Code Helper & Gene Sequence Analyzer

A comprehensive Python tool for analyzing DNA sequences from FASTA files. Features include ORF finding, codon usage analysis, and visualization.

🆕 Advanced Code Helper AI

New! We now include a powerful Streamlit web application that provides intelligent bioinformatics and coding assistance powered by OpenAI GPT-4!

• 🧬 Bioinformatics Support: FASTA, VCF, CSV analysis with AI-powered insights
• 💻 Coding Help: Code explanation, debugging, refactoring for Python, R, and more
• 📁 File Analysis: Automatic analysis of uploaded bioinformatics files
• 💬 Interactive Chat: Maintain conversation context for better assistance

➡️ See Advanced Code Helper AI Documentation

Quick Start

git clone https://github.com/JamieT18/code-helper.git
cd code-helper
pip install -r requirements.txt
streamlit run advanced_code_helper.py

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Features

• Robust FASTA parsing: Supports multiline sequences, ignores headers, handles whitespace and non-standard characters gracefully
• ORF finding: Identifies open reading frames (start/stop codons, configurable minimum length)
• Codon usage analysis: Frequency tables, visualization
• AI-powered code helper: Explains, debugs, refactors code snippets; answers bioinformatics questions
• File upload & analysis: Streamlit app analyzes FASTA, VCF, CSV, and script files
• Visualization: GC content plots, codon usage charts
• Modular architecture: Easily extend or modify components

Repository Contents

• gene_sequence_analyzer.py: Command-line tool for DNA sequence analysis
• advanced_code_helper.py: Streamlit web application for AI-powered bioinformatics and coding assistance
• requirements.txt: Python package dependencies
• ADVANCED_CODE_HELPER_README.md: Detailed documentation for the AI assistant app
• sample_sequence.fasta: Example FASTA file for testing

License

See LICENSE file for details.