GAIn Documentation
Contents:
Getting started on the web
Select annotation pipeline
Single annotation
Annotation jobs
Custom annotation pipeline
Getting started on CLI
Prerequisites
Installation
Browse available resources
Quick annotation test
Custom annotation pipelines
Using the VEP effect annotator
Caching resources
Parallelizing large annotation jobs
Annotating VCF input
Annotating positions and regions
Adding public GRRs
Adding local GRRs
Reannotation
Getting started with GRR
Create your first GRR
Connect the local GRR to GAIn
Add new resources to the local GRR
1: Toy genome
2: Genome (GRCh38.p14)
3: Gene models (MANE v1.4)
4: Toy position score
5: Position score (PhyloP7)
6: Toy allele score
7: Allele score (AlphaMissense)
8: Toy gene score
9: Gene score (pLI)
10: Toy gene sets
11: Gene sets (MSigDB)
12: Toy fragment score
13: Fragment score (Iossifov 2021)
Browse the local GRR
Annotate using the local GRR
mini-GRR: a template GRR
Genomic resources and repositories
Repository discovery
Repository configuration
Common fields
Repository types
Repository caching
Complete GRR definition example
Repository management
grr_manage
Rebuilding on demand:
--force
and
--dry-run
grr_browse
Searching resources
The search index
Indexed fields
Searching by label
List-valued labels
Limitations
Version control for GRRs
Initializing version control
Adding a resource to version control
Metadata-only updates
Genomic resource configuration
Genomes
Gene models
Liftover chains
Annotation pipelines
Position scores
table
scores
default_annotation
Score value types
Allele scores
Fragment scores
Gene scores
Gene set collections
Histogram configuration
VCF score auto-detection
Tabix indexing
GRR configuration files
How the CLI tools find the configuration
Configuration file structure
Common fields
Repository types
Search order
Resource caching
A complete annotated example
Annotation infrastructure
Annotation pipelines
Preamble
Annotators
Score annotators
position_score_annotator
allele_score_annotator
gene_score_annotator
Effect annotators
effect_annotator
simple_effect_annotator
Transforming annotators
liftover_annotator
normalize_allele_annotator
chrom_mapping
fragment_score_annotator
Requiring a substantial overlap
gene_set_annotator
spliceai_annotator
VEP annotators
vep_full_annotator
vep_effect_annotator
Command line tools
Notes on usage
annotate_tabular
annotate_vcf
annotate_doc
Example annotations
1: Effect annotation
2: Position score annotation
3: Allele score annotation
4: Gene score annotation
5: Liftover annotation
6. Fragment score annotation (CNVs)
7: Gene set annotation
Binning position scores with
binning_tool
The run definition
Reference genome
Bins
Binner entries
Track names
Coordinates and the grid
Running the tool
Dry run
Parallelism
Work directory and reruns
The output file
Reading the file back
A worked example
GAIn Web interface
Create annotation pipelines
Add annotators
Add resources
Registration and user accounts
Annotators Plugin Library
GAIn Python interface
1: Chromosome lengths
2: Position scores across a gene
3: Resource counts by genome
4: Annotating variants in Python
5: Creating an annotator plugin
GAIn Development
Working with resources in Python
Where the line falls
The shape of the API
Repositories and resources
Reference genomes
Gene models
Scores
Histograms
Adding a resource type
Not covered here
Complete module index
gain package
Subpackages
Submodules
gain.logging module
Module contents
Release Notes
GAIn Documentation
Index
Index
A
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B
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C
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D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
A
add() (gain.genomic_resources.repository.Manifest method)
add_batch() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.NumberHistogram method)
add_value() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.NullHistogram method)
(gain.genomic_resources.histogram.NumberHistogram method)
aggregate_region() (gain.genomic_resources.genomic_scores.GenomicScore method)
all_regions() (gain.genomic_resources.gene_models.TranscriptModel method)
AlleleAggregate (class in gain.genomic_resources.genomic_scores)
alleles_mode() (gain.genomic_resources.genomic_scores.AlleleScore method)
AlleleScore (class in gain.genomic_resources.genomic_scores)
AlleleScore.Mode (class in gain.genomic_resources.genomic_scores)
B
build_gene_models_from_resource_id() (in module gain.genomic_resources.gene_models)
build_genomic_resource_repository() (in module gain.genomic_resources.repository_factory)
build_reference_genome_from_resource_id() (in module gain.genomic_resources.reference_genome)
build_score_from_resource_id() (in module gain.genomic_resources.genomic_scores)
C
calc_frames() (gain.genomic_resources.gene_models.TranscriptModel method)
calc_info_hash() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
calc_statistics_hash() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
CategoricalHistogram (class in gain.genomic_resources.histogram)
CategoricalHistogramConfig (class in gain.genomic_resources.histogram)
cds_len() (gain.genomic_resources.gene_models.TranscriptModel method)
cds_regions() (gain.genomic_resources.gene_models.TranscriptModel method)
choose_bin_lin() (gain.genomic_resources.histogram.NumberHistogram method)
choose_bin_log() (gain.genomic_resources.histogram.NumberHistogram method)
chrom_length_source (gain.genomic_resources.genomic_scores.GenomicScore property)
chrom_prefix (gain.genomic_resources.reference_genome.ReferenceGenome property)
chromosomes (gain.genomic_resources.reference_genome.ReferenceGenome property)
close() (gain.genomic_resources.gene_models.GeneModels method)
(gain.genomic_resources.genomic_scores.GenomicScore method)
(gain.genomic_resources.reference_genome.ReferenceGenome method)
(gain.genomic_resources.repository.GenomicResourceRepo method)
collect_index_info() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
compile_filter() (gain.genomic_resources.genomic_scores.GenomicScore method)
contains() (gain.genomic_resources.gene_models.Exon method)
create_statistics_build_tasks() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
D
default_config() (gain.genomic_resources.histogram.CategoricalHistogramConfig static method)
(gain.genomic_resources.histogram.NullHistogramConfig static method)
(gain.genomic_resources.histogram.NumberHistogramConfig static method)
definition (gain.genomic_resources.repository.GenomicResourceRepo property)
deserialize() (gain.genomic_resources.histogram.CategoricalHistogram static method)
(gain.genomic_resources.histogram.NullHistogram static method)
(gain.genomic_resources.histogram.NumberHistogram static method)
display_values (gain.genomic_resources.histogram.CategoricalHistogram property)
E
Exon (class in gain.genomic_resources.gene_models)
F
fetch() (gain.genomic_resources.reference_genome.ReferenceGenome method)
fetch_allele_records() (gain.genomic_resources.genomic_scores.AlleleScore method)
fetch_allele_scores() (gain.genomic_resources.genomic_scores.AlleleScore method)
fetch_fragment_scores() (gain.genomic_resources.genomic_scores.FragmentScore method)
fetch_records() (gain.genomic_resources.genomic_scores.GenomicScore method)
fetch_region_allele_arrays() (gain.genomic_resources.genomic_scores.AlleleScore method)
fetch_region_segments_scores() (gain.genomic_resources.genomic_scores.GenomicScore method)
fetch_region_value_arrays() (gain.genomic_resources.genomic_scores.GenomicScore method)
file_exists() (gain.genomic_resources.repository.GenomicResource method)
files (gain.genomic_resources.resource_implementation.GenomicResourceImplementation property)
find_resource() (gain.genomic_resources.repository.GenomicResourceRepo method)
FragmentAggregate (class in gain.genomic_resources.genomic_scores)
FragmentScore (class in gain.genomic_resources.genomic_scores)
from_dict() (gain.genomic_resources.histogram.CategoricalHistogram static method)
(gain.genomic_resources.histogram.CategoricalHistogramConfig static method)
(gain.genomic_resources.histogram.NullHistogram static method)
(gain.genomic_resources.histogram.NullHistogramConfig static method)
(gain.genomic_resources.histogram.NumberHistogram static method)
(gain.genomic_resources.histogram.NumberHistogramConfig static method)
from_file_content() (gain.genomic_resources.repository.Manifest static method)
from_manifest_entries() (gain.genomic_resources.repository.Manifest static method)
G
gene_models_by_gene_name() (gain.genomic_resources.gene_models.GeneModels method)
gene_models_by_location() (gain.genomic_resources.gene_models.GeneModels method)
gene_names() (gain.genomic_resources.gene_models.GeneModels method)
GeneModels (class in gain.genomic_resources.gene_models)
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() (gain.genomic_resources.reference_genome.ReferenceGenome method)
get_all_chromosomes() (gain.genomic_resources.genomic_scores.GenomicScore method)
get_all_resources() (gain.genomic_resources.repository.GenomicResourceRepo method)
get_allele_scores_in_region_agg() (gain.genomic_resources.genomic_scores.AlleleScore method)
get_chrom_length() (gain.genomic_resources.reference_genome.ReferenceGenome method)
get_config() (gain.genomic_resources.genomic_scores.GenomicScore method)
(gain.genomic_resources.repository.GenomicResource method)
(gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
get_default_annotation_attribute() (gain.genomic_resources.genomic_scores.GenomicScore method)
get_default_annotation_attributes() (gain.genomic_resources.genomic_scores.GenomicScore method)
get_description() (gain.genomic_resources.repository.GenomicResource method)
get_file_content() (gain.genomic_resources.repository.GenomicResource method)
get_file_url() (gain.genomic_resources.repository.GenomicResource method)
get_files() (gain.genomic_resources.repository.Manifest method)
get_fragment_score_at_position() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_score_overlapping_region() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_score_overlapping_region_agg() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_score_starting_in_region() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_scores_at_position() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_scores_overlapping_region() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_scores_overlapping_region_agg() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_fragment_scores_starting_in_region() (gain.genomic_resources.genomic_scores.FragmentScore method)
get_full_id() (gain.genomic_resources.repository.GenomicResource method)
get_id() (gain.genomic_resources.repository.GenomicResource method)
get_info() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
get_labels() (gain.genomic_resources.repository.GenomicResource method)
get_loaded_manifest() (gain.genomic_resources.repository.GenomicResource method)
get_manifest() (gain.genomic_resources.repository.GenomicResource method)
get_memo_key() (gain.genomic_resources.repository.GenomicResource method)
get_meta() (gain.genomic_resources.repository.GenomicResource method)
get_public_url() (gain.genomic_resources.repository.GenomicResource method)
get_repo_public_url() (gain.genomic_resources.repository.GenomicResource method)
get_repo_url() (gain.genomic_resources.repository.GenomicResource method)
get_resource() (gain.genomic_resources.repository.GenomicResourceRepo method)
get_resource_implementation_builder() (in module gain.genomic_resources)
get_schema() (gain.genomic_resources.gene_models.GeneModels static method)
(gain.genomic_resources.genomic_scores.AlleleScore static method)
(gain.genomic_resources.genomic_scores.FragmentScore static method)
(gain.genomic_resources.genomic_scores.GenomicScore static method)
(gain.genomic_resources.genomic_scores.PositionScore static method)
(gain.genomic_resources.reference_genome.ReferenceGenome static method)
get_score_at_position() (gain.genomic_resources.genomic_scores.PositionScore method)
get_score_in_bins() (gain.genomic_resources.genomic_scores.PositionScore method)
get_score_in_region() (gain.genomic_resources.genomic_scores.PositionScore method)
get_score_in_region_agg() (gain.genomic_resources.genomic_scores.PositionScore method)
get_score_value_from_record() (gain.genomic_resources.genomic_scores.GenomicScore method)
get_score_values_from_record() (gain.genomic_resources.genomic_scores.GenomicScore method)
get_scores_at_position() (gain.genomic_resources.genomic_scores.PositionScore method)
get_scores_in_bins() (gain.genomic_resources.genomic_scores.PositionScore method)
get_scores_in_region() (gain.genomic_resources.genomic_scores.PositionScore method)
get_scores_in_region_agg() (gain.genomic_resources.genomic_scores.PositionScore method)
get_sequence() (gain.genomic_resources.reference_genome.ReferenceGenome method)
get_statistics() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
get_statistics_info() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
get_summary() (gain.genomic_resources.repository.GenomicResource method)
get_type() (gain.genomic_resources.repository.GenomicResource method)
get_url() (gain.genomic_resources.repository.GenomicResource method)
get_version_str() (gain.genomic_resources.repository.GenomicResource method)
H
has_chromosome() (gain.genomic_resources.gene_models.GeneModels method)
(gain.genomic_resources.genomic_scores.GenomicScore method)
has_view_range() (gain.genomic_resources.histogram.NumberHistogramConfig method)
I
invalidate() (gain.genomic_resources.repository.GenomicResource method)
(gain.genomic_resources.repository.GenomicResourceRepo method)
is_coding() (gain.genomic_resources.gene_models.TranscriptModel method)
is_loaded() (gain.genomic_resources.gene_models.GeneModels method)
is_open() (gain.genomic_resources.genomic_scores.GenomicScore method)
(gain.genomic_resources.reference_genome.ReferenceGenome method)
is_pseudoautosomal() (gain.genomic_resources.reference_genome.ReferenceGenome method)
J
join_gene_models() (gain.genomic_resources.gene_models.GeneModels static method)
L
load() (gain.genomic_resources.gene_models.GeneModels method)
load_histogram() (in module gain.genomic_resources.histogram)
M
Manifest (class in gain.genomic_resources.repository)
merge() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.NullHistogram method)
(gain.genomic_resources.histogram.NumberHistogram method)
N
names() (gain.genomic_resources.repository.Manifest method)
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() (gain.genomic_resources.genomic_scores.GenomicScore method)
(gain.genomic_resources.reference_genome.ReferenceGenome method)
open_bigwig_file() (gain.genomic_resources.repository.GenomicResource method)
open_fasta_file() (gain.genomic_resources.repository.GenomicResource method)
open_raw_file() (gain.genomic_resources.repository.GenomicResource method)
open_tabix_file() (gain.genomic_resources.repository.GenomicResource method)
open_vcf_file() (gain.genomic_resources.repository.GenomicResource method)
P
parse_array() (gain.genomic_resources.score_def.GenomicScoreDef method)
parse_value() (gain.genomic_resources.score_def.GenomicScoreDef method)
plot() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.NullHistogram method)
(gain.genomic_resources.histogram.NumberHistogram method)
PositionScore (class in gain.genomic_resources.genomic_scores)
R
raw_values (gain.genomic_resources.histogram.CategoricalHistogram property)
record_weight() (gain.genomic_resources.genomic_scores.AlleleScore class method)
(gain.genomic_resources.genomic_scores.FragmentScore class method)
(gain.genomic_resources.genomic_scores.GenomicScore class method)
(gain.genomic_resources.genomic_scores.PositionScore class method)
record_weights() (gain.genomic_resources.genomic_scores.GenomicScore class method)
ReferenceGenome (class in gain.genomic_resources.reference_genome)
region_values_from_records() (gain.genomic_resources.genomic_scores.GenomicScore method)
register_implementation() (in module gain.genomic_resources)
reload_statistics() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method)
repo_id (gain.genomic_resources.repository.GenomicResourceRepo property)
require_owner() (gain.genomic_resources.score_filter.ScoreFilter method)
resolve_aggregation_queries() (gain.genomic_resources.genomic_scores.AlleleScore method)
(gain.genomic_resources.genomic_scores.PositionScore method)
resolve_allele_key_scores() (gain.genomic_resources.genomic_scores.AlleleScore method)
resource_files() (gain.genomic_resources.genomic_scores.GenomicScore method)
resource_id (gain.genomic_resources.gene_models.GeneModels property)
(gain.genomic_resources.reference_genome.ReferenceGenome property)
(gain.genomic_resources.resource_implementation.GenomicResourceImplementation property)
S
ScoreFilter (class in gain.genomic_resources.score_filter)
search_resources() (gain.genomic_resources.repository.GenomicResourceRepo method)
search_resources_by_child() (gain.genomic_resources.repository.GenomicResourceRepo method)
select() (gain.genomic_resources.score_filter.ScoreFilter method)
serialize() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.NullHistogram method)
(gain.genomic_resources.histogram.NumberHistogram method)
serialize_truncated() (gain.genomic_resources.histogram.CategoricalHistogram method)
split_into_regions() (gain.genomic_resources.reference_genome.ReferenceGenome method)
substitutions_mode() (gain.genomic_resources.genomic_scores.AlleleScore method)
supports_region_allele_arrays() (gain.genomic_resources.genomic_scores.AlleleScore method)
supports_region_value_arrays() (gain.genomic_resources.genomic_scores.GenomicScore method)
T
test_frames() (gain.genomic_resources.gene_models.TranscriptModel method)
to_dict() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.CategoricalHistogramConfig method)
(gain.genomic_resources.histogram.NullHistogram method)
(gain.genomic_resources.histogram.NullHistogramConfig method)
(gain.genomic_resources.histogram.NumberHistogram method)
(gain.genomic_resources.histogram.NumberHistogramConfig method)
to_manifest_entries() (gain.genomic_resources.repository.Manifest method)
total_count (gain.genomic_resources.histogram.CategoricalHistogram property)
total_len() (gain.genomic_resources.gene_models.TranscriptModel method)
TranscriptModel (class in gain.genomic_resources.gene_models)
U
unique_values (gain.genomic_resources.histogram.CategoricalHistogram property)
update() (gain.genomic_resources.repository.Manifest method)
update_frames() (gain.genomic_resources.gene_models.TranscriptModel method)
utr3_len() (gain.genomic_resources.gene_models.TranscriptModel method)
utr3_regions() (gain.genomic_resources.gene_models.TranscriptModel method)
utr5_len() (gain.genomic_resources.gene_models.TranscriptModel method)
utr5_regions() (gain.genomic_resources.gene_models.TranscriptModel method)
V
values_domain() (gain.genomic_resources.histogram.CategoricalHistogram method)
(gain.genomic_resources.histogram.NullHistogram method)
(gain.genomic_resources.histogram.NumberHistogram method)
view_max() (gain.genomic_resources.histogram.NumberHistogram method)
view_min() (gain.genomic_resources.histogram.NumberHistogram method)