GIMS Parsing

Parse GIMS 📄 PDF-based PGx reports to stuctured ⭐ star alleles.

The parse.py script reads all PDF files provided in the data directory and creates JSON files containing star allele information in the results directory.

Docker Setup

• Clone this repo and start a terminal in the repository directory
• Build the Docker image docker build -t gims-parsing .
• Run the script using Docker docker run -v $(pwd):/gims-parsing gims-parsing python3 parse.py

Manual Setup

Of course you can also setup everything without Docker and execute the parse.py script; please refer to the Dockerfile for required packages.