comparative-analysis-among-strains

Install environment

git clone https://github.com/SATAY-LL/comparative-analysis-among-strains.git 
cd Data-analysis-multiple-strains
conda env create --file environment.yml
conda activate satay-analysis

The pergene files must be tab separated instead of comma separated.

This is a bash code to convert comma separated files to tab separated files, if needed.

cat oldfile.txt | tr '[,]' '[\t]' > newfile.txt

To version control the notebooks for the analysis

1. Convert the modified notebooks to .py files with jupytext
   • jupytext --to py <your-notebook>.ipynb
2. Add and commit the .py files to the repository
   • git add <your-notebook>.py
   • git commit -m "<commit -message>"
3. Push the changes to the repository

This way of versioning the notebooks are taken from this blog Version Control With Jupyter Notebook.