Blast+ must be installed. Check this page to download the version for your system.
python3 -m venv <path>/<to>/<environment>
pip3 install -r requirements.txt
You can see the help running:
python3 malivhu.py -h or python3 malivhu.py --help
The basic way to run the script is:
python3 malivhu.py -iv <input virus file path> -o <output directory path> -p <last phase to run>
If you're running up to the fourth phase, you also need to add the path to the human file:
python3 malivhu.py -iv <input virus file path> -ih <input human file path> -o <output directory path> -p 4
You can also run the fourth phase only by adding the -p4 or --phase4only flag and specifying what virus do the virus proteins belong to with the -v or --virus flag. It accepts 'cov1', 'cov2' and 'mers'.
python3 malivhu.py -iv <input virus file path> -ih <input human file path> -o <output directory path> -p 4 -p4 -v cov1