dae package
Subpackages
- dae.annotation package
- Submodules
- dae.annotation.annotatable module
- dae.annotation.annotate_columns module
- dae.annotation.annotate_doc module
- dae.annotation.annotate_schema2_parquet module
- dae.annotation.annotate_utils module
- dae.annotation.annotate_vcf module
- dae.annotation.annotation_config module
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
AnnotatorInfo
AttributeInfo
ParamsUsageMonitor
RawFullConfig
RawPreamble
- 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
AnnotatorDecorator
FullReannotationPipeline
InputAnnotableAnnotatorDecorator
ReannotationPipeline
ValueTransformAnnotatorDecorator
- dae.annotation.annotator_base module
- dae.annotation.cnv_collection_annotator module
- dae.annotation.debug_annotator module
- dae.annotation.docker_annotator module
- dae.annotation.effect_annotator module
- dae.annotation.format_handlers module
- dae.annotation.gene_score_annotator module
- dae.annotation.gene_set_annotator module
- dae.annotation.genomic_context module
- dae.annotation.liftover_annotator module
- dae.annotation.normalize_allele_annotator module
- dae.annotation.parquet module
- dae.annotation.reannotate_instance module
- dae.annotation.record_to_annotatable module
- dae.annotation.score_annotator module
- dae.annotation.simple_effect_annotator module
- Module contents
- dae.common_reports package
- dae.configuration package
- 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
- dae.configuration.schemas package
- 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
- dae.configuration.study_config_builder module
- dae.configuration.utils module
- Module contents
- Subpackages
- dae.dask package
- dae.duckdb_storage package
- Submodules
- dae.duckdb_storage.duckdb2_variants module
- dae.duckdb_storage.duckdb_connection_factory module
- dae.duckdb_storage.duckdb_genotype_storage module
- dae.duckdb_storage.duckdb_import_storage module
- dae.duckdb_storage.duckdb_legacy_genotype_storage module
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
- 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
DuckDbVariants
- 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
- dae.effect_annotation.effect_checkers package
- Submodules
- dae.effect_annotation.annotation_effects module
- 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
- dae.effect_annotation.annotator module
- dae.effect_annotation.cli module
- dae.effect_annotation.effect module
AlleleEffects
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
EffectTranscript
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
- dae.effect_annotation.variant module
- Module contents
- Subpackages
- dae.enrichment_tool package
- Subpackages
- Submodules
- dae.enrichment_tool.base_enrichment_background module
- dae.enrichment_tool.build_coding_length_enrichment_background module
- dae.enrichment_tool.build_ur_synonymous_enrichment_background module
- dae.enrichment_tool.enrichment_builder module
- dae.enrichment_tool.enrichment_cache_builder module
- dae.enrichment_tool.enrichment_helper module
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
EnrichmentResult
EnrichmentSingleResult
EventCountersResult
EventsCounter
EventsResult
GeneEventsCounter
VariantEventsResult
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
- dae.enrichment_tool.genotype_helper module
- dae.enrichment_tool.samocha_background module
- Module contents
- dae.gene_profile package
- dae.gene_scores package
- Subpackages
- 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
ScoreDef
ScoreDesc
build_gene_score_from_resource()
build_gene_score_from_resource_id()
- Module contents
- dae.gene_sets package
- Subpackages
- 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
- dae.gene_sets.denovo_gene_sets_config module
DGSCQuery
DGSSpec
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
RecurrentCriteria
SexesCriteria
SingleCriteria
TripleCriteria
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
BaseResourceSchema
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
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
MetaSchema
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
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
- Module contents
- dae.genomic_resources package
- Subpackages
- dae.genomic_resources.gene_models package
- 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.aggregators module
- 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
cache_resources()
- dae.genomic_resources.cli module
- dae.genomic_resources.draw_score_histograms module
- 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
- dae.genomic_resources.genomic_context_cli module
- dae.genomic_resources.genomic_scores module
AlleleScore
AlleleScoreAggr
AlleleScoreQuery
CNV
CnvCollection
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
PositionScoreAggr
PositionScoreQuery
ScoreDef
ScoreLine
build_score_from_resource()
build_score_from_resource_id()
- dae.genomic_resources.group_repository module
- 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
NullHistogram
NullHistogramConfig
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
- 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
GenomicResourceRepo
Manifest
ManifestEntry
ManifestUpdate
Mode
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
is_gr_id_token()
is_version_constraint_satisfied()
parse_gr_id_version_token()
parse_resource_id_version()
version_string_to_suffix()
version_tuple_to_string()
version_tuple_to_suffix()
- dae.genomic_resources.repository_factory module
- dae.genomic_resources.resource_implementation module
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
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
- 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()
- Subpackages
- dae.genomic_scores package
- dae.genotype_storage package
- Submodules
- dae.genotype_storage.genotype_storage module
- dae.genotype_storage.genotype_storage_registry module
GenotypeStorageRegistry
GenotypeStorageRegistry.get_all_genotype_storage_ids()
GenotypeStorageRegistry.get_all_genotype_storages()
GenotypeStorageRegistry.get_default_genotype_storage()
GenotypeStorageRegistry.get_genotype_storage()
GenotypeStorageRegistry.register_default_storage()
GenotypeStorageRegistry.register_genotype_storage()
GenotypeStorageRegistry.register_storage_config()
GenotypeStorageRegistry.register_storages_configs()
GenotypeStorageRegistry.shutdown()
- Module contents
- dae.gpf_instance package
- Subpackages
- 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
- dae.import_tools package
- Submodules
- dae.import_tools.cli module
- dae.import_tools.import_config module
- dae.import_tools.import_tools module
Bucket
ImportConfigNormalizer
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
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
- dae.inmemory_storage.inmemory_genotype_storage module
- dae.inmemory_storage.inmemory_import_storage module
- dae.inmemory_storage.raw_variants module
RawFamilyVariants
RawFamilyVariants.build_family_variants_query_runner()
RawFamilyVariants.build_summary_variants_query_runner()
RawFamilyVariants.family_variant_filter_function()
RawFamilyVariants.family_variants_iterator()
RawFamilyVariants.filter_allele()
RawFamilyVariants.filter_family_variant()
RawFamilyVariants.filter_gene_effects()
RawFamilyVariants.filter_real_attr()
RawFamilyVariants.filter_regions()
RawFamilyVariants.filter_summary_allele()
RawFamilyVariants.filter_summary_variant()
RawFamilyVariants.full_variants_iterator()
RawFamilyVariants.query_summary_variants()
RawFamilyVariants.query_variants()
RawFamilyVariants.summary_variant_filter_function()
RawFamilyVariants.summary_variants_iterator()
RawMemoryVariants
RawVariantsQueryRunner
- Module contents
- dae.parquet package
- Subpackages
- Submodules
- dae.parquet.helpers module
- dae.parquet.parquet_writer module
- dae.parquet.partition_descriptor module
PartitionDescriptor
PartitionDescriptor.dataset_family_partition()
PartitionDescriptor.dataset_summary_partition()
PartitionDescriptor.family_partition()
PartitionDescriptor.get_variant_partitions()
PartitionDescriptor.has_coding_bins()
PartitionDescriptor.has_family_bins()
PartitionDescriptor.has_family_partitions()
PartitionDescriptor.has_frequency_bins()
PartitionDescriptor.has_partitions()
PartitionDescriptor.has_region_bins()
PartitionDescriptor.has_summary_partitions()
PartitionDescriptor.make_all_region_bins()
PartitionDescriptor.make_coding_bin()
PartitionDescriptor.make_family_bin()
PartitionDescriptor.make_frequency_bin()
PartitionDescriptor.make_region_bin()
PartitionDescriptor.make_region_bins_regions()
PartitionDescriptor.parse()
PartitionDescriptor.parse_dict()
PartitionDescriptor.parse_string()
PartitionDescriptor.partition_directory()
PartitionDescriptor.partition_filename()
PartitionDescriptor.path_to_partitions()
PartitionDescriptor.region_bins_count()
PartitionDescriptor.region_to_region_bins()
PartitionDescriptor.schema1_partition()
PartitionDescriptor.serialize()
PartitionDescriptor.summary_partition()
PartitionDescriptor.to_dict()
- Module contents
- dae.parquet_storage package
- dae.pedigrees package
- Submodules
- dae.pedigrees.drawing module
- 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
- dae.pedigrees.family_tag_builder module
FamilyTagsBuilder
check_affected_dad_family()
check_affected_mom_family()
check_affected_prb_family()
check_affected_sib_family()
check_control_family()
check_family_tags_query()
check_female_prb_family()
check_male_prb_family()
check_missing_dad_family()
check_missing_mom_family()
check_multiplex_family()
check_nuclear_family()
check_quad_family()
check_simplex_family()
check_tag()
check_trio_family()
check_unaffected_dad_family()
check_unaffected_mom_family()
check_unaffected_prb_family()
check_unaffected_sib_family()
set_attr()
set_tag()
tag_affected_dad_family()
tag_affected_mom_family()
tag_affected_prb_family()
tag_affected_sib_family()
tag_control_family()
tag_female_prb_family()
tag_male_prb_family()
tag_missing_dad_family()
tag_missing_mom_family()
tag_multiplex_family()
tag_nuclear_family()
tag_quad_family()
tag_simplex_family()
tag_trio_family()
tag_unaffected_dad_family()
tag_unaffected_mom_family()
tag_unaffected_prb_family()
tag_unaffected_sib_family()
unset_tag()
- dae.pedigrees.layout module
- dae.pedigrees.loader module
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
IndividualGroup
Interval
IntervalForVertex
MatingUnit
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
SandwichSolver
SibshipUnit
copy_graph()
- dae.pedigrees.testing module
- Module contents
- dae.person_filters package
- Submodules
- dae.person_filters.person_filters module
- Module contents
- dae.person_sets package
- Submodules
- dae.person_sets.person_sets module
AttributeQueriesUnsupportedException
ChildrenBySex
ChildrenStats
PSCQuery
PersonSet
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
PersonSetConfig
SourceConfig
parse_person_set_collection_config()
parse_person_set_collections_study_config()
parse_person_set_config()
- Module contents
ChildrenBySex
ChildrenStats
PSCQuery
PersonSet
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
PersonSetConfig
SourceConfig
parse_person_set_collection_config()
parse_person_set_collections_study_config()
parse_person_set_config()
- dae.pheno package
- Subpackages
- 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
- 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
GPFInstanceConfig
ImportManifest
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
InstrumentDescriptionsConfig
InstrumentDictionaryConfig
InstrumentDictionaryConfig.delimiter
InstrumentDictionaryConfig.description_column
InstrumentDictionaryConfig.instrument
InstrumentDictionaryConfig.instrument_column
InstrumentDictionaryConfig.model_computed_fields
InstrumentDictionaryConfig.model_config
InstrumentDictionaryConfig.model_fields
InstrumentDictionaryConfig.path
MeasureDescriptionsConfig
MeasureHistogramConfigs
MeasureType
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
RegressionMeasure
StudyConfig
- dae.pheno.db module
- dae.pheno.graphs module
- dae.pheno.import_tools module
- dae.pheno.pheno_data module
Instrument
Measure
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
MeasureReport
add_pheno_common_inference()
collect_instruments()
create_import_tasks()
create_tables()
determine_destination()
generate_phenotype_data_config()
get_gpf_instance()
get_output_parquet_files_dir()
handle_measure_inference_tasks()
import_pheno_data()
infer_measures()
load_histogram_configs()
load_inference_configs()
load_instrument_description_file()
load_instrument_descriptions()
load_measure_description_file()
load_measure_descriptions()
main()
merge_histogram_configs()
merge_inference_configs()
open_file()
pheno_cli_parser()
read_and_classify_measure()
read_instrument_measure_names()
read_pedigree()
transform_cli_args()
write_descriptions()
write_reports_to_parquet()
write_results()
write_to_parquet()
- dae.pheno.prepare_data module
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
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
- Module contents
- dae.pheno_tool package
- dae.query_variants package
- Subpackages
- Submodules
- dae.query_variants.attribute_queries module
AttributeQueryTransformer
AttributeQueryTransformerFunction
AttributeQueryTransformerSQL
AttributeQueryTransformerSQLLegacy
CompoundStripTransformer
Matcher
QueryCompoundAdditionTransformer
QueryCompoundAdditionTransformer.all()
QueryCompoundAdditionTransformer.and_()
QueryCompoundAdditionTransformer.any()
QueryCompoundAdditionTransformer.compound()
QueryCompoundAdditionTransformer.grouping()
QueryCompoundAdditionTransformer.literal()
QueryCompoundAdditionTransformer.neg()
QueryCompoundAdditionTransformer.or_()
SyntaxSugarTransformer
create_and_node()
create_or_node()
transform_attribute_query_to_function()
transform_attribute_query_to_sql_expression()
transform_attribute_query_to_sql_expression_schema1()
update_attribute_query_with_compounds()
- dae.query_variants.base_query_variants module
QueryVariants
QueryVariants.build_family_variants_query_runner()
QueryVariants.build_summary_variants_query_runner()
QueryVariants.has_affected_status_queries()
QueryVariants.query_summary_variants()
QueryVariants.query_variants()
QueryVariants.tags_to_family_ids()
QueryVariants.transform_roles_to_single_role_string()
QueryVariantsBase
- dae.query_variants.query_runners module
- Module contents
- dae.schema2_storage package
- dae.studies package
- Submodules
- dae.studies.dataset_helpers module
- dae.studies.study module
CommonStudyMixin
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
GenotypeDataStudy
PSCQueryAdjustments
- 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
- dae.task_graph.cli_tools module
- dae.task_graph.demo_graphs_cli module
- dae.task_graph.executor module
- dae.task_graph.graph module
- dae.task_graph.logging module
- Module contents
- dae.testing package
- Submodules
- dae.testing.acgt_import module
- dae.testing.alla_import module
- dae.testing.foobar_import module
- dae.testing.import_helpers module
- dae.testing.setup_helpers module
- dae.testing.t4c8_import module
- Module contents
StudyInputLayout
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
- dae.tools.dae2vcf module
- dae.tools.dae_liftover module
- dae.tools.denovo2vcf module
- dae.tools.denovo_liftover module
- dae.tools.draw_pedigree module
- dae.tools.generate_common_report module
- dae.tools.generate_denovo_gene_sets module
- dae.tools.gpf_convert_study_config module
- dae.tools.gpf_validation_runner module
- dae.tools.grr_cache_repo module
- dae.tools.ped2ped module
- dae.tools.simple_study_import module
- dae.tools.to_gpf_gene_models_format module
- dae.tools.vcf2tsv module
- dae.tools.vcf_liftover module
- Module contents
- dae.utils package
- Submodules
- dae.utils.cnv_utils module
- dae.utils.dae_utils module
- dae.utils.debug_closing module
- dae.utils.dict_utils module
- dae.utils.filehash module
- dae.utils.fixtures module
- dae.utils.fs_utils module
- dae.utils.helpers module
- dae.utils.progress module
- dae.utils.regions module
BedRegion
Region
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
- dae.utils.stats_collection module
- dae.utils.variant_utils module
BitmaskEnumTranslator
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
- Module contents
- dae.variants package
- Submodules
- dae.variants.attributes module
GeneticModel
Inheritance
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
Status
TransmissionType
Zygosity
bitmask2inheritance()
- dae.variants.core module
- 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
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
VariantDesc
VariantDetails
allele_type_from_cshl_variant()
allele_type_from_name()
cshl_format()
tandem_repeat()
vcf2cshl()
- Module contents
- dae.variants_loaders package