Update phenopacket
create_updated_phenopacket(gene_identifier, phenopacket_path, output_dir)
Update the gene context within the interpretations for a Phenopacket and writes the updated Phenopacket.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gene_identifier |
str
|
Identifier used to update the gene context. |
required |
phenopacket_path |
Path
|
The path to the input Phenopacket file. |
required |
output_dir |
Path
|
The directory where the updated Phenopacket will be written. |
required |
Notes
The gene_identifier parameter should be chosen from ensembl_id, hgnc_id, or entrez_id to update to the current gene identifier in the Phenopacket. We recommend using the ENSEMBL namespace to describe the gene identifiers.
Source code in src/pheval/prepare/update_phenopacket.py
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create_updated_phenopackets(gene_identifier, phenopacket_dir, output_dir)
Update the gene context within the interpretations for a directory of Phenopackets and writes the updated Phenopackets.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gene_identifier |
str
|
Identifier used to update the gene context. |
required |
phenopacket_dir |
Path
|
The path to the input Phenopacket directory. |
required |
output_dir |
Path
|
The directory where the updated Phenopackets will be written. |
required |
Notes
The gene_identifier parameter should be chosen from ensembl_id, hgnc_id, or entrez_id to update to the current gene identifier in the Phenopacket. We recommend using the ENSEMBL namespace to describe the gene identifiers.
Source code in src/pheval/prepare/update_phenopacket.py
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update_outdated_gene_context(phenopacket_path, gene_identifier, hgnc_data)
Update the gene context of the Phenopacket.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
phenopacket_path |
Path
|
The path to the Phenopacket file. |
required |
gene_identifier |
str
|
Identifier to update the gene context. |
required |
hgnc_data |
defaultdict
|
The HGNC data used for updating. |
required |
Returns:
Type | Description |
---|---|
Union[Phenopacket, Family]
|
Union[Phenopacket, Family]: The updated Phenopacket or Family. |
Notes
This function updates the gene context within the Phenopacket or Family instance. The gene_identifier parameter should be chosen from ensembl_id, hgnc_id, or entrez_id to update to the current gene identifier in the Phenopacket. We recommend using the ENSEMBL namespace to describe the gene identifiers.
Source code in src/pheval/prepare/update_phenopacket.py
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update_phenopackets(gene_identifier, phenopacket_path, phenopacket_dir, output_dir)
Update the gene identifiers in either a single phenopacket or a directory of phenopackets.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gene_identifier |
str
|
The gene identifier to be updated. |
required |
phenopacket_path |
Path
|
The path to a single Phenopacket file. |
required |
phenopacket_dir |
Path
|
The directory containing multiple Phenopacket files. |
required |
output_dir |
Path
|
The output directory to save the updated Phenopacket files. |
required |
Notes
The gene_identifier parameter should be chosen from ensembl_id, hgnc_id, or entrez_id to update to the current gene identifier in the Phenopacket. We recommend using the ENSEMBL namespace to describe the gene identifiers.
Source code in src/pheval/prepare/update_phenopacket.py
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