ISEQPHARMGKB
Scripts that allow you to:
- Create databases (clinical and variant) from PharmGKB
- Get clinical or variant annotations from PharmGKB for own queries
Install iseqpharmgkb library
Optional steps (create virtual environment):
python3 -m venv venv
source venv/bin/activate
Obligatory steps:
python3 -m pip install --upgrade pip
pip install iseqpharmgkb
Requirements
- python >=3.6
- pandas >= 1.2.4
- requests >= 2.22.0
- SQLAlchemy >= 1.3.17
Create databases
create_database
Get clinical annotations
get_clinical_annotation --queries /path/to/query.json --output-filename /output/filename.json
An example query.json file should look like this:
{
"rs1050828": "CC",
"rs5030868": "CC",
"CYP2D6*2": "*2",
"CYP2D6*1": "*1/*1"
}
Get variant annotations
get_variant_annotation --queries /path/to/query.json --output-filename /output/filename.json
An example query.json file should look like this:
{
"rs1050828": "CC",
"rs5030868": "CC",
"CYP2D6*2": "*2",
"CYP2D6*1": "*1/*1"
}
1 maintainer
Metadata
1 maintainer
Release files for iseqpharmgkb 0.0.9
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| File | Size | Uploaded | Provenance | |
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| iseqpharmgkb-0.0.9.tar.gz | 9.1 kB | Without provenance | Details |
Release files / iseqpharmgkb-0.0.9.tar.gz
| Download URL | iseqpharmgkb-0.0.9.tar.gz |
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| Size | 9.1 kB |
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