# ISEQPHARMGKB
Scripts that allow you to:
1) Create databases (clinical and variant) from [PharmGKB](https://www.pharmgkb.org/)
2) 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"
}
```
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