pharmvar-tools 0.5.0

Python tools to work with Pharmvar data.

Introduction

Set of tools to work with pharmvar data.

Installation (Linux)

python3 -m venv
source venv/bin/activate
pip install -r requirements.txt

Installation (Windows)

1. Install Windows subsystem for Linux (WSL).

wsl --install

2. Navigate to the repository and install the Linux/Python dependencies.

cd /mnt/c/[path]/pharmvar-tools

sudo apt update
sudo apt upgrade
sudo apt install python3.10-venv python-is-python3 python3-pip

sudo python -m venv venv
source ./venv/bin/activate
python -m pip install -r requirements.txt

Data requirements

For each gene of interest the sequence fasta of the NC and the NG should be downloaded (from the NCBI) into the data/ directory, e.g., data/NC_000022.11.fasta and data/NG_008376.4.fasta for CYP2D6.

In addition, for the check functionality, also the complete download zipfile from pharmvar is required. It needs to be unzipped in the data directory, e.g., the fasta file for CYP2D6 should be located in data/pharmvar-5.2.19/CYP2D6/CYP2D6.haplotypes.fasta.

Usage

Pharmvar data consistency check

python check.py --gene CYP2D6 --all

Calculating relations between alleles and variants based on variant algebra

python compare.py --gene CYP2D6 > data/pharmvar_5.2.19_CYP2D6_relations.txt

Visualizing relations

Requires graphviz (sudo apt install graphviz).

python to_dot.py --gene CYP2D6 < data/pharmvar_5.2.19_CYP2D6_relations.txt | fdp -Tpdf > /tmp/CYP2D6.pdf