MetExtract II - Python 3 Version

A comprehensive metabolite extraction and analysis tool, migrated from Python 2.7 to Python 3 with modern dependency management using UV.

Installation

Optional: Install uv

Please install uv. For instruction see https://docs.astral.sh/uv/getting-started/installation/

Clone MetExtract II

# Clone the repository
git clone https://github.com/chrboku/MetExtract-II
cd MetExtract-II

Setup virtual environment

uv sync

Quick Start

uv run python -m src.MExtract

Usage

Running the Applications

# Main application (MExtract) - Primary metabolite extraction interface
uv run python -m src.MExtract

# MetExtract II Main Interface - Alternative main interface
uv run python -m src.MetExtractII_Main

Module Descriptions

• MExtract: The primary GUI application for metabolite extraction and analysis
• MetExtractII_Main: Main interface for MetExtract II functionality
• FragExtract: Specialized tool for extracting and analyzing mass spectrometry fragments
• FTICRModule: Module for handling Fourier Transform Ion Cyclotron Resonance mass spectrometry data

Code Formatting

# Format code with Black
uvx ruff format

Migration Notes

This version has been migrated from Python 2.7 (published version) to Python 3.11+ with the following major changes:

Key Changes Made:

• Python 3 Compatibility: All Python 2.7 syntax updated to Python 3
• PyQt4 → PyQt5: GUI framework updated for modern compatibility
• Print Statements: All print statements converted to print() function calls
• Dictionary Methods: .has_key() replaced with in operator, .iteritems() with .items()
• String Handling: Unicode handling updated for Python 3
• Integer Division: Updated / to // where floor division intended
• Exception Handling: Modern except Exception as e: syntax
• Import System: Relative imports updated to absolute imports where needed

New Features:

• UV Package Management: Modern, fast dependency resolution and virtual environment management
• Type Hints: Gradual addition of type annotations
• Modern Setup: Uses pyproject.toml instead of setup.py
• Code Quality: Black formatting and linting support