carvemegut 0.3.3

A Python package for metabolic modeling

CarveMeGut

CarveMeGut is a Python package designed for metabolic model reconstruction and curation, particularly tailored for gut microbiome studies. It automates the process of extracting, curating, and refining genome-scale metabolic models using various datasets and computational methods.

Features

• Automated metabolic model reconstruction from genome sequences
• Integration with public metabolic databases
• Gap-filling for incomplete metabolic networks
• Support for various file formats (FASTA, SBML, etc.)
• CLI tools for streamlined workflows

Installation

CarveMeGut requires Python 3.7 or higher. Install it using pip:

pip install carvemegut

Alternatively, you can install the latest development version from GitHub:

git clone https://github.com/yourusername/carvemegut.git
cd carvemegut
pip install .

Usage

CLI Usage

CarveMeGut provides a command-line interface (CLI) for ease of use. After installation, you can use:

carvemegut build-universe --input genome.fasta --output model.xml

For a list of available commands:

carvemegut --help

Python API

You can also use CarveMeGut as a Python module:

import carvemegut

model = carvemegut.build_universe("genome.fasta")
model.save("model.xml")

Configuration

CarveMeGut allows customization through a configuration file (config.cfg). This file contains parameters for model reconstruction, database paths, and computational settings.

Data Sources

CarveMeGut integrates with multiple external metabolic databases, including:

• BiGG Models
• MetaNetX
• KEGG

Contributing

We welcome contributions! To contribute:

1. Fork the repository
2. Create a feature branch (git checkout -b feature-branch)
3. Commit changes (git commit -m "Add new feature")
4. Push to the branch (git push origin feature-branch)
5. Open a Pull Request

License

CarveMeGut is released under the MIT License.

Contact

For questions or issues, please open an issue on GitHub.