dnaviz 0.2.0

A package for DNA/RNA visualization

DNAviz 🧬

An simple interactive DNA/RNA sequence visualization tool. Useful to check the structures or binding of complex sequences to ensure the correct pairing.

Features

• 🧬 Interactive DNA/RNA sequence visualization
• 🔄 Real-time base pairing detection
• 🖱️ Drag-and-drop base manipulation
• 📏 Dynamic scaling with grid snapping
• 💾 Save/load visualization states
• 📸 Export as PNG

Installation

pip install dnaviz

Quick Start

# Basic DNA sequence visualization
dnaviz ATGC GCTA

# RNA sequence with specified directions
dnaviz AUGC GCAU -d 53 -d 35

# Multiple strands
dnaviz ATGC GCTA TACG -d 53 -d 35 -d 53

Interactive Controls

Mouse Controls

• Click and Drag: Move bases
• Shift + Click: Select multiple bases
• Click and Drag Scale Bar: Adjust visualization scale
• Click and Drag Empty Space: Selection box

Keyboard Shortcuts

• Arrow Keys: Scroll the view
• R: Reset selected strand positions
• Cmd/Ctrl + S: Save current state
• Shift + Cmd/Ctrl + S: Save as PNG
• Cmd/Ctrl + L: Load last saved state
• ESC: Quit

File Management

• Save files are stored in ~/.dna_visualizer/
• PNG exports include timestamps
• State files are saved as JSON with timestamps

Base Pairing Rules

• A pairs with T (DNA) or U (RNA)
• G pairs with C
• Correct pairing is shown in green
• Incorrect direction pairing is shown in orange
• Unpaired bases are shown in gray

Examples

Basic DNA Visualization

dnaviz ATGC GCTA

RNA Sequence

dnaviz AUGC GCAU

Multiple Strands with Directions

dnaviz ATGC GCTA TACG -d 53 -d 35 -d 53

JavaScript Version

There is a JavaScript version of the visualizer available in the web_visualizer.html file. This version is not as feature-rich as the Python version, but it can be useful for quick visualizations or for sharing visualizations with others.

To use the JavaScript version, simply open the web_visualizer.html file in your browser. You can then enter sequences and directions, and the visualizer will update in real-time.