GenPPI Python Interface

A Python interface for GenPPI (Genomic-based Protein-Protein Interaction prediction).

Installation

From PyPI (Recommended)

pip install genppi-py

Windows Users - Important Notes

Python Version Requirements:

• Python 3.10 or higher is required
• Use only official Python from python.org
• Do NOT use Python from Microsoft Store (may cause compatibility issues)
• Ensure "Add Python to PATH" is checked during installation

Development Tools (if installation fails): Some Python packages require compilation. If you encounter errors, install:

• Microsoft C++ Build Tools from: https://developer.microsoft.com/en-us/windows/downloads/sdk-archive/
• Or Visual Studio Community with C++ support

Command Usage: After installation, use genppi command (not genppi.py).

From TestPyPI (Development)

pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ genppi-py

From Source

git clone https://github.com/santosardr/genppi.git
cd genppi
pip install .

Project Structure

genppi/
├── genppi_py/          # Main package code
├── docs/               # Documentation (LaTeX/PDF)
├── scripts/            # Development and deployment scripts
├── tests/              # Automated tests
├── tools/              # Development tools and configurations
├── README.md           # This file
├── setup.py            # Installation configuration
└── pyproject.toml      # Modern project configuration

For Developers

• docs/ - Technical documentation in LaTeX/PDF
• scripts/ - Scripts for build, test and deployment
• tests/ - Automated tests
• tools/ - Development tools and configurations

Usage

Command Line Interface

After installation, you can use GenPPI from the command line:

# Basic usage
genppi -dir /path/to/protein/files

# With gene fusion
genppi -dir /path/to/protein/files -genefusion

# Using machine learning
genppi -dir /path/to/protein/files -ml

Download Model and Samples

# Download machine learning model
genppi-download-model

# Download sample data
genppi-download-samples

Python API

from genppi_py.genppi import run_genppi

# Run GenPPI with arguments
run_genppi(['-dir', '/path/to/protein/files', '-genefusion'])

How it Works

When you install the package, it will:

1. Download the appropriate pre-compiled GenPPI executables for your operating system
2. Download and extract the machine learning model file (model.dat) using py7zr
3. Install the Python wrapper that provides a command-line interface

The package uses py7zr library exclusively for extracting multivolume 7z archives (model.7z.001, model.7z.002, model.7z.003).

Dependencies

• Python 3.10+ (minimum required version)
• py7zr >= 1.1.3 (for 7z extraction, resolving CVE-2026-23879)
• multivolumefile >= 0.2.3 (for multivolume support)

All dependencies are installed automatically.

Development

Quick Setup

# Clone repository
git clone https://github.com/santosardr/genppi.git
cd genppi

# Install development dependencies
pip install -r tools/requirements-dev.txt

# Install in development mode
pip install -e .

Development Scripts

# Quick check
python scripts/quick_check.py

# Build and test
python scripts/build_and_test.py

# Deploy to TestPyPI
python scripts/deploy_test.py

# Deploy to PyPI
python scripts/deploy_production.py

Running Tests

# Run all tests
python -m pytest tests/

# Run specific test
python tests/test_genppi.py

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.