This repository contains all data used and all figures generated in the study to build bedaquilne catalogues containing minor alleles.
To run the notebooks you will first have to clone the repository via
git clone git@github.com:fowler-lab/tb-bdq-cat.git
Navigate into project directory and setup an environment either with conda or pip:
conda env create -f env.yml
conda activate BDQ_env
or
python -m venv bdq_venv
source bdq_venv/bin/activate (On Windows, use: venv\Scripts\activate)
pip install -r requirements.txt
The methods.ipynb, results.ipynb, and supplement.ipynb notebooks correspond to the methods, sections, and supplementary sections in the manuscript. Notebook cells are presented in a similar order and structure as the manuscript.
All generated catalogues can be found in the catalogues folder and can all be parsed by Piezo. Catalogue naming (ie catomatic_1.csv) correspond to the catalogue names in the manuscript, and can be cross referenced.
All data used to build and test the catalogues can be found in the data/ directory.
While results.ipynb does itself act as a demo on how to use catomatic's Python interface, a dedicated demo notebook can also be found in the package repository, and a CLI demo in the repository's readme (github.com/fowlerlab/catomatic).