data_config()
      • GPFInstance.get_phenotype_data_ids()
      • GPFInstance.get_transcript_models()
      • GPFInstance.grr
      • GPFInstance.has_gene_score()
      • GPFInstance.has_phenotype_data()
      • GPFInstance.list_gp_gene_symbols()
      • GPFInstance.load()
      • GPFInstance.make_enrichment_builder()
      • GPFInstance.make_pheno_tool_adapter()
      • GPFInstance.phenotype_storages
      • GPFInstance.query_gp_statistics()
      • GPFInstance.reference_genome
      • GPFInstance.register_enrichment_builder()
      • GPFInstance.register_pheno_tool_adapter()
      • GPFInstance.reload()
• dae.gpf_instance_plugin package
  • Submodules
  • dae.gpf_instance_plugin.gpf_instance_context_plugin module
    • GPFInstanceContextProvider
      • GPFInstanceContextProvider.add_argparser_arguments()
      • GPFInstanceContextProvider.init()
    • GPFInstanceGenomicContext
      • GPFInstanceGenomicContext.get_context_keys()
      • GPFInstanceGenomicContext.get_context_object()
      • GPFInstanceGenomicContext.get_source()
  • Module contents
• dae.import_tools package
  • Submodules
  • dae.import_tools.cli module
    • main()
    • run_with_project()
  • dae.import_tools.import_config module
  • dae.import_tools.import_tools module
    • Bucket
      • Bucket.index
      • Bucket.region_bin
      • Bucket.regions
      • Bucket.type
    • ImportConfigNormalizer
      • ImportConfigNormalizer.normalize()
    • ImportProject
      • ImportProject.build_annotation_pipeline()
      • ImportProject.build_from_config()
      • ImportProject.build_from_file()
      • ImportProject.del_loader_prefix()
      • ImportProject.get_annotation_pipeline_config()
      • ImportProject.get_genotype_storage()
      • ImportProject.get_gpf_instance()
      • ImportProject.get_import_storage()
      • ImportProject.get_import_variants_buckets()
      • ImportProject.get_input_filenames()
      • ImportProject.get_parquet_dataset_dir()
      • ImportProject.get_partition_descriptor()
      • ImportProject.get_pedigree()
      • ImportProject.get_pedigree_filename()
      • ImportProject.get_pedigree_loader()
      • ImportProject.get_pedigree_params()
      • ImportProject.get_processing_annotation_batch_size()
      • ImportProject.get_processing_parquet_dataset_dir()
      • ImportProject.get_row_group_size()
      • ImportProject.get_variant_loader()
      • ImportProject.get_variant_loader_chrom_lens()
      • ImportProject.get_variant_loader_chromosomes()
      • ImportProject.get_variant_loader_types()
      • ImportProject.get_variant_params()
      • ImportProject.get_variants_blob_serializer()
      • ImportProject.has_denovo_variants()
      • ImportProject.has_genotype_storage()
      • ImportProject.has_variants()
      • ImportProject.include_reference
      • ImportProject.input_dir
      • ImportProject.study_id
      • ImportProject.work_dir
    • ImportStorage
      • ImportStorage.generate_import_task_graph()
    • construct_import_annotation_pipeline()
    • construct_import_annotation_pipeline_config()
    • get_import_storage_factory()
    • get_import_storage_types()
    • register_import_storage_factory()
    • save_study_config()
  • Module contents
• dae.inmemory_storage package
  • Submodules
  • dae.inmemory_storage.annotation_serialization module
    • build_annotation_filename()
    • variants_loader_annotate_and_save()
    • variants_loader_load_annotation()
  • dae.inmemory_storage.inmemory_genotype_storage module
    • InmemoryGenotypeStorage
      • InmemoryGenotypeStorage.VALIDATION_SCHEMA
      • InmemoryGenotypeStorage.build_backend()
      • InmemoryGenotypeStorage.get_data_dir()
      • InmemoryGenotypeStorage.get_storage_types()
      • InmemoryGenotypeStorage.shutdown()
      • InmemoryGenotypeStorage.start()
      • InmemoryGenotypeStorage.validate_and_normalize_config()
  • dae.inmemory_storage.inmemory_import_storage module
    • InmemoryImportStorage
      • InmemoryImportStorage.generate_import_task_graph()
  • 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
      • RawMemoryVariants.full_variants
      • RawMemoryVariants.full_variants_iterator()
      • RawMemoryVariants.has_affected_status_queries()
    • RawVariantsQueryRunner
      • RawVariantsQueryRunner.run()
  • Module contents
• dae.parquet package
  • Subpackages
    • dae.parquet.schema2 package
      • Submodules
      • dae.parquet.schema2.parquet_io module
      • dae.parquet.schema2.serializers module
      • Module contents
  • Submodules
  • dae.parquet.helpers module
    • merge_parquets()
    • url_to_pyarrow_fs()
  • dae.parquet.parquet_writer module
    • add_missing_parquet_fields()
    • append_meta_to_parquet()
    • collect_pedigree_parquet_schema()
    • fill_family_bins()
    • merge_variants_parquets()
    • pedigree_parquet_schema()
    • save_ped_df_to_parquet()
    • serialize_summary_schema()
  • 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_storage package
  • Submodules
  • dae.parquet_storage.storage module
    • ParquetGenotypeStorage
      • ParquetGenotypeStorage.VALIDATION_SCHEMA
      • ParquetGenotypeStorage.build_backend()
      • ParquetGenotypeStorage.get_storage_types()
      • ParquetGenotypeStorage.import_dataset()
      • ParquetGenotypeStorage.shutdown()
      • ParquetGenotypeStorage.start()
      • ParquetGenotypeStorage.validate_and_normalize_config()
    • ParquetImportStorage
      • ParquetImportStorage.generate_import_task_graph()
    • ParquetLoaderVariants
      • ParquetLoaderVariants.build_family_variants_query_runner()
      • ParquetLoaderVariants.build_summary_variants_query_runner()
      • ParquetLoaderVariants.families
  • Module contents
• dae.pedigrees package
  • Submodules
  • dae.pedigrees.drawing module
    • OffsetLayoutDrawer
      • OffsetLayoutDrawer.GAP
      • OffsetLayoutDrawer.draw()
    • PDFLayoutDrawer
      • PDFLayoutDrawer.add_page()
  • dae.pedigrees.families_data module
    • FamiliesData
      • FamiliesData.broken_families
      • FamiliesData.combine()
      • FamiliesData.copy()
      • FamiliesData.families_of_persons()
      • FamiliesData.from_families()
      • FamiliesData.from_family_persons()
      • FamiliesData.from_pedigree_df()
      • FamiliesData.get()
      • FamiliesData.items()
      • FamiliesData.keys()
      • FamiliesData.ped_df
      • FamiliesData.pedigree_samples()
      • FamiliesData.persons_with_parents()
      • FamiliesData.persons_without_parents()
      • FamiliesData.real_persons
      • FamiliesData.redefine()
      • FamiliesData.values()
    • merge_families()
    • tag_families_data()
  • dae.pedigrees.family module
    • Family
      • Family.add_members()
      • Family.from_persons()
      • Family.from_records()
      • Family.full_members
      • Family.get_columns()
      • Family.get_member()
      • Family.get_members_with_roles()
      • Family.get_members_with_statuses()
      • Family.has_members()
      • Family.member_has_both_parents()
      • Family.member_has_dad()
      • Family.member_has_mom()
      • Family.member_has_parent()
      • Family.member_is_child()
      • Family.member_is_parent()
      • Family.members_ids
      • Family.members_in_order
      • Family.members_index()
      • Family.redefine()
      • Family.samples_index
      • Family.set_tag()
      • Family.tag_labels
      • Family.tags
      • Family.to_json()
      • Family.trios
      • Family.unset_tag()
    • FamilyTag
      • FamilyTag.AFFECTED_DAD
      • FamilyTag.AFFECTED_MOM
      • FamilyTag.AFFECTED_PRB
      • FamilyTag.AFFECTED_SIB
      • FamilyTag.CONTROL
      • FamilyTag.FEMALE_PRB
      • FamilyTag.MALE_PRB
      • FamilyTag.MISSING_DAD
      • FamilyTag.MISSING_MOM
      • FamilyTag.MULTIPLEX
      • FamilyTag.NUCLEAR
      • FamilyTag.QUAD
      • FamilyTag.SIMPLEX
      • FamilyTag.TRIO
      • FamilyTag.UNAFFECTED_DAD
      • FamilyTag.UNAFFECTED_MOM
      • FamilyTag.UNAFFECTED_PRB
      • FamilyTag.UNAFFECTED_SIB
      • FamilyTag.all_labels()
      • FamilyTag.all_tags()
      • FamilyTag.from_label()
      • FamilyTag.label
    • Person
      • Person.all_tag_labels()
      • Person.diff()
      • Person.family_bin
      • Person.generated
      • Person.get_attr()
      • Person.has_attr()
      • Person.has_tag()
      • Person.layout
      • Person.member_index
      • Person.missing
      • Person.not_sequenced
      • Person.redefine()
      • Person.role
      • Person.sample_index
      • Person.set_attr()
      • Person.set_tag()
      • Person.sex
      • Person.status
      • Person.tags
      • Person.to_json()
      • Person.unset_tag()
    • get_pedigree_column_names()
  • dae.pedigrees.family_role_builder module
    • FamilyRoleBuilder
      • FamilyRoleBuilder.build_roles()
    • Mating
      • Mating.build_id()
      • Mating.parents_id()
  • dae.pedigrees.family_tag_builder module
    • FamilyTagsBuilder
      • FamilyTagsBuilder.TAGS
      • FamilyTagsBuilder.add_tagger()
      • FamilyTagsBuilder.clear_tags()
      • FamilyTagsBuilder.tag_family()
      • FamilyTagsBuilder.tag_family_type()
    • 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
    • IndividualWithCoordinates
      • IndividualWithCoordinates.SIZE
      • IndividualWithCoordinates.x_center
      • IndividualWithCoordinates.y_center
    • Layout
      • Layout.BBox
      • Layout.apply_to_family()
      • Layout.from_family()
      • Layout.from_family_layout()
      • Layout.get_bbox()
      • Layout.id_to_position
      • Layout.individuals_by_rank
      • Layout.scale()
      • Layout.translate()
    • Line
      • Line.curve_p0()
      • Line.curve_p1()
      • Line.curve_p2()
      • Line.curve_p3()
      • Line.curve_y_at()
      • Line.curved
      • Line.inverse_curve_p1()
      • Line.inverse_curve_p2()
      • Line.inverse_curve_y_at()
    • Point
      • Point.x
      • Point.y
    • layout_parser()
  • dae.pedigrees.loader module
    • FamiliesLoader
      • FamiliesLoader.build_families_data_from_pedigree()
      • FamiliesLoader.flexible_pedigree_read()
      • FamiliesLoader.load()
      • FamiliesLoader.load_pedigree_file()
      • FamiliesLoader.load_simple_families_file()
      • FamiliesLoader.parse_cli_arguments()
      • FamiliesLoader.save_families()
      • FamiliesLoader.save_pedigree()
      • FamiliesLoader.to_tsv()
  • dae.pedigrees.pedigrees module
    • FamilyConnections
      • FamilyConnections.add_missing_members()
      • FamilyConnections.add_ranks()
      • FamilyConnections.connected_components()
      • FamilyConnections.create_sandwich_instance()
      • FamilyConnections.from_family()
      • FamilyConnections.get_graph()
      • FamilyConnections.get_individual()
      • FamilyConnections.get_individuals()
      • FamilyConnections.get_individuals_with_rank()
      • FamilyConnections.get_mating_units()
      • FamilyConnections.get_sibship_units()
      • FamilyConnections.is_connected()
      • FamilyConnections.is_valid_family()
      • FamilyConnections.max_rank()
      • FamilyConnections.members
    • Individual
      • Individual.NO_RANK
      • Individual.add_rank()
      • Individual.are_mates()
      • Individual.are_siblings()
      • Individual.children_set()
      • Individual.individual_set()
      • Individual.is_individual()
    • IndividualGroup
      • IndividualGroup.children_set()
      • IndividualGroup.generation_ranks()
      • IndividualGroup.individual_set()
      • IndividualGroup.is_individual()
    • Interval
      • Interval.intersection()
    • IntervalForVertex
    • MatingUnit
      • MatingUnit.children_set()
      • MatingUnit.individual_set()
      • MatingUnit.other_parent()
    • Realization
      • Realization.can_extend()
      • Realization.copy()
      • Realization.dangling()
      • Realization.dangling_set()
      • Realization.degree()
      • Realization.extend()
      • Realization.force_extend()
      • Realization.get_active_vertex_edges()
      • Realization.get_active_vertices()
      • Realization.get_interval()
      • Realization.get_maximal_set()
      • Realization.is_active_vertex()
      • Realization.is_in_interval_order()
      • Realization.is_maximal()
    • SandwichInstance
      • SandwichInstance.from_sets()
    • SandwichSolver
      • SandwichSolver.solve()
      • SandwichSolver.try_solve()
    • SibshipUnit
      • SibshipUnit.children_set()
      • SibshipUnit.individual_set()
    • copy_graph()
  • dae.pedigrees.testing module
    • build_families_data()
    • build_family()
  • Module contents
• dae.person_filters package
  • Submodules
  • dae.person_filters.person_filters module
    • CriteriaFilter
      • CriteriaFilter.apply()
    • FamilyFilter
      • FamilyFilter.apply()
      • FamilyFilter.apply_to_df()
    • PersonFilter
      • PersonFilter.apply()
      • PersonFilter.apply_to_df()
    • PersonFilterRange
      • PersonFilterRange.apply_to_df()
    • PersonFilterSet
      • PersonFilterSet.apply_to_df()
    • PhenoFilter
      • PhenoFilter.apply()
    • PhenoFilterRange
    • PhenoFilterSet
    • make_pedigree_filter()
    • make_pheno_filter()
    • make_pheno_filter_beta()
  • Module contents
    • FamilyFilter
      • FamilyFilter.apply()
      • FamilyFilter.apply_to_df()
    • PersonFilter
      • PersonFilter.apply()
      • PersonFilter.apply_to_df()
    • PersonFilterRange
      • PersonFilterRange.apply_to_df()
    • PersonFilterSet
      • PersonFilterSet.apply_to_df()
    • PhenoFilter
      • PhenoFilter.apply()
    • PhenoFilterRange
    • PhenoFilterSet
    • make_pedigree_filter()
    • make_pheno_filter()
    • make_pheno_filter_beta()
• dae.person_sets package
  • Submodules
  • dae.person_sets.person_sets module
    • AttributeQueriesUnsupportedException
    • ChildrenBySex
      • ChildrenBySex.female
      • ChildrenBySex.male
      • ChildrenBySex.unspecified
    • ChildrenStats
      • ChildrenStats.female
      • ChildrenStats.male
      • ChildrenStats.total
      • ChildrenStats.unspecified
    • PSCQuery
      • PSCQuery.psc_id
      • PSCQuery.selected_person_sets
    • PersonSet
      • PersonSet.from_json()
      • PersonSet.get_children()
      • PersonSet.get_children_by_sex()
      • PersonSet.get_children_count()
      • PersonSet.get_children_stats()
      • PersonSet.to_json()
    • PersonSetCollection
      • PersonSetCollection.collect_person_collection_attributes()
      • PersonSetCollection.combine()
      • PersonSetCollection.config_json()
      • PersonSetCollection.domain_json()
      • PersonSetCollection.from_families()
      • PersonSetCollection.get_person_color()
      • PersonSetCollection.get_person_set()
      • PersonSetCollection.get_person_set_of_person()
      • PersonSetCollection.get_query_person_set_ids()
      • PersonSetCollection.get_stats()
      • PersonSetCollection.is_pedigree_only()
      • PersonSetCollection.legend_json()
      • PersonSetCollection.merge_configs()
      • PersonSetCollection.query_fpids()
      • PersonSetCollection.query_person_ids()
      • PersonSetCollection.remove_empty_person_sets()
      • PersonSetCollection.transform_ps_query_to_attribute_queries()
    • PersonSetCollectionConfig
      • PersonSetCollectionConfig.default
      • PersonSetCollectionConfig.domain
      • PersonSetCollectionConfig.id
      • PersonSetCollectionConfig.model_computed_fields
      • PersonSetCollectionConfig.model_config
      • PersonSetCollectionConfig.model_fields
      • PersonSetCollectionConfig.name
      • PersonSetCollectionConfig.sources
    • PersonSetConfig
      • PersonSetConfig.color
      • PersonSetConfig.id
      • PersonSetConfig.model_computed_fields
      • PersonSetConfig.model_config
      • PersonSetConfig.model_fields
      • PersonSetConfig.name
      • PersonSetConfig.values
    • SourceConfig
      • SourceConfig.from_
      • SourceConfig.model_computed_fields
      • SourceConfig.model_config
      • SourceConfig.model_fields
      • SourceConfig.source
    • parse_person_set_collection_config()
    • parse_person_set_collections_study_config()
    • parse_person_set_config()
  • Module contents
    • ChildrenBySex
      • ChildrenBySex.female
      • ChildrenBySex.male
      • ChildrenBySex.unspecified
    • ChildrenStats
      • ChildrenStats.female
      • ChildrenStats.male
      • ChildrenStats.total
      • ChildrenStats.unspecified
    • PSCQuery
      • PSCQuery.psc_id
      • PSCQuery.selected_person_sets
    • PersonSet
      • PersonSet.from_json()
      • PersonSet.get_children()
      • PersonSet.get_children_by_sex()
      • PersonSet.get_children_count()
      • PersonSet.get_children_stats()
      • PersonSet.to_json()
    • PersonSetCollection
      • PersonSetCollection.collect_person_collection_attributes()
      • PersonSetCollection.combine()
      • PersonSetCollection.config_json()
      • PersonSetCollection.domain_json()
      • PersonSetCollection.from_families()
      • PersonSetCollection.get_person_color()
      • PersonSetCollection.get_person_set()
      • PersonSetCollection.get_person_set_of_person()
      • PersonSetCollection.get_query_person_set_ids()
      • PersonSetCollection.get_stats()
      • PersonSetCollection.is_pedigree_only()
      • PersonSetCollection.legend_json()
      • PersonSetCollection.merge_configs()
      • PersonSetCollection.query_fpids()
      • PersonSetCollection.query_person_ids()
      • PersonSetCollection.remove_empty_person_sets()
      • PersonSetCollection.transform_ps_query_to_attribute_queries()
    • PersonSetCollectionConfig
      • PersonSetCollectionConfig.default
      • PersonSetCollectionConfig.domain
      • PersonSetCollectionConfig.id
      • PersonSetCollectionConfig.model_computed_fields
      • PersonSetCollectionConfig.model_config
      • PersonSetCollectionConfig.model_fields
      • PersonSetCollectionConfig.name
      • PersonSetCollectionConfig.sources
    • PersonSetConfig
      • PersonSetConfig.color
      • PersonSetConfig.id
      • PersonSetConfig.model_computed_fields
      • PersonSetConfig.model_config
      • PersonSetConfig.model_fields
      • PersonSetConfig.name
      • PersonSetConfig.values
    • SourceConfig
      • SourceConfig.from_
      • SourceConfig.model_computed_fields
      • SourceConfig.model_config
      • SourceConfig.model_fields
      • SourceConfig.source
    • parse_person_set_collection_config()
    • parse_person_set_collections_study_config()
    • parse_person_set_config()
• dae.pheno package
  • Subpackages
    • dae.pheno.prepare package
      • Submodules
      • dae.pheno.prepare.measure_classifier module
      • Module contents
    • dae.pheno.utils package
      • Submodules
      • dae.pheno.utils.commons module
      • dae.pheno.utils.lin_regress module
      • Module contents
  • Submodules
  • dae.pheno.browser module
    • PhenoBrowser
      • PhenoBrowser.PAGE_SIZE
      • PhenoBrowser.count_measures()
      • PhenoBrowser.create_browser_tables()
      • PhenoBrowser.has_instrument_descriptions
      • PhenoBrowser.has_measure_descriptions
      • PhenoBrowser.regression_display_names
      • PhenoBrowser.regression_display_names_with_ids
      • PhenoBrowser.regression_ids
      • PhenoBrowser.save()
      • PhenoBrowser.save_descriptions()
      • PhenoBrowser.save_regression()
      • PhenoBrowser.save_regression_values()
      • PhenoBrowser.search_measures()
  • dae.pheno.build_pheno_browser module
    • build_pheno_browser()
    • main()
    • pheno_cli_parser()
  • dae.pheno.common module
    • DataDictionaryConfig
      • DataDictionaryConfig.delimiter
      • DataDictionaryConfig.description_column
      • DataDictionaryConfig.instrument
      • DataDictionaryConfig.instrument_column
      • DataDictionaryConfig.measure_column
      • DataDictionaryConfig.model_computed_fields
      • DataDictionaryConfig.model_config
      • DataDictionaryConfig.model_fields
      • DataDictionaryConfig.path
    • DestinationConfig
      • DestinationConfig.model_computed_fields
      • DestinationConfig.model_config
      • DestinationConfig.model_fields
      • DestinationConfig.storage_dir
      • DestinationConfig.storage_id
    • GPFInstanceConfig
      • GPFInstanceConfig.model_computed_fields
      • GPFInstanceConfig.model_config
      • GPFInstanceConfig.model_fields
      • GPFInstanceConfig.path
    • ImportManifest
      • ImportManifest.create_table()
      • ImportManifest.from_row()
      • ImportManifest.from_table()
      • ImportManifest.import_config
      • ImportManifest.is_older_than()
      • ImportManifest.model_computed_fields
      • ImportManifest.model_config
      • ImportManifest.model_fields
      • ImportManifest.unix_timestamp
      • ImportManifest.write_to_db()
    • InferenceConfig
      • InferenceConfig.categorical
      • InferenceConfig.continuous
      • InferenceConfig.histogram_type
      • InferenceConfig.min_individuals
      • InferenceConfig.model_computed_fields
      • InferenceConfig.model_config
      • InferenceConfig.model_fields
      • InferenceConfig.non_numeric_cutoff
      • InferenceConfig.ordinal
      • InferenceConfig.skip
      • InferenceConfig.value_max_len
      • InferenceConfig.value_type
    • InstrumentConfig
      • InstrumentConfig.delimiter
      • InstrumentConfig.instrument
      • InstrumentConfig.model_computed_fields
      • InstrumentConfig.model_config
      • InstrumentConfig.model_fields
      • InstrumentConfig.path
      • InstrumentConfig.person_column
    • InstrumentDescriptionsConfig
      • InstrumentDescriptionsConfig.dictionary
      • InstrumentDescriptionsConfig.files
      • InstrumentDescriptionsConfig.model_computed_fields
      • InstrumentDescriptionsConfig.model_config
      • InstrumentDescriptionsConfig.model_fields
    • InstrumentDictionaryConfig
      • InstrumentDictionaryConfig.delimiter
      • InstrumentDictionaryConfig.description_column
      • InstrumentDictionaryConfig.instrument
      • InstrumentDictionaryConfig.instrument_column
      • InstrumentDictionaryConfig.model_computed_fields
      • InstrumentDictionaryConfig.model_config
      • InstrumentDictionaryConfig.model_fields
      • InstrumentDictionaryConfig.path
    • MeasureDescriptionsConfig
      • MeasureDescriptionsConfig.dictionary
      • MeasureDescriptionsConfig.files
      • MeasureDescriptionsConfig.model_computed_fields
      • MeasureDescriptionsConfig.model_config
      • MeasureDescriptionsConfig.model_fields
    • MeasureHistogramConfigs
      • MeasureHistogramConfigs.categorical_config
      • MeasureHistogramConfigs.model_computed_fields
      • MeasureHistogramConfigs.model_config
      • MeasureHistogramConfigs.model_fields
      • MeasureHistogramConfigs.number_config
    • MeasureType
      • MeasureType.categorical
      • MeasureType.continuous
      • MeasureType.from_str()
      • MeasureType.is_numeric()
      • MeasureType.is_text()
      • MeasureType.ordinal
      • MeasureType.other
      • MeasureType.raw
      • MeasureType.skipped
      • MeasureType.text
    • PhenoImportConfig
      • PhenoImportConfig.data_dictionary
      • PhenoImportConfig.delimiter
      • PhenoImportConfig.destination
      • PhenoImportConfig.gpf_instance
      • PhenoImportConfig.histogram_configs
      • PhenoImportConfig.id
      • PhenoImportConfig.inference_config
      • PhenoImportConfig.input_dir
      • PhenoImportConfig.instrument_dictionary
      • PhenoImportConfig.instrument_files
      • PhenoImportConfig.model_computed_fields
      • PhenoImportConfig.model_config
      • PhenoImportConfig.model_fields
      • PhenoImportConfig.pedigree
      • PhenoImportConfig.person_column
      • PhenoImportConfig.skip_pedigree_measures
      • PhenoImportConfig.study_config
      • PhenoImportConfig.work_dir
    • RankRange
      • RankRange.max_rank
      • RankRange.min_rank
      • RankRange.model_computed_fields
      • RankRange.model_config
      • RankRange.model_fields
    • RegressionMeasure
      • RegressionMeasure.display_name
      • RegressionMeasure.instrument_name
      • RegressionMeasure.jitter
      • RegressionMeasure.measure_names
      • RegressionMeasure.model_computed_fields
      • RegressionMeasure.model_config
      • RegressionMeasure.model_fields
    • StudyConfig
      • StudyConfig.common_report
      • StudyConfig.model_computed_fields
      • StudyConfig.model_config
      • StudyConfig.model_fields
      • StudyConfig.person_set_collections
      • StudyConfig.regressions
  • dae.pheno.db module
    • PhenoDb
      • PhenoDb.find_instrument_values_tables()
      • PhenoDb.get_measures_df()
      • PhenoDb.get_pedigree_df()
      • PhenoDb.get_people_measure_values()
      • PhenoDb.get_people_measure_values_df()
      • PhenoDb.get_persons_df()
      • PhenoDb.save_descriptions()
    • generate_instrument_table_name()
    • safe_db_name()
  • dae.pheno.graphs module
    • GraphColumn
      • GraphColumn.all_count()
      • GraphColumn.build()
      • GraphColumn.females_count()
      • GraphColumn.label
      • GraphColumn.males_count()
    • column_counts()
    • draw_categorical_violin_distribution()
    • draw_linregres()
    • draw_measure_violinplot()
    • draw_ordinal_violin_distribution()
    • gender_palette()
    • gender_palette_light()
    • get_columns_to_draw()
    • male_female_legend()
    • role_labels()
    • set_figure_size()
  • dae.pheno.import_tools module
    • main()
    • pheno_cli_parser()
  • dae.pheno.pheno_data module
    • Instrument
    • Measure
      • Measure.domain
      • Measure.from_record()
      • Measure.to_json()
    • PhenotypeData
      • PhenotypeData.browser
      • PhenotypeData.build_and_save()
      • PhenotypeData.build_report()
      • PhenotypeData.close()
      • PhenotypeData.count_measures()
      • PhenotypeData.create_browser()
      • PhenotypeData.families
      • PhenotypeData.generate_import_manifests()
      • PhenotypeData.get_children_ids()
      • PhenotypeData.get_common_report()
      • PhenotypeData.get_image()
      • PhenotypeData.get_instrument_measures()
      • PhenotypeData.get_instruments()
      • PhenotypeData.get_measure()
      • PhenotypeData.get_measure_description()
      • PhenotypeData.get_measures()
      • PhenotypeData.get_measures_info()
      • PhenotypeData.get_pedigree_df()
      • PhenotypeData.get_people_measure_values()
      • PhenotypeData.get_people_measure_values_df()
      • PhenotypeData.get_person_roles()
      • PhenotypeData.get_person_set_collection()
      • PhenotypeData.get_persons()
      • PhenotypeData.get_persons_df()
      • PhenotypeData.get_regressions()
      • PhenotypeData.has_measure()
      • PhenotypeData.instruments
      • PhenotypeData.is_browser_outdated()
      • PhenotypeData.is_group
      • PhenotypeData.measures
      • PhenotypeData.person_set_collections
      • PhenotypeData.pheno_id
      • PhenotypeData.search_measures()
    • PhenotypeGroup
      • PhenotypeGroup.count_measures()
      • PhenotypeGroup.families
      • PhenotypeGroup.generate_import_manifests()
      • PhenotypeGroup.get_children_ids()
      • PhenotypeGroup.get_leaves()
      • PhenotypeGroup.get_measures_info()
      • PhenotypeGroup.get_pedigree_df()
      • PhenotypeGroup.get_people_measure_values()
      • PhenotypeGroup.get_people_measure_values_df()
      • PhenotypeGroup.get_person_roles()
      • PhenotypeGroup.get_persons_df()
      • PhenotypeGroup.get_regressions()
      • PhenotypeGroup.is_group
      • PhenotypeGroup.person_set_collections
    • PhenotypeStudy
      • PhenotypeStudy.count_measures()
      • PhenotypeStudy.families
      • PhenotypeStudy.generate_import_manifests()
      • PhenotypeStudy.get_children_ids()
      • PhenotypeStudy.get_measures_info()
      • PhenotypeStudy.get_pedigree_df()
      • PhenotypeStudy.get_people_measure_values()
      • PhenotypeStudy.get_people_measure_values_df()
      • PhenotypeStudy.get_persons_df()
      • PhenotypeStudy.get_regressions()
      • PhenotypeStudy.person_set_collections
    • get_pheno_browser_images_dir()
    • get_pheno_db_dir()
  • dae.pheno.pheno_import module
    • ImportInstrument
      • ImportInstrument.delimiter
      • ImportInstrument.files
      • ImportInstrument.name
      • ImportInstrument.person_column
    • MeasureReport
      • MeasureReport.db_name
      • MeasureReport.inference_report
      • MeasureReport.instrument_name
      • MeasureReport.measure_name
      • MeasureReport.measure_type
      • MeasureReport.model_computed_fields
      • MeasureReport.model_config
      • MeasureReport.model_fields
    • 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
    • PreparePhenoBrowserBase
      • PreparePhenoBrowserBase.LARGE_DPI
      • PreparePhenoBrowserBase.SMALL_DPI
      • PreparePhenoBrowserBase.add_measure_task()
      • PreparePhenoBrowserBase.browsable_figure_path()
      • PreparePhenoBrowserBase.build_regression()
      • PreparePhenoBrowserBase.build_values_categorical_distribution()
      • PreparePhenoBrowserBase.build_values_ordinal_distribution()
      • PreparePhenoBrowserBase.build_values_violinplot()
      • PreparePhenoBrowserBase.collect_child_configs()
      • PreparePhenoBrowserBase.do_measure_build()
      • PreparePhenoBrowserBase.figure_filepath()
      • PreparePhenoBrowserBase.get_regression_measures()
      • PreparePhenoBrowserBase.run()
      • PreparePhenoBrowserBase.save_fig()
  • dae.pheno.registry module
    • PhenoRegistry
      • PhenoRegistry.CACHE_LOCK
      • PhenoRegistry.get_all_phenotype_data()
      • PhenoRegistry.get_phenotype_data()
      • PhenoRegistry.get_phenotype_data_config()
      • PhenoRegistry.get_phenotype_data_ids()
      • PhenoRegistry.has_phenotype_data()
      • PhenoRegistry.load_configurations()
      • PhenoRegistry.register_phenotype_data()
      • PhenoRegistry.register_study_config()
      • PhenoRegistry.shutdown()
  • dae.pheno.storage module
    • PhenotypeStorage
      • PhenotypeStorage.build_phenotype_study()
      • PhenotypeStorage.from_config()
      • PhenotypeStorage.shutdown()
    • PhenotypeStorageRegistry
      • PhenotypeStorageRegistry.get_all_phenotype_storage_ids()
      • PhenotypeStorageRegistry.get_all_phenotype_storages()
      • PhenotypeStorageRegistry.get_default_phenotype_storage()
      • PhenotypeStorageRegistry.get_phenotype_storage()
      • PhenotypeStorageRegistry.register_default_storage()
      • PhenotypeStorageRegistry.register_phenotype_storage()
      • PhenotypeStorageRegistry.register_storage_config()
      • PhenotypeStorageRegistry.register_storages_configs()
      • PhenotypeStorageRegistry.shutdown()
  • dae.pheno.update_pheno_descriptions module
    • main()
    • pheno_cli_parser()
    • save_descriptions()
  • Module contents
• dae.pheno_tool package
  • Submodules
  • dae.pheno_tool.pheno_tool_adapter module
    • PhenoToolAdapter
      • PhenoToolAdapter.align_na_results()
      • PhenoToolAdapter.build_report_description()
      • PhenoToolAdapter.calc_by_effect()
      • PhenoToolAdapter.calc_variants()
      • PhenoToolAdapter.get_result_by_sex()
    • PhenoToolAdapterBase
      • PhenoToolAdapterBase.calc_by_effect()
      • PhenoToolAdapterBase.calc_variants()
  • dae.pheno_tool.tool module
    • PhenoResult
      • PhenoResult.set_negative_stats()
      • PhenoResult.set_positive_stats()
    • PhenoTool
      • PhenoTool.calc()
      • PhenoTool.create_df()
      • PhenoTool.get_normalize_measure_id()
      • PhenoTool.init_normalize_measures()
      • PhenoTool.join_pheno_df_with_variants()
    • PhenoToolHelper
      • PhenoToolHelper.genotype_data_persons()
      • PhenoToolHelper.genotype_data_variants()
  • Module contents
• dae.query_variants package
  • Subpackages
    • dae.query_variants.sql package
      • Subpackages
      • Module contents
  • Submodules
  • dae.query_variants.attribute_queries module
    • AttributeQueryTransformer
    • AttributeQueryTransformerFunction
      • AttributeQueryTransformerFunction.and_()
      • AttributeQueryTransformerFunction.compound()
      • AttributeQueryTransformerFunction.grouping()
      • AttributeQueryTransformerFunction.literal()
      • AttributeQueryTransformerFunction.neg()
      • AttributeQueryTransformerFunction.or_()
    • AttributeQueryTransformerSQL
      • AttributeQueryTransformerSQL.and_()
      • AttributeQueryTransformerSQL.compound()
      • AttributeQueryTransformerSQL.grouping()
      • AttributeQueryTransformerSQL.literal()
      • AttributeQueryTransformerSQL.neg()
      • AttributeQueryTransformerSQL.or_()
    • AttributeQueryTransformerSQLLegacy
      • AttributeQueryTransformerSQLLegacy.compound()
      • AttributeQueryTransformerSQLLegacy.literal()
    • CompoundStripTransformer
      • CompoundStripTransformer.compound()
    • Matcher
    • QueryCompoundAdditionTransformer
      • QueryCompoundAdditionTransformer.all()
      • QueryCompoundAdditionTransformer.and_()
      • QueryCompoundAdditionTransformer.any()
      • QueryCompoundAdditionTransformer.compound()
      • QueryCompoundAdditionTransformer.grouping()
      • QueryCompoundAdditionTransformer.literal()
      • QueryCompoundAdditionTransformer.neg()
      • QueryCompoundAdditionTransformer.or_()
    • SyntaxSugarTransformer
      • SyntaxSugarTransformer.all()
      • SyntaxSugarTransformer.any()
    • 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
      • QueryVariantsBase.RUNNER_CLASS
      • QueryVariantsBase.deserialize_family_variant()
      • QueryVariantsBase.deserialize_summary_variant()
      • QueryVariantsBase.has_affected_status_queries()
  • dae.query_variants.query_runners module
    • QueryResult
      • QueryResult.CHECK_VERBOSITY
      • QueryResult.close()
      • QueryResult.get()
      • QueryResult.is_done()
      • QueryResult.start()
    • QueryRunner
      • QueryRunner.adapt()
      • QueryRunner.close()
      • QueryRunner.is_closed()
      • QueryRunner.is_done()
      • QueryRunner.is_started()
      • QueryRunner.put_value_in_result_queue()
      • QueryRunner.result_queue
      • QueryRunner.run()
      • QueryRunner.set_result_queue()
      • QueryRunner.set_study_id()
      • QueryRunner.start()
  • Module contents
• dae.schema2_storage package
  • Submodules
  • dae.schema2_storage.schema2_import_storage module
    • Schema2ImportStorage
      • Schema2ImportStorage.BATCH_SIZE
      • Schema2ImportStorage.generate_import_task_graph()
      • Schema2ImportStorage.generate_reannotate_task_graph()
      • Schema2ImportStorage.load_meta()
    • schema2_project_dataset_layout()
  • dae.schema2_storage.schema2_layout module
    • Schema2DatasetLayout
      • Schema2DatasetLayout.base_dir
      • Schema2DatasetLayout.family
      • Schema2DatasetLayout.has_variants()
      • Schema2DatasetLayout.meta
      • Schema2DatasetLayout.pedigree
      • Schema2DatasetLayout.study
      • Schema2DatasetLayout.summary
    • create_schema2_dataset_layout()
    • load_schema2_dataset_layout()
  • Module contents
• dae.studies package
  • Submodules
  • dae.studies.dataset_helpers module
    • DatasetHelpers
      • DatasetHelpers.disable_study_config()
      • DatasetHelpers.find_genotype_data_config()
      • DatasetHelpers.find_genotype_data_config_file()
      • DatasetHelpers.get_genotype_storage()
      • DatasetHelpers.remove_study_config()
      • DatasetHelpers.rename_study_config()
  • dae.studies.study module
    • CommonStudyMixin
      • CommonStudyMixin.description
    • GenotypeData
      • GenotypeData.add_parent()
      • GenotypeData.build_and_save()
      • GenotypeData.build_report()
      • GenotypeData.close()
      • GenotypeData.create_query_runners()
      • GenotypeData.create_summary_query_runners()
      • GenotypeData.families
      • GenotypeData.get_common_report()
      • GenotypeData.get_leaf_children()
      • GenotypeData.get_person_set_collection()
      • GenotypeData.get_query_leaf_studies()
      • GenotypeData.get_studies_ids()
      • GenotypeData.has_cnv
      • GenotypeData.has_complex
      • GenotypeData.has_denovo
      • GenotypeData.has_transmitted
      • GenotypeData.has_zygosity
      • GenotypeData.is_group
      • GenotypeData.name
      • GenotypeData.parents
      • GenotypeData.person_set_collections
      • GenotypeData.phenotype
      • GenotypeData.pub_med
      • GenotypeData.query_result_summary_variants()
      • GenotypeData.query_result_variants()
      • GenotypeData.query_summary_variants()
      • GenotypeData.query_variants()
      • GenotypeData.study_id
      • GenotypeData.study_type
      • GenotypeData.year
    • GenotypeDataGroup
      • GenotypeDataGroup.create_query_runners()
      • GenotypeDataGroup.create_summary_query_runners()
      • GenotypeDataGroup.families
      • GenotypeDataGroup.get_studies_ids()
      • GenotypeDataGroup.has_denovo
      • GenotypeDataGroup.has_transmitted
      • GenotypeDataGroup.is_group
      • GenotypeDataGroup.rebuild_families()
    • GenotypeDataStudy
      • GenotypeDataStudy.backend
      • GenotypeDataStudy.create_query_runners()
      • GenotypeDataStudy.create_summary_query_runners()
      • GenotypeDataStudy.families
      • GenotypeDataStudy.get_studies_ids()
      • GenotypeDataStudy.is_group
      • GenotypeDataStudy.study_phenotype
    • PSCQueryAdjustments
      • PSCQueryAdjustments.affected_statues
      • PSCQueryAdjustments.person_ids
      • PSCQueryAdjustments.roles
      • PSCQueryAdjustments.sexes
  • dae.studies.variants_db module
    • VariantsDb
      • VariantsDb.get()
      • VariantsDb.get_all_genotype_data()
      • VariantsDb.get_all_genotype_group_ids()
      • VariantsDb.get_all_genotype_groups()
      • VariantsDb.get_all_genotype_studies()
      • VariantsDb.get_all_genotype_study_ids()
      • VariantsDb.get_genotype_group()
      • VariantsDb.get_genotype_group_config()
      • VariantsDb.get_genotype_study()
      • VariantsDb.get_genotype_study_config()
      • VariantsDb.register_genotype_data()
      • VariantsDb.reload()
      • VariantsDb.unregister_genotype_data()
  • Module contents
• dae.task_graph package
  • Submodules
  • dae.task_graph.cache module
    • CacheRecord
      • CacheRecord.error
      • CacheRecord.result
      • CacheRecord.result_or_error
      • CacheRecord.type
    • CacheRecordType
      • CacheRecordType.COMPUTED
      • CacheRecordType.ERROR
      • CacheRecordType.NEEDS_COMPUTE
    • FileTaskCache
      • FileTaskCache.cache()
      • FileTaskCache.load()
    • NoTaskCache
      • NoTaskCache.cache()
      • NoTaskCache.load()
    • TaskCache
      • TaskCache.cache()
      • TaskCache.create()
      • TaskCache.load()
  • dae.task_graph.cli_tools module
    • TaskGraphCli
      • TaskGraphCli.add_arguments()
      • TaskGraphCli.create_executor()
      • TaskGraphCli.process_graph()
  • dae.task_graph.demo_graphs_cli module
    • build_demo_graph()
    • main()
  • dae.task_graph.executor module
    • AbstractTaskGraphExecutor
      • AbstractTaskGraphExecutor.close()
      • AbstractTaskGraphExecutor.execute()
    • DaskExecutor
      • DaskExecutor.MIN_QUEUE_SIZE
      • DaskExecutor.close()
    • SequentialExecutor
    • TaskGraphExecutor
      • TaskGraphExecutor.close()
      • TaskGraphExecutor.execute()
    • task_graph_all_done()
    • task_graph_run()
    • task_graph_run_with_results()
    • task_graph_status()
  • dae.task_graph.graph module
    • Task
      • Task.args
      • Task.deps
      • Task.func
      • Task.input_files
      • Task.task_id
    • TaskGraph
      • TaskGraph.create_task()
      • TaskGraph.prune()
  • dae.task_graph.logging module
    • FsspecHandler
      • FsspecHandler.close()
    • configure_task_logging()
    • ensure_log_dir()
    • safe_task_id()
  • Module contents
• dae.testing package
  • Submodules
  • dae.testing.acgt_import module
    • acgt_gpf()
  • dae.testing.alla_import module
    • alla_gpf()
  • dae.testing.foobar_import module
    • foobar_genes()
    • foobar_genome()
    • foobar_gpf()
  • dae.testing.import_helpers module
    • StudyInputLayout
      • StudyInputLayout.cnv
      • StudyInputLayout.dae
      • StudyInputLayout.denovo
      • StudyInputLayout.pedigree
      • StudyInputLayout.study_id
      • StudyInputLayout.vcf
    • cnv_import()
    • cnv_study()
    • dae_import()
    • dae_study()
    • denovo_import()
    • denovo_study()
    • pedigree_import()
    • setup_dataset()
    • setup_dataset_config()
    • setup_import_project()
    • setup_import_project_config()
    • study_update()
    • update_study_config()
    • vcf_import()
    • vcf_study()
  • dae.testing.setup_helpers module
    • setup_gpf_instance()
  • dae.testing.t4c8_import module
    • t4c8_genes()
    • t4c8_genome()
    • t4c8_gpf()
    • t4c8_grr()
  • Module contents
    • StudyInputLayout
      • StudyInputLayout.cnv
      • StudyInputLayout.dae
      • StudyInputLayout.denovo
      • StudyInputLayout.pedigree
      • StudyInputLayout.study_id
      • StudyInputLayout.vcf
    • acgt_gpf()
    • alla_gpf()
    • cnv_import()
    • cnv_study()
    • convert_to_tab_separated()
    • denovo_import()
    • denovo_study()
    • foobar_gpf()
    • setup_dae_transmitted()
    • setup_dataset()
    • setup_denovo()
    • setup_directories()
    • setup_empty_gene_models()
    • setup_gene_models()
    • setup_genome()
    • setup_gpf_instance()
    • setup_import_project()
    • setup_pedigree()
    • setup_vcf()
    • study_update()
    • t4c8_gpf()
    • update_study_config()
    • vcf_import()
    • vcf_study()
• dae.tools package
  • Submodules
  • dae.tools.cnv_liftover module
    • main()
    • parse_cli_arguments()
  • dae.tools.dae2vcf module
    • main()
    • parse_cli_arguments()
  • dae.tools.dae_liftover module
    • main()
    • parse_cli_arguments()
  • dae.tools.denovo2vcf module
    • main()
    • parse_cli_arguments()
  • dae.tools.denovo_liftover module
    • main()
    • parse_cli_arguments()
  • dae.tools.draw_pedigree module
    • build_families_report()
    • build_family_layout()
    • draw_families()
    • draw_families_report()
    • draw_pedigree()
    • main()
  • dae.tools.generate_common_report module
    • main()
  • dae.tools.generate_denovo_gene_sets module
    • main()
  • dae.tools.gpf_convert_study_config module
    • load_study_config()
    • main()
  • dae.tools.gpf_validation_runner module
    • AbstractRunner
      • AbstractRunner.counter()
      • AbstractRunner.error_case_count
      • AbstractRunner.failed_case_count
      • AbstractRunner.passed_case_count
    • BaseGenotypeBrowserRunner
    • GenotypeBrowserRunner
      • GenotypeBrowserRunner.run()
      • GenotypeBrowserRunner.store_results()
    • MainRunner
      • MainRunner.collect_expectations()
      • MainRunner.counter()
      • MainRunner.errors_case_count
      • MainRunner.failed_case_count
      • MainRunner.main()
      • MainRunner.make_validation_runner()
      • MainRunner.passed_case_count
      • MainRunner.store_junit_results()
      • MainRunner.store_results()
      • MainRunner.summary()
    • TestResult
      • TestResult.to_xml_element()
    • TestStatus
      • TestStatus.ERROR
      • TestStatus.FAIL
      • TestStatus.NOTSET
      • TestStatus.PASSED
    • TestSuite
      • TestSuite.append()
      • TestSuite.to_xml_element()
    • main()
  • dae.tools.grr_cache_repo module
    • cli_cache_repo()
  • dae.tools.ped2ped module
    • main()
  • dae.tools.simple_study_import module
    • build_import_project()
    • cli_arguments()
    • main()
  • dae.tools.to_gpf_gene_models_format module
    • main()
  • dae.tools.vcf2tsv module
    • main()
    • parse_cli_arguments()
  • dae.tools.vcf_liftover module
    • liftover_header()
    • main()
    • parse_cli_arguments()
    • report_alleles()
    • report_variant()
    • report_vcf_variant()
  • Module contents
• dae.utils package
  • Submodules
  • dae.utils.cnv_utils module
    • cnv_variant_type()
    • cshl2cnv_variant()
  • dae.utils.dae_utils module
    • cshl2vcf_variant()
    • dae2vcf_variant()
    • join_line()
    • split_iterable()
  • dae.utils.debug_closing module
    • closing
      • closing.close()
  • dae.utils.dict_utils module
    • recursive_dict_update()
    • recursive_dict_update_inplace()
  • dae.utils.filehash module
    • hashsum()
    • md5sum()
    • sha256sum()
  • dae.utils.fixtures module
    • change_environment()
    • path_to_fixtures()
  • dae.utils.fs_utils module
    • abspath()
    • containing_path()
    • copy()
    • exists()
    • find_directory_with_a_file()
    • glob()
    • is_s3url()
    • join()
    • modified()
    • rm_file()
    • sign()
    • tabix_index_filename()
  • dae.utils.helpers module
    • camelize_string()
    • convert_size()
    • isnan()
    • str2bool()
    • study_id_from_path()
    • to_response_json()
  • dae.utils.progress module
    • progress()
    • progress_nl()
    • red_print()
  • dae.utils.regions module
    • BedRegion
      • BedRegion.begin
      • BedRegion.end
      • BedRegion.from_str()
      • BedRegion.start
      • BedRegion.stop
    • Region
      • Region.begin
      • Region.contains()
      • Region.end
      • Region.from_str()
      • Region.intersection()
      • Region.intersects()
      • Region.isin()
      • Region.start
      • Region.stop
    • all_regions_from_chrom()
    • bedfile2regions()
    • calc_bin_begin()
    • calc_bin_end()
    • calc_bin_index()
    • coalesce()
    • collapse()
    • collapse_no_chrom()
    • connected_component()
    • difference()
    • get_chromosome_length_tabix()
    • intersection()
    • regions2bedfile()
    • split_into_regions()
    • total_length()
    • union()
    • unique_regions()
  • dae.utils.sql_utils module
    • fill_query_parameters()
    • glot_and()
    • to_duckdb_transpile()
  • dae.utils.stats_collection module
    • StatsCollection
      • StatsCollection.inc()
      • StatsCollection.save()
  • dae.utils.variant_utils module
    • BitmaskEnumTranslator
      • BitmaskEnumTranslator.apply_mask()
    • best2gt()
    • complement()
    • fgt2str()
    • get_interval_locus_ploidy()
    • get_locus_ploidy()
    • gt2str()
    • is_all_reference_genotype()
    • is_all_unknown_genotype()
    • is_reference_genotype()
    • is_unknown_genotype()
    • mat2str()
    • reference_genotype()
    • reverse_complement()
    • str2fgt()
    • str2gt()
    • str2lists()
    • str2mat()
    • str2mat_adjust_colsep()
    • trim_parsimonious()
    • trim_str_left()
    • trim_str_left_right()
    • trim_str_right()
    • trim_str_right_left()
  • dae.utils.verbosity_configuration module
    • VerbosityConfiguration
      • VerbosityConfiguration.set()
      • VerbosityConfiguration.set_arguments()
      • VerbosityConfiguration.set_verbosity()
  • Module contents
• dae.variants package
  • Submodules
  • dae.variants.attributes module
    • GeneticModel
      • GeneticModel.X
      • GeneticModel.X_broken
      • GeneticModel.autosomal
      • GeneticModel.autosomal_broken
      • GeneticModel.pseudo_autosomal
    • Inheritance
      • Inheritance.denovo
      • Inheritance.from_name()
      • Inheritance.from_value()
      • Inheritance.mendelian
      • Inheritance.missing
      • Inheritance.omission
      • Inheritance.other
      • Inheritance.possible_denovo
      • Inheritance.possible_omission
      • Inheritance.reference
      • Inheritance.unknown
    • Role
      • Role.child
      • Role.dad
      • Role.display_name
      • Role.from_name()
      • Role.from_value()
      • Role.half_sibling
      • Role.maternal_aunt
      • Role.maternal_cousin
      • Role.maternal_grandfather
      • Role.maternal_grandmother
      • Role.maternal_half_sibling
      • Role.maternal_uncle
      • Role.mom
      • Role.not_role()
      • Role.parent
      • Role.paternal_aunt
      • Role.paternal_cousin
      • Role.paternal_grandfather
      • Role.paternal_grandmother
      • Role.paternal_half_sibling
      • Role.paternal_uncle
      • Role.prb
      • Role.sib
      • Role.spouse
      • Role.step_dad
      • Role.step_mom
      • Role.to_name()
      • Role.to_value()
      • Role.unknown
    • Sex
      • Sex.F
      • Sex.M
      • Sex.U
      • Sex.aliases()
      • Sex.female
      • Sex.from_name()
      • Sex.from_value()
      • Sex.male
      • Sex.short()
      • Sex.to_name()
      • Sex.to_value()
      • Sex.unspecified
    • Status
      • Status.affected
      • Status.from_name()
      • Status.from_value()
      • Status.short()
      • Status.to_name()
      • Status.to_value()
      • Status.unaffected
      • Status.unspecified
    • TransmissionType
      • TransmissionType.denovo
      • TransmissionType.transmitted
      • TransmissionType.unknown
    • Zygosity
      • Zygosity.from_name()
      • Zygosity.from_value()
      • Zygosity.heterozygous
      • Zygosity.homozygous
      • Zygosity.undefined
    • bitmask2inheritance()
  • dae.variants.core module
    • Allele
      • Allele.DISPLAY_NAME_TYPE
      • Allele.TYPE_DISPLAY_NAME
      • Allele.Type
      • Allele.allele_type
      • Allele.alternative
      • Allele.build_cnv_allele()
      • Allele.build_position_allele()
      • Allele.build_vcf_allele()
      • Allele.chrom
      • Allele.chromosome
      • Allele.end_position
      • Allele.get_annotatable()
      • Allele.position
      • Allele.reference
  • dae.variants.family_variant module
    • FamilyAllele
      • FamilyAllele.allele_in_members
      • FamilyAllele.allele_in_roles
      • FamilyAllele.allele_in_sexes
      • FamilyAllele.allele_in_statuses
      • FamilyAllele.allele_index
      • FamilyAllele.allele_type
      • FamilyAllele.alternative
      • FamilyAllele.attributes
      • FamilyAllele.best_st
      • FamilyAllele.best_state
      • FamilyAllele.calc_inheritance_trio()
      • FamilyAllele.check_denovo_trio()
      • FamilyAllele.check_mendelian_trio()
      • FamilyAllele.check_omission_trio()
      • FamilyAllele.chrom
      • FamilyAllele.chromosome
      • FamilyAllele.details
      • FamilyAllele.effects
      • FamilyAllele.end_position
      • FamilyAllele.family_attributes
      • FamilyAllele.family_index
      • FamilyAllele.genetic_model
      • FamilyAllele.genotype
      • FamilyAllele.get_attribute()
      • FamilyAllele.gt_flatten()
      • FamilyAllele.has_attribute()
      • FamilyAllele.inheritance_in_members
      • FamilyAllele.position
      • FamilyAllele.reference
      • FamilyAllele.summary_allele
      • FamilyAllele.summary_attributes
      • FamilyAllele.summary_index
      • FamilyAllele.transmission_type
      • FamilyAllele.update_attributes()
      • FamilyAllele.variant_in_members
      • FamilyAllele.variant_in_members_fpid
      • FamilyAllele.variant_in_members_objects
      • FamilyAllele.variant_in_roles
      • FamilyAllele.variant_in_sexes
      • FamilyAllele.variant_in_statuses
      • FamilyAllele.zygosity_in_roles
      • FamilyAllele.zygosity_in_sexes
      • FamilyAllele.zygosity_in_status
    • FamilyDelegate
      • FamilyDelegate.family_id
      • FamilyDelegate.members_fpids
      • FamilyDelegate.members_ids
      • FamilyDelegate.members_in_order
    • FamilyVariant
      • FamilyVariant.allele_count
      • FamilyVariant.allele_indexes
      • FamilyVariant.alleles
      • FamilyVariant.best_st
      • FamilyVariant.best_state
      • FamilyVariant.calc_alleles()
      • FamilyVariant.calc_alt_alleles()
      • FamilyVariant.chrom
      • FamilyVariant.chromosome
      • FamilyVariant.end_position
      • FamilyVariant.family_allele_indexes
      • FamilyVariant.family_alleles
      • FamilyVariant.family_alt_alleles
      • FamilyVariant.family_best_state
      • FamilyVariant.family_genotype
      • FamilyVariant.family_index
      • FamilyVariant.fvuid
      • FamilyVariant.genetic_model
      • FamilyVariant.genotype
      • FamilyVariant.gt_flatten()
      • FamilyVariant.is_reference()
      • FamilyVariant.is_unknown()
      • FamilyVariant.position
      • FamilyVariant.reference
      • FamilyVariant.summary_index
      • FamilyVariant.to_record()
      • FamilyVariant.variant_in_members
      • FamilyVariant.zygosity_in_roles
      • FamilyVariant.zygosity_in_sexes
      • FamilyVariant.zygosity_in_status
    • calculate_simple_best_state()
  • dae.variants.variant module
    • SummaryAllele
      • SummaryAllele.allele_index
      • SummaryAllele.attributes
      • SummaryAllele.create_reference_allele()
      • SummaryAllele.cshl_location
      • SummaryAllele.cshl_position
      • SummaryAllele.cshl_variant
      • SummaryAllele.cshl_variant_full
      • SummaryAllele.details
      • SummaryAllele.effect_gene_symbols
      • SummaryAllele.effect_genes
      • SummaryAllele.effect_types
      • SummaryAllele.effects
      • SummaryAllele.frequency
      • SummaryAllele.get_attribute()
      • SummaryAllele.has_attribute()
      • SummaryAllele.is_reference_allele
      • SummaryAllele.summary_index
      • SummaryAllele.to_record()
      • SummaryAllele.transmission_type
      • SummaryAllele.update_attributes()
      • SummaryAllele.variant_type
      • SummaryAllele.worst_effect
    • SummaryVariant
      • SummaryVariant.allele_count
      • SummaryVariant.alleles
      • SummaryVariant.alt_alleles
      • SummaryVariant.alternative
      • SummaryVariant.attributes
      • SummaryVariant.chrom
      • SummaryVariant.chromosome
      • SummaryVariant.cshl_location
      • SummaryVariant.cshl_variant
      • SummaryVariant.cshl_variant_full
      • SummaryVariant.details
      • SummaryVariant.effect_gene_symbols
      • SummaryVariant.effect_types
      • SummaryVariant.effects
      • SummaryVariant.end_position
      • SummaryVariant.frequencies
      • SummaryVariant.get_attribute()
      • SummaryVariant.has_attribute()
      • SummaryVariant.location
      • SummaryVariant.matched_alleles
      • SummaryVariant.matched_alleles_indexes
      • SummaryVariant.matched_gene_effects
      • SummaryVariant.position
      • SummaryVariant.ref_allele
      • SummaryVariant.reference
      • SummaryVariant.set_matched_alleles()
      • SummaryVariant.summary_index
      • SummaryVariant.svuid
      • SummaryVariant.to_record()
      • SummaryVariant.transmission_type
      • SummaryVariant.update_attributes()
      • SummaryVariant.variant_types
    • SummaryVariantFactory
      • SummaryVariantFactory.summary_allele_from_record()
      • SummaryVariantFactory.summary_variant_from_records()
      • SummaryVariantFactory.summary_variant_from_vcf()
    • VariantDesc
      • VariantDesc.combine()
      • VariantDesc.to_cshl_full()
      • VariantDesc.to_cshl_short()
    • VariantDetails
      • VariantDetails.from_cnv()
      • VariantDetails.from_vcf()
    • allele_type_from_cshl_variant()
    • allele_type_from_name()
    • cshl_format()
    • tandem_repeat()
    • vcf2cshl()
  • Module contents
• dae.variants_loaders package
  • Subpackages
    • dae.variants_loaders.cnv package
      • Submodules
      • dae.variants_loaders.cnv.flexible_cnv_loader module
      • dae.variants_loaders.cnv.loader module
      • Module contents
    • dae.variants_loaders.dae package
      • Submodules
      • dae.variants_loaders.dae.loader module
      • Module contents
    • dae.variants_loaders.parquet package
      • Submodules
      • dae.variants_loaders.parquet.loader module
      • Module contents
    • dae.variants_loaders.raw package
      • Submodules
      • dae.variants_loaders.raw.flexible_variant_loader module
      • dae.variants_loaders.raw.loader module
      • Module contents
    • dae.variants_loaders.vcf package
      • Submodules
      • dae.variants_loaders.vcf.loader module
      • dae.variants_loaders.vcf.serializer module
      • Module contents
  • Module contents

Module contents