DNA Helix Visualizer

A simple tool for visualizing DNA sequences in both 2D and 3D, with support for interactive exploration. This project provides multiple visualization methods including static 2D/3D renders and interactive molecular viewing.

Features

• 2D DNA helix visualization using Matplotlib
• 3D static visualization using PyVista
• Interactive 3D visualization using py3Dmol
• Support for AncestryDNA data format
• Color-coded base pairs (A, T, C, G)
• Multiple output formats (PNG, interactive)
• Configurable visualization parameters
• Multi-threaded processing for large datasets

Example interactive view

Installation

Create and activate a virtual environment:

python3 -m venv venv
source venv/bin/activate
pip3 install numpy matplotlib pyvista pyyaml nglview mdtraj biopython py3dmol jupyter

Project structure

dna-visualizer/
├── config/
│   └── settings.yaml
├── helix_drawer.py
├── view_dna.ipynb
├── output/
└── README.md

Configuration

Create config/settings.yaml with:

dna_file_path: "path/to/your/dna_data.txt"
base_pairs: 200
output_path: "output"

Usage

Static Visualizations Generate both 2D and 3D static visualizations:

python3 helix_drawer.py

Interactive Visualization

jupyter notebook

Open view_dna.ipynb Run all cells to see the interactive 3D visualization

Input Data Format

The DNA input file should be tab-separated with these columns:

• Chromosome
• Position
• rsid
• Genotype

Example Data

1   752721  rs3131972   AG
1   776546  rs12124819  AA
1   832918  rs4040617   GA

Output Files

The program generates:

• dna_helix_[timestamp].png: 2D visualization
• dna_helix_3d_[timestamp].png: 3D static visualization
• Interactive 3D model in Jupyter notebook

Color Coding

Base pairs are represented with distinct colors:

• Adenine (A): Red
• Thymine (T): Blue
• Cytosine (C): Green
• Guanine (G): Yellow

Requirements

• Python 3.8+
• Modern web browser for interactive visualization
• 2GB RAM minimum
• Graphics support for 3D rendering

Testing and Development

Test Data Generation

The project includes a test data generator that creates synthetic DNA data files in AncestryDNA format. Located in tests/generate_test_data.py: The generator creates realistic test data with:

• Random chromosomes (1-22, X, Y, MT)
• Valid position values
• Random rsid values
• Valid base pair combinations

Test Files Structure

tests/
├── generate_test_data.py
├── test_ancestry_data.txt
└── large_test_ancestry_data

To use the test data generator, run:

python3 -m tests.generate_test_data

This will create a test file with 500,000 DNA entries, perfect for testing the visualization features without requiring real genetic data.