colordna

A Go command-line tool that colorizes DNA/RNA sequences and quality scores for better visualization in the terminal.

Features

• Multiple file format support: FASTA, FASTQ, SAM, VCF with automatic format detection
• Custom color schemes: Define your own color schemes or use built-in ones
• Quality score coloring: Gradient coloring for Phred quality scores in FASTQ/SAM files
• Pipe support: Works with standard input for streaming data processing

Installation

From Source

bash git clone https://github.com/benekenobi/colordna.git cd colordna go build -o colordna sudo mv colordna /usr/local/bin/

Using Go Install

bash go install github.com/benekenobi/colordna@latest

Development

```bash

Clone the repository

git clone https://github.com/benekenobi/colordna.git cd colordna

Download dependencies

go mod download

Build

go build -o colordna

Run tests

go test ./...

Format code

go fmt ./...

Vet code

go vet ./...

Install locally

go install ```

Usage

Basic Usage

```bash

Colorize a FASTA file

colordna sequences.fasta

Colorize a FASTQ file with quality scores

colordna reads.fastq

Use a specific color scheme

colordna --scheme classic sequences.fasta

Process multiple files

colordna file1.fasta file2.fastq file3.sam

Use with pipes

cat sequences.fasta | colordna samtools view alignment.bam | colordna ```

Command Options

-s, --scheme string Color scheme to use (default "bright") --config string Config file (default "~/.colordna.yaml") -v, --verbose Verbose output -h, --help Show help

Color Schemes

Built-in Schemes

1. bright (default): Font-only coloring with bright colors, no background

   • A: Bright red
   • T: Bright green
   • G: Bright yellow
   • C: Bright blue
   • U: Bright magenta
   • N: Dark gray

2. classic: Background coloring similar to original dnacol

   • Colored backgrounds with contrasting text

3. pastel: Light background colors with black text

4. monochrome: Text styling only (bold, italic, underline, etc.)

Custom Color Schemes

Edit ~/.colordna.yaml to add custom color schemes:

yaml color_schemes: my_custom: a: "\033[31m" # Red t: "\033[32m" # Green g: "\033[33m" # Yellow c: "\033[34m" # Blue u: "\033[35m" # Magenta "n": "\033[90m" # Dark gray quality: gradient # gradient, mono, or none background: false # Use background colors

Color Codes

Use ANSI escape sequences for colors:

Font Colors

• \033[31m - Red
• \033[32m - Green
• \033[33m - Yellow
• \033[34m - Blue
• \033[35m - Magenta
• \033[36m - Cyan
• \033[91m - Bright red
• \033[92m - Bright green
• etc.

Background Colors

• \033[41m - Red background
• \033[42m - Green background
• etc.

Text Styles

• \033[1m - Bold
• \033[2m - Dim
• \033[3m - Italic
• \033[4m - Underline

Acknowledgments

Inspired by the dnacol Python project by koelling.