Setup

To install conda environment for our parsing, run

conda env create -f amrenv.yml
conda activate amrenv

Testing

To use test data, run

AMR_TEST=test python clean.py

Preparing antibiogram from messy data

Parsing chevron files and create antibiogram

Create a symbolic link to our lab data to ../input_data

Download latest revision of the lookup table chevron-lookup-table as an xls to that directory.

Run script

./run.sh

or just execute commands from there