mvgem is a tiny CLI application to convert between Genome-scale Metabolic formats.

1. Clone this repository:

git clone https://github.com/carrascommj/mvgem.git
cd mvgem

2. Install the requirements:

pip install -r requirements.txt

3. Put the script under your path. For instance:

mv mvgem.py ~/.local/bin/mvgem

Personally, I prefer to remove the extension.

All of these packages are specified in the requirements file with pinned versions:

• click: CLI package.
• cobra: IO operations.
• scipy: required to handle matlab format.

Usage: mvgem.py [OPTIONS] INPUT_MODEL OUTPUT_MODEL

Convert GEM format INPUT_MODEL to OUTPUT_MODEL.

The format will be infered based on the extension of OUTPUT_MODEL.
Supported formats: .sbml, .xml, .json, .mat.

Options:
  --help  Show this message and exit.