Genomic Resources

Classes and Functions

• dae.genomic_resources package
  • Subpackages
    • dae.genomic_resources.gene_models package
    • dae.genomic_resources.genomic_position_table package
    • dae.genomic_resources.implementations package
    • dae.genomic_resources.statistics package
  • Submodules
  • dae.genomic_resources.aggregators module
    • Aggregator
    • ConcatAggregator
    • CountAggregator
    • DictAggregator
    • JoinAggregator
    • ListAggregator
    • MaxAggregator
    • MeanAggregator
    • MedianAggregator
    • MinAggregator
    • ModeAggregator
    • build_aggregator()
    • create_aggregator()
    • create_aggregator_definition()
    • get_aggregator_class()
    • validate_aggregator()
  • dae.genomic_resources.cached_repository module
    • CacheResource
    • CachingProtocol
    • GenomicResourceCachedRepo
    • 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
    • FsspecReadWriteProtocol
    • build_fsspec_protocol()
    • build_inmemory_protocol()
    • build_local_resource()
  • dae.genomic_resources.genomic_context module
    • DefaultRepositoryContextProvider
    • clear_registered_contexts()
    • context_providers_add_argparser_arguments()
    • context_providers_init()
    • context_providers_init_with_argparser()
    • get_genomic_context()
    • register_context()
    • register_context_provider()
  • dae.genomic_resources.genomic_context_base module
    • Key Constants
    • See Also
    • GenomicContext
    • GenomicContextProvider
    • PriorityGenomicContext
    • SimpleGenomicContext
  • dae.genomic_resources.genomic_context_cli module
    • CLIGenomicContextProvider
  • dae.genomic_resources.genomic_scores module
    • AlleleScore
    • AlleleScoreAggr
    • AlleleScoreQuery
    • CNV
    • CnvCollection
    • GenomicScore
    • PositionScore
    • PositionScoreAggr
    • PositionScoreQuery
    • ScoreDef
    • ScoreLine
    • build_score_from_resource()
    • build_score_from_resource_id()
  • dae.genomic_resources.group_repository module
    • GenomicResourceGroupRepo
  • dae.genomic_resources.histogram module
    • CategoricalHistogram
    • CategoricalHistogramConfig
    • HistogramError
    • HistogramStatisticMixin
    • NullHistogram
    • NullHistogramConfig
    • NumberHistogram
    • NumberHistogramConfig
    • build_default_histogram_conf()
    • build_empty_histogram()
    • build_histogram_config()
    • load_histogram()
    • plot_histogram()
    • save_histogram()
  • dae.genomic_resources.liftover_chain module
    • LiftoverChain
    • build_liftover_chain_from_resource()
    • build_liftover_chain_from_resource_id()
  • dae.genomic_resources.reference_genome module
    • ReferenceGenome
    • build_reference_genome_from_file()
    • build_reference_genome_from_resource()
    • build_reference_genome_from_resource_id()
  • dae.genomic_resources.repository module
    • GenomicResource
    • GenomicResourceProtocolRepo
    • GenomicResourceRepo
    • Manifest
    • ManifestEntry
    • ManifestUpdate
    • Mode
    • ReadOnlyRepositoryProtocol
    • ReadWriteRepositoryProtocol
    • ResourceFileState
    • is_gr_id_token()
    • is_version_constraint_satisfied()
    • parse_gr_id_version_token()
    • parse_resource_id_version()
    • version_string_to_suffix()
    • version_tuple_to_string()
    • version_tuple_to_suffix()
  • dae.genomic_resources.repository_factory module
    • 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
    • InfoImplementationMixin
    • ResourceConfigValidationMixin
    • ResourceStatistics
    • 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
    • get_resource_implementation_builder()