Documentation for Annotation¶
cnv: CNVRegionAnnotation
instance-attribute
¶
count_gene_types()
¶
Count the number of genes of each type in GenesDB
Returns:
| Type | Description |
|---|---|
GenesDBGeneTypesCounter
|
A dictionary with the count of each gene type. |
count_regulatory_types()
¶
Count the number of regulatory element types in the database
Returns:
| Type | Description |
|---|---|
RegulatoryTypesCounter
|
A dictionary with the count of each regulatory type. |
Notes
The regulatory database entries are looped over and their "type" element is checked for presence in any of existing regulatory types.
Unknown regulatory types are counted as 'other'. To get a count of all regulatory types, sum the values.
get_annotated_genes()
¶
Get list of names for genes that are morbid or associated with a disease
Returns:
| Type | Description |
|---|---|
AnnotatedGenesList
|
Dictionary with two lists of gene names: 'morbid_genes' and 'associated_with_disease' |
get_benign_cnvs_gs_outer(frequency_threshold)
¶
Get Benign CNV GS outer entries with no defined frequency or higher than the threshold
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
frequency_threshold
|
float
|
Minimum frequency for a benign CNV GS outer entry to be considered |
required |
Returns:
| Type | Description |
|---|---|
list[dict[str, Any]]
|
List of benign CNV GS outer entries |
See Also
core.MIN_FREQUENCY_BENIGN Minimum frequency for a benign CNV GS outer entry to be considered
get_common_variability_regions()
¶
Get GnomAD regions that intersect with the CNV and are in the specified populations
Returns:
| Type | Description |
|---|---|
list[CommonVariabilityRegion]
|
List of common variability regions that intersect with the CNV |
See Also
core.POPULATION_FOR_COMMON_VARIABILITY List of populations for common variability core.COMMON_VARIABILITY_FREQUENCY_THRESHOLD Minimum frequency for a common variability region to be considered
get_gene_by_name(gene_name)
¶
Get 'Genes' entry with gene_name
get_gene_transcript_regions(gene_name)
¶
Get transcript regions for a gene
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
gene_name
|
str
|
Name of the gene |
required |
Returns:
| Type | Description |
|---|---|
list[TranscriptRegion]
|
List of transcript regions for the gene |
get_genes(gene_type=None, overlap=enums.Overlap.ANY)
¶
Get 'Genes' entries whose gene_type is 'gene_type' and overlaps the CNV region in that manner
get_haploinsufficient_gene_names(overlap_type, valid_scores)
¶
Get names of genes with sufficient Haploinsufficiency Score
get_haploinsufficient_genes(overlap_type, valid_scores)
¶
Get all HiGene entries with sufficient Haploinsufficiency Score
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
overlap_type
|
Overlap
|
Type of overlap to consider. |
required |
valid_scores
|
list[int]
|
List of valid scores to consider. Entry scores are coerced to integers. |
required |
Returns:
| Type | Description |
|---|---|
list[HiGeneEntry]
|
List of HiGene entries with sufficient Haploinsufficiency Score |
get_haploinsufficient_regions(overlap_type, valid_scores)
¶
Get all HiRegion entries with sufficient Haploinsufficiency Score
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
overlap_type
|
Overlap
|
Type of overlap to consider. |
required |
valid_scores
|
list[int]
|
List of valid scores to consider. Entry scores are coerced to integers. |
required |
Returns:
| Type | Description |
|---|---|
list[HiRegionEntry]
|
List of HiRegion entries with sufficient Haploinsufficiency Score |
get_high_risk_loss_genes()
¶
Get genes with high risk loss predictors
Raises:
| Type | Description |
|---|---|
HighRiskForDuplicationError
|
If the CNV region is a duplication, not a loss |
Returns:
| Type | Description |
|---|---|
list[dict[str, Any]]
|
List of genes with high risk loss predictors |
See Also
core.HIGH_RISK_PREDICTORS List of high risk predictors core.HIGH_RISK_PREDICTORS_COUNT_THRESHOLD Minimum number of high risk predictors for a gene to be considered high risk
get_triplosensitivity_gene_names(overlap_type, valid_scores)
¶
Get names of genes with sufficient Triplosensitivity Score
get_triplosensitivity_genes(overlap_type, valid_scores)
¶
Get all HiGene entries with sufficient Triplosensitivity Score
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
overlap_type
|
Overlap
|
Type of overlap to consider. |
required |
valid_scores
|
list[int]
|
List of valid scores to consider. Entry scores are coerced to integers. |
required |
Returns:
| Type | Description |
|---|---|
list[HiGeneEntry]
|
List of HiGene entries with sufficient Triplosensitivity Score |
get_triplosensitivity_regions(overlap_type, valid_scores)
¶
Get all HiRegion entries with sufficient Triplosensitivity Score
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
overlap_type
|
Overlap
|
Type of overlap to consider. |
required |
valid_scores
|
list[int]
|
List of valid scores to consider. Entry scores are coerced to integers. |
required |
Returns:
| Type | Description |
|---|---|
list[HiRegionEntry]
|
List of HiRegion entries with sufficient Triplosensitivity Score |
load_from_json(json_file)
classmethod
¶
Load annotation from a JSON file
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
json_file
|
str
|
Path to the JSON file. Can be gzipped. |
required |
Returns:
| Type | Description |
|---|---|
Annotation
|
Annotation object loaded from the JSON file. |
Raises:
| Type | Description |
|---|---|
FileNotFoundError
|
If the file does not exist. |
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