Index

_

_do_annotate() (AnnotatorBase method) _do_batch_annotate() (AnnotatorBase method) _empty_result() (AnnotatorBase method)

_every() (AnnotatorBase method) _from_sources() (AnnotatorBase method) _pair_aggregated() (AnnotatorBase method) _pair_all() (AnnotatorBase method)

A

ACCEPTED_RESOURCE_TYPES (AnnotatorBase attribute) add_annotator() (AnnotationPipeline method) add_arguments() (TaskGraphCli static method) add_batch() (CategoricalHistogram method) (NumberHistogram method) add_task() (TaskGraph method) add_tasks() (TaskGraph method) add_value() (CategoricalHistogram method) (NullHistogram method) (NumberHistogram method) all_regions() (TranscriptModel method) allele_key() (in module gain.genomic_resources.genomic_scores) AlleleAggregate (class in gain.genomic_resources.genomic_scores) AlleleEntry (class in gain.genomic_resources.genomic_scores) AlleleMultiplicityError (class in gain.genomic_resources.genomic_scores) alleles_mode() (AlleleScore method) AlleleScore (class in gain.genomic_resources.genomic_scores) AlleleScore.Mode (class in gain.genomic_resources.genomic_scores) AlleleScore.Multiplicity (class in gain.genomic_resources.genomic_scores)

alt (AlleleEntry attribute) (VCFAllele property) alternative (VCFAllele property) Annotatable (class in gain.annotation.annotatable) Annotatable.Type (class in gain.annotation.annotatable) annotate() (AnnotationPipeline method) (Annotator method) (AnnotatorBase method) AnnotatedValues (class in gain.annotation.annotator_base) AnnotationConfigurationError (class in gain.annotation.annotation_config) AnnotationPipeline (class in gain.annotation.annotation_pipeline) Annotator (class in gain.annotation.annotation_pipeline) AnnotatorBase (class in gain.annotation.annotator_base) AnnotatorInfo (class in gain.annotation.annotation_config) as_dict() (AttributeSpec method) (ParamsUsageMonitor method) Attribute (class in gain.annotation.annotation_config) attributes (Annotator property) (AnnotatorBase property) AttributeSpec (class in gain.annotation.annotation_pipeline)

B

batch_annotate() (AnnotationPipeline method) (Annotator method) (AnnotatorBase method) build_allele_score_from_resource() (in module gain.genomic_resources.genomic_scores) build_allele_score_from_resource_id() (in module gain.genomic_resources.genomic_scores) build_annotatable_from_dict() (in module gain.annotation.record_to_annotatable) build_annotation_pipeline() (in module gain.annotation.annotation_factory) build_fragment_score_from_resource() (in module gain.genomic_resources.genomic_scores) build_fragment_score_from_resource_id() (in module gain.genomic_resources.genomic_scores) build_gene_models_from_resource() (in module gain.genomic_resources.gene_models) build_gene_models_from_resource_id() (in module gain.genomic_resources.gene_models) build_gene_score_from_resource() (in module gain.gene_scores.gene_scores) build_gene_score_from_resource_id() (in module gain.gene_scores.gene_scores)

build_gene_set_collection_from_resource() (in module gain.gene_sets.gene_set) build_gene_set_collection_from_resource_id() (in module gain.gene_sets.gene_set) build_genomic_resource_group_repository() (in module gain.genomic_resources.repository_factory) build_genomic_resource_repository() (in module gain.genomic_resources.repository_factory) build_liftover_chain_from_resource() (in module gain.genomic_resources.liftover_chain) build_liftover_chain_from_resource_id() (in module gain.genomic_resources.liftover_chain) build_position_score_from_resource() (in module gain.genomic_resources.genomic_scores) build_position_score_from_resource_id() (in module gain.genomic_resources.genomic_scores) build_record_to_annotatable() (in module gain.annotation.record_to_annotatable) build_reference_genome_from_resource() (in module gain.genomic_resources.reference_genome) build_reference_genome_from_resource_id() (in module gain.genomic_resources.reference_genome) build_score_from_resource() (in module gain.genomic_resources.genomic_scores) build_score_from_resource_id() (in module gain.genomic_resources.genomic_scores) build_score_help() (GeneScore method)

C

cache() (FileTaskCache method) (NoTaskCache method) (TaskCache method) CacheRecord (class in gain.task_graph.cache) CacheRecordType (class in gain.task_graph.cache) calc_frames() (TranscriptModel method) calc_info_hash() (GenomicResourceImplementation method) calc_statistics_hash() (GenomicResourceImplementation method) CategoricalHistogram (class in gain.genomic_resources.histogram) CategoricalHistogramConfig (class in gain.genomic_resources.histogram) cds_len() (TranscriptModel method) cds_regions() (TranscriptModel method) chain_tasks() (in module gain.task_graph.graph) chrom (Annotatable property) chrom_length_source (GenomicScore property) chrom_length_sources (GenomicScore property) chrom_prefix (ReferenceGenome property) chromosome (Annotatable property) chromosomes (ReferenceGenome property)

close() (AnnotationPipeline method) (Annotator method) (DaskExecutor method) (GeneModels method) (GenomicResourceRepo method) (GenomicScore method) (LiftoverChain method) (ProcessPoolTaskExecutor method) (ReferenceGenome method) (SequentialExecutor method) (TaskGraphExecutor method) CNVAllele (class in gain.annotation.annotatable) compile_filter() (GenomicScore method) contains() (Exon method) convert_coordinate() (LiftoverChain method) count (NumberHistogram property) create() (TaskCache static method) create_executor() (TaskGraphCli static method) create_statistics_build_tasks() (GenomicResourceImplementation method) create_task() (TaskGraph method)

D

DaskExecutor (class in gain.task_graph.dask_executor) DEFAULT_AGGREGATORS (AlleleScore attribute) (FragmentScore attribute) default_config() (CategoricalHistogramConfig static method) (NullHistogramConfig static method) (NumberHistogramConfig static method)

definition (GenomicResourceRepo property) deserialize() (CategoricalHistogram static method) (NullHistogram static method) (NumberHistogram static method) display_values (CategoricalHistogram property) DockerAnnotator (class in gain.annotation.docker_annotator)

E

empty() (TaskGraph method) end_position (Annotatable property) error (CacheRecord property)

execute() (TaskGraphExecutor method) (TaskGraphExecutorBase method) Exon (class in gain.genomic_resources.gene_models)

F

fetch() (ReferenceGenome method) fetch_records() (GenomicScore method) fetch_region_allele_arrays() (AlleleScore method) fetch_region_segments_scores() (GenomicScore method) fetch_region_value_arrays() (GenomicScore method) file_exists() (GenomicResource method) files (GeneScore property) (GeneSetCollection property) (GenomicResourceImplementation property) (LiftoverChain property) FileTaskCache (class in gain.task_graph.cache) find_resource() (GenomicResourceRepo method) fold() (Attribute method) fold_own_values() (in module gain.annotation.annotator_base) format_plan() (ReannotationPipeline method) FragmentAggregate (class in gain.genomic_resources.genomic_scores)

FragmentScore (class in gain.genomic_resources.genomic_scores) frame (Exon property) from_dict() (CategoricalHistogram static method) (CategoricalHistogramConfig static method) (NullHistogram static method) (NullHistogramConfig static method) (NumberHistogram static method) (NumberHistogramConfig static method) from_file_content() (Manifest static method) from_name() (AlleleScore.Mode static method) from_string() (Annotatable static method) (Annotatable.Type static method) (CNVAllele static method) (Position static method) (Region static method) (VCFAllele static method) from_transcript_models() (GeneModels class method)

G

gene_models_by_gene_name() (GeneModels method) gene_models_by_location() (GeneModels method) gene_names() (GeneModels method) GeneModels (class in gain.genomic_resources.gene_models) GeneScore (class in gain.gene_scores.gene_scores) GeneScoreDef (class in gain.gene_scores.gene_scores) GeneSet (class in gain.gene_sets.gene_set) GeneSetCollection (class in gain.gene_sets.gene_set) GenomicResource (class in gain.genomic_resources.repository) GenomicResourceImplementation (class in gain.genomic_resources.resource_implementation) GenomicResourceRepo (class in gain.genomic_resources.repository) GenomicScore (class in gain.genomic_resources.genomic_scores) GenomicScoreDef (class in gain.genomic_resources.score_def) get_all_chrom_lengths() (GenomicScore method) (ReferenceGenome method) get_all_chromosomes() (GenomicScore method) get_all_gene_sets() (GeneSetCollection method) get_all_resources() (GenomicResourceRepo method) get_allele_score_for_allele() (AlleleScore method) get_allele_score_for_allele_agg() (AlleleScore method) get_allele_score_for_allele_rows() (AlleleScore method) get_allele_score_in_region_rows() (AlleleScore method) get_allele_scores_for_allele() (AlleleScore method) get_allele_scores_for_allele_agg() (AlleleScore method) get_allele_scores_for_allele_rows() (AlleleScore method) get_allele_scores_in_region_agg() (AlleleScore method) get_allele_scores_in_region_rows() (AlleleScore method) get_annotator_by_attribute_info() (AnnotationPipeline method) get_annotator_factory() (in module gain.annotation.annotation_factory) get_attribute_defaults() (AnnotatorBase method) get_attribute_info() (AnnotationPipeline method) get_attribute_specs() (Annotator method) get_attributes() (AnnotationPipeline method) get_attributes_by_type() (AnnotationPipeline method) get_available_annotator_types() (in module gain.annotation.annotation_factory) get_chrom_length() (GenomicScore method) (ReferenceGenome method) get_chrom_length_source() (GenomicScore method) get_config() (GenomicResource method) (GenomicResourceImplementation method) (GenomicScore method) get_default_grr_definition() (in module gain.genomic_resources.repository_factory) get_default_grr_definition_path() (in module gain.genomic_resources.repository_factory) get_description() (GenomicResource method) get_file_content() (GenomicResource method) get_file_url() (GenomicResource method) get_files() (Manifest method) get_fragment_arrays_overlapping_region() (FragmentScore method) get_fragment_arrays_starting_in_region() (FragmentScore method) get_fragment_score_at_position() (FragmentScore method) get_fragment_score_overlapping_region() (FragmentScore method) get_fragment_score_overlapping_region_agg() (FragmentScore method) get_fragment_score_starting_in_region() (FragmentScore method) get_fragment_scores_at_position() (FragmentScore method) get_fragment_scores_overlapping_region() (FragmentScore method) get_fragment_scores_overlapping_region_agg() (FragmentScore method) get_fragment_scores_starting_in_region() (FragmentScore method) get_full_id() (GenomicResource method) get_gene_collection_count_statistics() (GeneSetCollection method) get_gene_set() (GeneSetCollection method)

get_gene_sets_list_statistics() (GeneSetCollection method) get_gene_sets_per_gene_hist() (GeneSetCollection method) get_gene_value() (GeneScore method) get_genes() (GeneScore method) get_genes_per_gene_set_hist() (GeneSetCollection method) get_genomic_context() (in module gain.genomic_resources.genomic_context) get_grr_from_context() (in module gain.genomic_resources.genomic_context) get_id() (GenomicResource method) get_info() (AnnotationPipeline method) (Annotator method) (GenomicResourceImplementation method) get_integer() (ParamsUsageMonitor method) get_labels() (GenomicResource method) get_loaded_manifest() (GenomicResource method) get_manifest() (GenomicResource method) get_max() (GeneScore method) get_meta() (GenomicResource method) get_min() (GeneScore method) get_number() (ParamsUsageMonitor method) get_public_url() (GenomicResource method) get_record() (FileTaskCache method) (NoTaskCache method) (TaskCache method) get_repo_public_url() (GenomicResource method) get_repo_url() (GenomicResource method) get_resource() (GenomicResourceRepo method) get_resource_ids() (AnnotationPipeline method) get_resource_implementation_builder() (in module gain.genomic_resources) get_schema() (AlleleScore static method) (FragmentScore static method) (GeneModels static method) (GeneScore static method) (LiftoverChain static method) (PositionScore static method) (ReferenceGenome static method) get_score_at_position() (PositionScore method) get_score_df() (GeneScore method) get_score_in_bins() (PositionScore method) get_score_in_region() (PositionScore method) get_score_in_region_agg() (PositionScore method) get_score_value_from_record() (GenomicScore method) get_scores_at_position() (PositionScore method) get_scores_in_bins() (FragmentScore method) (PositionScore method) get_scores_in_region() (PositionScore method) get_scores_in_region_agg() (PositionScore method) get_sequence() (ReferenceGenome method) get_statistics() (GenomicResourceImplementation method) get_statistics_info() (GenomicResourceImplementation method) get_summary() (GenomicResource method) get_task_desc() (TaskGraph method) get_type() (GenomicResource method) get_unused_keys() (ParamsUsageMonitor method) get_url() (GenomicResource method) get_used_keys() (ParamsUsageMonitor method) get_value_type() (Attribute method) get_values() (GeneScore method) get_version_str() (GenomicResource method) get_x_scale() (GeneScore method) get_y_scale() (GeneScore method)

H

has_chromosome() (GeneModels method) (GenomicScore method) has_task() (TaskGraph method) has_view_range() (NumberHistogramConfig method)

HISTOGRAM_COUNT_UNIT (AlleleScore attribute) (FragmentScore attribute) (GeneScore attribute) (PositionScore attribute)

I

inject() (ParamsUsageMonitor method) invalidate() (GenomicResourceRepo method) is_coding() (TranscriptModel method) is_loaded() (GeneModels method) (GeneSetCollection method)

is_open() (Annotator method) (GenomicScore method) (LiftoverChain method) (ReferenceGenome method) is_pseudoautosomal() (ReferenceGenome method)

J

join_gene_models() (GeneModels static method)

L

LiftoverChain (class in gain.genomic_resources.liftover_chain) load() (GeneModels method) (GeneSetCollection method) load_ann_data_from_resource() (in module gain.genomic_resources.ann_data_resource) load_ann_data_from_resource_id() (in module gain.genomic_resources.ann_data_resource)

load_data_frame_from_resource() (in module gain.genomic_resources.data_frame_resource) load_data_frame_from_resource_id() (in module gain.genomic_resources.data_frame_resource) load_histogram() (in module gain.genomic_resources.histogram) load_pipeline_from_file() (in module gain.annotation.annotation_factory) load_pipeline_from_file_or_resource() (in module gain.annotation.annotation_factory) load_pipeline_from_yaml() (in module gain.annotation.annotation_factory)

M

make_task() (TaskGraph static method) Manifest (class in gain.genomic_resources.repository) map_chromosome() (LiftoverChain static method) mean (NumberHistogram property) merge() (CategoricalHistogram method) (NullHistogram method) (NumberHistogram method)

moments (NumberHistogram property) moments_summary() (CategoricalHistogram method) (NullHistogram method) (NumberHistogram method) multiplicity (AlleleScore property)

N

names() (Manifest method) NoTaskCache (class in gain.task_graph.cache) NullHistogram (class in gain.genomic_resources.histogram)

NullHistogramConfig (class in gain.genomic_resources.histogram) NumberHistogram (class in gain.genomic_resources.histogram) NumberHistogramConfig (class in gain.genomic_resources.histogram)

O

open() (AnnotationPipeline method) (Annotator method) (AnnotatorBase method) (DockerAnnotator method) (GenomicScore method) (LiftoverChain method) (ReferenceGenome method)

open_bigwig_file() (GenomicResource method) open_fasta_file() (GenomicResource method) open_raw_file() (GenomicResource method) open_tabix_file() (GenomicResource method) open_vcf_file() (GenomicResource method)

P

ParamsUsageMonitor (class in gain.annotation.annotation_config) parse_array() (GenomicScoreDef method) parse_value() (GenomicScoreDef method) plot() (CategoricalHistogram method) (NullHistogram method) (NumberHistogram method) pos (AlleleEntry attribute) (Annotatable property)

pos_end (Annotatable property) position (Annotatable property) Position (class in gain.annotation.annotatable) PositionScore (class in gain.genomic_resources.genomic_scores) print() (AnnotationPipeline method) print_plan() (ReannotationPipeline method) process_graph() (TaskGraphCli static method) ProcessPoolTaskExecutor (class in gain.task_graph.process_pool_executor) prune() (TaskGraph method)

R

raw_values (CategoricalHistogram property) ReannotationPipeline (class in gain.annotation.annotation_pipeline) ref (AlleleEntry attribute) (VCFAllele property) reference (VCFAllele property) ReferenceGenome (class in gain.genomic_resources.reference_genome) Region (class in gain.annotation.annotatable) register_annotator_factory() (in module gain.annotation.annotation_factory) register_implementation() (in module gain.genomic_resources) reload_statistics() (GenomicResourceImplementation method) repo_id (GenomicResourceRepo property)

require_owner() (ScoreFilter method) resolve_aggregation_queries() (PositionScore method) resolve_attribute_parameter() (AnnotationPipeline method) resolve_input_gene_list() (AnnotatorBase static method) resolve_resource() (AnnotatorBase class method) resource_id (GeneModels property) (GenomicResourceImplementation property) (ReferenceGenome property) resource_ids (Annotator property) resources (Annotator property) result (CacheRecord property)

S

ScoreFilter (class in gain.genomic_resources.score_filter) search_resources() (GenomicResourceRepo method) search_resources_by_child() (GenomicResourceRepo method) select() (ScoreFilter method) SequentialExecutor (class in gain.task_graph.sequential_executor) serialize() (CategoricalHistogram method) (NullHistogram method) (NumberHistogram method) serialize_gzipped() (CategoricalHistogram method)

serialize_truncated() (CategoricalHistogram method) setup_client() (in module gain.dask.named_cluster) setup_client_from_config() (in module gain.dask.named_cluster) split_into_regions() (ReferenceGenome method) start (Exon property) std (NumberHistogram property) stop (Exon property) substitutions_mode() (AlleleScore method) supports_region_allele_arrays() (AlleleScore method) supports_region_value_arrays() (GenomicScore method)

T

Task (class in gain.task_graph.graph) task_graph_run() (in module gain.task_graph.cli_tools) task_graph_run_with_results() (in module gain.task_graph.cli_tools) TaskCache (class in gain.task_graph.cache) TaskDesc (class in gain.task_graph.graph) TaskGraph (class in gain.task_graph.graph) TaskGraphCli (class in gain.task_graph.cli_tools) TaskGraphExecutor (class in gain.task_graph.executor) TaskGraphExecutorBase (class in gain.task_graph.base_executor) tasks (TaskGraph property) test_frames() (TranscriptModel method) to_dict() (Annotatable method) (AnnotatorInfo method) (CategoricalHistogram method) (CategoricalHistogramConfig method) (CNVAllele method) (GeneScore method) (NullHistogram method) (NullHistogramConfig method) (NumberHistogram method) (NumberHistogramConfig method) (Position method) (Region method) (VCFAllele method)

to_tsv() (GeneScore method) tokenize() (Annotatable static method) topological_order() (TaskGraph method) total_count (CategoricalHistogram property) total_len() (TranscriptModel method) TranscriptModel (class in gain.genomic_resources.gene_models)

U

unique_values (CategoricalHistogram property) update_frames() (TranscriptModel method) used_context_attributes (Annotator property)

utr3_len() (TranscriptModel method) utr3_regions() (TranscriptModel method) utr5_len() (TranscriptModel method) utr5_regions() (TranscriptModel method)

V

values (AlleleEntry attribute) values_domain() (CategoricalHistogram method) (NullHistogram method) (NumberHistogram method)

VCFAllele (class in gain.annotation.annotatable) view_max() (NumberHistogram method) view_min() (NumberHistogram method)