iseqpharmgkb 0.0.9

Package for creating database from PharmGKB and querying for specific variant/allele

ISEQPHARMGKB

Scripts that allow you to:

1. Create databases (clinical and variant) from PharmGKB
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"
}