gain package
Subpackages
- gain.annotation package
- Submodules
- gain.annotation.annotatable module
- gain.annotation.annotate_columns module
- gain.annotation.annotate_doc module
- gain.annotation.annotate_utils module
- gain.annotation.annotate_vcf module
- gain.annotation.annotation_config module
AnnotationConfigParserAnnotationConfigParser.ANNOTATION_CONFIG_GRAMMARAnnotationConfigParser.WILDCARD_LIMITAnnotationConfigParser.build_labels_query()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()
AnnotationConfigurationErrorAnnotationPreambleAnnotatorInfoAttributeInfoErrorMarkParamsUsageMonitorRawFullConfigRawPreamble
- gain.annotation.annotation_factory module
build_annotation_pipeline()build_pipeline_annotator()check_for_repeated_attributes_in_annotator()check_for_repeated_attributes_in_pipeline()check_for_unused_parameters()get_annotator_factory()get_available_annotator_types()load_pipeline_from_file()load_pipeline_from_grr()load_pipeline_from_yaml()register_annotator_factory()resolve_repeated_attributes()
- gain.annotation.annotation_genomic_context_cli module
- gain.annotation.annotation_pipeline module
AnnotationPipelineAnnotationPipeline.add_annotator()AnnotationPipeline.annotate()AnnotationPipeline.batch_annotate()AnnotationPipeline.close()AnnotationPipeline.get_annotator_by_attribute_info()AnnotationPipeline.get_attribute_info()AnnotationPipeline.get_attributes()AnnotationPipeline.get_attributes_by_type()AnnotationPipeline.get_info()AnnotationPipeline.get_resource_ids()AnnotationPipeline.open()AnnotationPipeline.print()
AnnotatorAnnotatorDecoratorAttributeDescInputAnnotableAnnotatorDecoratorReannotationPipelineValueTransformAnnotatorDecorator
- gain.annotation.annotator_base module
- gain.annotation.chrom_mapping_annotator module
- gain.annotation.cnv_collection_annotator module
- gain.annotation.debug_annotator module
- gain.annotation.docker_annotator module
- gain.annotation.effect_annotator module
- gain.annotation.gene_score_annotator module
- gain.annotation.gene_set_annotator module
- gain.annotation.liftover_annotator module
AbstractLiftoverAnnotatorAbstractLiftoverAnnotator.close()AbstractLiftoverAnnotator.get_all_attribute_descriptions()AbstractLiftoverAnnotator.liftover_allele()AbstractLiftoverAnnotator.liftover_cnv()AbstractLiftoverAnnotator.liftover_position()AbstractLiftoverAnnotator.liftover_region()AbstractLiftoverAnnotator.open()
BasicLiftoverAnnotatorBcfLiftoverAnnotatorLiftoverFunctionbasic_liftover_allele()basic_liftover_variant()bcf_liftover_allele()bcf_liftover_variant()build_liftover_annotator()
- gain.annotation.normalize_allele_annotator module
- gain.annotation.processing_pipeline module
- gain.annotation.record_to_annotatable module
- gain.annotation.score_annotator module
AlleleScoreAnnotatorGenomicScoreAnnotatorBaseGenomicScoreAnnotatorBase.GENOMIC_SCORE_HELPGenomicScoreAnnotatorBase.SCORE_HISTOGRAMGenomicScoreAnnotatorBase.add_score_aggregator_documentation()GenomicScoreAnnotatorBase.build_attribute_help()GenomicScoreAnnotatorBase.build_score_aggregator_documentation()GenomicScoreAnnotatorBase.close()GenomicScoreAnnotatorBase.get_all_attribute_descriptions()GenomicScoreAnnotatorBase.is_open()GenomicScoreAnnotatorBase.open()
PositionScoreAnnotatorbuild_allele_score_annotator()build_np_score_annotator()build_position_score_annotator()get_genomic_resource()
- gain.annotation.simple_effect_annotator module
SimpleEffectSimpleEffectAnnotatorSimpleEffectAnnotator.annotate()SimpleEffectAnnotator.call_region()SimpleEffectAnnotator.cds_intron_regions()SimpleEffectAnnotator.cds_regions()SimpleEffectAnnotator.effect_types()SimpleEffectAnnotator.get_all_attribute_descriptions()SimpleEffectAnnotator.noncoding_regions()SimpleEffectAnnotator.open()SimpleEffectAnnotator.peripheral_regions()SimpleEffectAnnotator.run_annotate()
build_simple_effect_annotator()
- gain.annotation.utils module
- Module contents
- gain.dask package
- gain.effect_annotation package
- Subpackages
- gain.effect_annotation.effect_checkers package
- Submodules
- gain.effect_annotation.effect_checkers.coding module
- gain.effect_annotation.effect_checkers.effect_checker module
- gain.effect_annotation.effect_checkers.frame_shift module
- gain.effect_annotation.effect_checkers.intron module
- gain.effect_annotation.effect_checkers.promoter module
- gain.effect_annotation.effect_checkers.protein_change module
- gain.effect_annotation.effect_checkers.splice_site module
- gain.effect_annotation.effect_checkers.start_loss module
- gain.effect_annotation.effect_checkers.stop_loss module
- gain.effect_annotation.effect_checkers.utr module
- Module contents
- gain.effect_annotation.effect_checkers package
- Submodules
- gain.effect_annotation.annotation_effects module
- gain.effect_annotation.annotation_request module
BaseAnnotationRequestBaseAnnotationRequest.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()
NegativeStrandAnnotationRequestNegativeStrandAnnotationRequest.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
- gain.effect_annotation.annotator module
- gain.effect_annotation.cli module
- gain.effect_annotation.effect module
AlleleEffectsAnnotationEffectAnnotationEffect.SEVERITYAnnotationEffect.create_effect_details()AnnotationEffect.effect_severity()AnnotationEffect.effects_description()AnnotationEffect.filter_gene_effects()AnnotationEffect.filter_genes()AnnotationEffect.gene_effects()AnnotationEffect.genes()AnnotationEffect.simplify_effects()AnnotationEffect.sort_effects()AnnotationEffect.transcript_effects()AnnotationEffect.worst_effect()
EffectFactoryEffectFactory.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()
EffectGeneEffectTranscriptEffectTypesMixinEffectTypesMixin.EFFECT_GROUPSEffectTypesMixin.EFFECT_TYPESEffectTypesMixin.EFFECT_TYPES_MAPPINGEffectTypesMixin.EFFECT_TYPES_UI_NAMINGEffectTypesMixin.build_effect_types()EffectTypesMixin.build_effect_types_groups()EffectTypesMixin.build_effect_types_list()EffectTypesMixin.get_effect_types()
expand_effect_types()gd2str()ge2str()gene_effect_get_genes()gene_effect_get_genes_worst()gene_effect_get_worst_effect()
- gain.effect_annotation.gene_codes module
- gain.effect_annotation.variant module
- Module contents
- Subpackages
- gain.gene_scores package
- Subpackages
- Submodules
- gain.gene_scores.gene_scores module
GeneScoreGeneScore.filesGeneScore.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_schema()GeneScore.get_score_df()GeneScore.get_score_histogram()GeneScore.get_score_range()GeneScore.get_scores()GeneScore.get_values()GeneScore.get_x_scale()GeneScore.get_y_scale()GeneScore.open()GeneScore.to_tsv()
GeneScoresDbScoreDefScoreDescbuild_gene_score_from_resource()build_gene_score_from_resource_id()
- Module contents
- gain.gene_sets package
- Subpackages
- Submodules
- gain.gene_sets.gene_set module
BaseGeneSetCollectionBaseResourceSchemaCategoricalHistogramSchemaCategoricalHistogramSchema.displayed_values_countCategoricalHistogramSchema.displayed_values_percentCategoricalHistogramSchema.enforce_typeCategoricalHistogramSchema.label_rotationCategoricalHistogramSchema.model_computed_fieldsCategoricalHistogramSchema.model_configCategoricalHistogramSchema.model_fieldsCategoricalHistogramSchema.natural_orderCategoricalHistogramSchema.plot_functionCategoricalHistogramSchema.typeCategoricalHistogramSchema.value_orderCategoricalHistogramSchema.y_log_scale
GeneSetGeneSetCollectionGeneSetCollection.filesGeneSetCollection.get_all_gene_sets()GeneSetCollection.get_gene_collection_count_statistics()GeneSetCollection.get_gene_set()GeneSetCollection.get_gene_sets_list_statistics()GeneSetCollection.get_gene_sets_per_gene_hist()GeneSetCollection.get_gene_sets_per_gene_hist_filename()GeneSetCollection.get_gene_sets_per_gene_hist_image_filename()GeneSetCollection.get_genes_per_gene_set_hist()GeneSetCollection.get_genes_per_gene_set_hist_filename()GeneSetCollection.get_genes_per_gene_set_hist_image_filename()GeneSetCollection.is_loaded()GeneSetCollection.load()GeneSetCollection.load_gene_sets()
GeneSetResourceSchemaGeneSetResourceSchema.directoryGeneSetResourceSchema.filenameGeneSetResourceSchema.histogramsGeneSetResourceSchema.model_computed_fieldsGeneSetResourceSchema.model_configGeneSetResourceSchema.model_fieldsGeneSetResourceSchema.resource_formatGeneSetResourceSchema.resource_idGeneSetResourceSchema.web_format_strGeneSetResourceSchema.web_label
MetaSchemaNumericHistogramSchemaNumericHistogramSchema.displayed_values_countNumericHistogramSchema.model_computed_fieldsNumericHistogramSchema.model_configNumericHistogramSchema.model_fieldsNumericHistogramSchema.number_of_binsNumericHistogramSchema.plot_functionNumericHistogramSchema.typeNumericHistogramSchema.value_orderNumericHistogramSchema.view_rangeNumericHistogramSchema.x_log_scaleNumericHistogramSchema.x_min_logNumericHistogramSchema.y_log_scale
ViewRangeSchemabuild_gene_set_collection_from_file()build_gene_set_collection_from_resource()build_gene_set_collection_from_resource_id()
- gain.gene_sets.gene_term module
- Module contents
- gain.genomic_resources package
- Subpackages
- gain.genomic_resources.gene_models package
- Submodules
- gain.genomic_resources.gene_models.gene_models module
- gain.genomic_resources.gene_models.gene_models_factory module
- gain.genomic_resources.gene_models.parsers module
- gain.genomic_resources.gene_models.serialization module
- gain.genomic_resources.gene_models.transcript_models module
- Module contents
- gain.genomic_resources.genomic_position_table package
- Submodules
- gain.genomic_resources.genomic_position_table.line module
- gain.genomic_resources.genomic_position_table.table module
- gain.genomic_resources.genomic_position_table.table_bigwig module
- gain.genomic_resources.genomic_position_table.table_inmemory module
- gain.genomic_resources.genomic_position_table.table_tabix module
- gain.genomic_resources.genomic_position_table.table_vcf module
- gain.genomic_resources.genomic_position_table.utils module
- Module contents
- gain.genomic_resources.implementations package
- Submodules
- gain.genomic_resources.implementations.annotation_pipeline_impl module
- gain.genomic_resources.implementations.gene_models_impl module
- gain.genomic_resources.implementations.genomic_scores_impl module
- gain.genomic_resources.implementations.liftover_chain_impl module
- gain.genomic_resources.implementations.reference_genome_impl module
- Module contents
- gain.genomic_resources.statistics package
- gain.genomic_resources.gene_models package
- Submodules
- gain.genomic_resources.aggregators module
- gain.genomic_resources.cached_repository module
CacheResourceCachingProtocolCachingProtocol.file_exists()CachingProtocol.get_all_resources()CachingProtocol.get_all_resources_dict()CachingProtocol.get_public_url()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_repository_sqlite3_metadata_db()CachingProtocol.open_tabix_file()CachingProtocol.open_vcf_file()CachingProtocol.refresh_cached_resource()CachingProtocol.refresh_cached_resource_file()
GenomicResourceCachedRepocache_resources()
- gain.genomic_resources.cli module
- gain.genomic_resources.draw_score_histograms module
- gain.genomic_resources.explore_grr_search module
- gain.genomic_resources.fsspec_protocol module
FsspecReadOnlyProtocolFsspecReadOnlyProtocol.close()FsspecReadOnlyProtocol.file_exists()FsspecReadOnlyProtocol.get_all_resources()FsspecReadOnlyProtocol.get_all_resources_dict()FsspecReadOnlyProtocol.get_public_url()FsspecReadOnlyProtocol.get_url()FsspecReadOnlyProtocol.invalidate()FsspecReadOnlyProtocol.load_contents()FsspecReadOnlyProtocol.load_manifest()FsspecReadOnlyProtocol.md5_contents()FsspecReadOnlyProtocol.open_bigwig_file()FsspecReadOnlyProtocol.open_raw_file()FsspecReadOnlyProtocol.open_repository_sqlite3_metadata_db()FsspecReadOnlyProtocol.open_tabix_file()FsspecReadOnlyProtocol.open_vcf_file()
FsspecReadWriteProtocolFsspecReadWriteProtocol.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_all_resources_dict()FsspecReadWriteProtocol.get_content_file_path()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()
- gain.genomic_resources.genomic_context module
- gain.genomic_resources.genomic_context_base module
- gain.genomic_resources.genomic_context_cli module
- gain.genomic_resources.genomic_scores module
AlleleScoreAlleleScoreAggrAlleleScoreQueryCNVCnvCollectionGenomicScoreGenomicScore.close()GenomicScore.fetch_region_values()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_schema()GenomicScore.get_score_definition()GenomicScore.get_score_histogram()GenomicScore.get_score_range()GenomicScore.is_open()GenomicScore.open()
PositionScorePositionScoreAggrPositionScoreQueryScoreDefScoreLinebuild_score_from_resource()build_score_from_resource_id()
- gain.genomic_resources.group_repository module
- gain.genomic_resources.histogram module
CategoricalHistogramCategoricalHistogram.UNIQUE_VALUES_LIMITCategoricalHistogram.add_value()CategoricalHistogram.deserialize()CategoricalHistogram.display_valuesCategoricalHistogram.from_dict()CategoricalHistogram.merge()CategoricalHistogram.plot()CategoricalHistogram.raw_valuesCategoricalHistogram.serialize()CategoricalHistogram.to_dict()CategoricalHistogram.typeCategoricalHistogram.values_domain()
CategoricalHistogramConfigCategoricalHistogramConfig.allow_only_whole_values_yCategoricalHistogramConfig.default_config()CategoricalHistogramConfig.displayed_values_countCategoricalHistogramConfig.displayed_values_percentCategoricalHistogramConfig.enforce_typeCategoricalHistogramConfig.from_dict()CategoricalHistogramConfig.label_rotationCategoricalHistogramConfig.natural_orderCategoricalHistogramConfig.plot_functionCategoricalHistogramConfig.to_dict()CategoricalHistogramConfig.value_orderCategoricalHistogramConfig.y_log_scale
HistogramErrorHistogramStatisticMixinNullHistogramNullHistogramConfigNumberHistogramNumberHistogram.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.typeNumberHistogram.values_domain()NumberHistogram.view_max()NumberHistogram.view_min()
NumberHistogramConfigNumberHistogramConfig.default_config()NumberHistogramConfig.from_dict()NumberHistogramConfig.has_view_range()NumberHistogramConfig.number_of_binsNumberHistogramConfig.plot_functionNumberHistogramConfig.to_dict()NumberHistogramConfig.view_rangeNumberHistogramConfig.x_log_scaleNumberHistogramConfig.x_min_logNumberHistogramConfig.y_log_scale
build_default_histogram_conf()build_empty_histogram()build_histogram_config()load_histogram()plot_histogram()save_histogram()
- gain.genomic_resources.liftover_chain module
- gain.genomic_resources.reference_genome module
ReferenceGenomeReferenceGenome.chrom_prefixReferenceGenome.chromosomesReferenceGenome.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_idReferenceGenome.split_into_regions()
build_reference_genome_from_file()build_reference_genome_from_resource()build_reference_genome_from_resource_id()
- gain.genomic_resources.repository module
GenomicResourceGenomicResource.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_public_url()GenomicResource.get_repo_public_url()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()
GenomicResourceProtocolRepoGenomicResourceRepoManifestManifestEntryManifestUpdateModeReadOnlyRepositoryProtocolReadOnlyRepositoryProtocol.CHUNK_SIZEReadOnlyRepositoryProtocol.build_genomic_resource()ReadOnlyRepositoryProtocol.compute_md5_sum()ReadOnlyRepositoryProtocol.file_exists()ReadOnlyRepositoryProtocol.find_resource()ReadOnlyRepositoryProtocol.get_all_resources()ReadOnlyRepositoryProtocol.get_all_resources_dict()ReadOnlyRepositoryProtocol.get_file_content()ReadOnlyRepositoryProtocol.get_id()ReadOnlyRepositoryProtocol.get_manifest()ReadOnlyRepositoryProtocol.get_public_url()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_repository_sqlite3_metadata_db()ReadOnlyRepositoryProtocol.open_tabix_file()ReadOnlyRepositoryProtocol.open_vcf_file()ReadOnlyRepositoryProtocol.search_resources()
ReadWriteRepositoryProtocolReadWriteRepositoryProtocol.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()
ResourceFileStateis_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()
- gain.genomic_resources.repository_factory module
- gain.genomic_resources.resource_implementation module
GenomicResourceImplementationGenomicResourceImplementation.calc_info_hash()GenomicResourceImplementation.calc_statistics_hash()GenomicResourceImplementation.create_statistics_build_tasks()GenomicResourceImplementation.filesGenomicResourceImplementation.get_config()GenomicResourceImplementation.get_info()GenomicResourceImplementation.get_statistics()GenomicResourceImplementation.get_statistics_info()GenomicResourceImplementation.reload_statistics()GenomicResourceImplementation.resource_id
InfoImplementationMixinResourceConfigValidationMixinResourceStatisticsget_base_resource_schema()
- gain.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()
- gain.genomic_resources.utils module
- gain.genomic_resources.variant_utils module
- Module contents
- Subpackages
- gain.task_graph package
- Submodules
- gain.task_graph.base_executor module
- gain.task_graph.cache module
- gain.task_graph.cli_tools module
- gain.task_graph.dask_executor module
- gain.task_graph.demo_graphs_cli module
- gain.task_graph.executor module
- gain.task_graph.graph module
TaskTaskDescTaskGraphTaskGraph.add_task()TaskGraph.add_tasks()TaskGraph.as_directed_graph()TaskGraph.create_task()TaskGraph.empty()TaskGraph.extract_tasks()TaskGraph.get_task_deps()TaskGraph.get_task_desc()TaskGraph.has_task()TaskGraph.make_task()TaskGraph.process_completed_tasks()TaskGraph.prune()TaskGraph.ready_tasks()TaskGraph.tasksTaskGraph.topological_order()
chain_tasks()sync_tasks()
- gain.task_graph.logging module
- gain.task_graph.process_pool_executor module
- gain.task_graph.sequential_executor module
- Module contents
- gain.testing package
- gain.utils package
- Submodules
- gain.utils.cnv_utils module
- gain.utils.dae_utils module
- gain.utils.debug_closing module
- gain.utils.dict_utils module
- gain.utils.fs_utils module
- gain.utils.helpers module
- gain.utils.processing_pipeline module
- gain.utils.regions module
BedRegionRegionall_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()
- gain.utils.sql_utils module
- gain.utils.stats_collection module
- gain.utils.variant_utils module
- gain.utils.verbosity_configuration module
- Module contents