Helix 🧬

A lightweight functional programming-inspired bioinformatics library for Scala 3.
Helix makes it easy to work with DNA sequences, including validation, nucleotide counting, and random sequence generation, all in a clean and expressive way.

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✨ Features

• ✅ Validate DNA sequences
• ✅ Convert DNA from/to strings
• ✅ Count nucleotide frequencies
• ✅ Generate random DNA sequences
• ✅ Pretty-print results in the terminal with colors and tables
• ✅ Fully immutable and FP-oriented design

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📦 Installation

Currently, you can clone the repository and use it locally:

git clone https://github.com/Deyan2306/helix.git
cd helix

Then build/run with:

• Scala CLI

  scala-cli run src

• sbt

  sbt run

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🛠 Usage

✅ Example Code

Create a Main.scala in your project:

import co.helix._
import scala.util.Random

object Main extends App {
  val dnaStr = "ACGTACGT"
  val dnaResult = DNA.fromString(dnaStr)

  // Pretty print validation
  PrettyPrinter.printValidation(dnaResult)

  dnaResult match {
    case Right(validDNA) =>
      // Count nucleotides
      val counts = Helix.countNucleotides(validDNA)
      PrettyPrinter.printCounts(counts)

      // Generate and print random DNA
      val randomDNA = Helix.randomDNA(10, new Random())
      PrettyPrinter.printRandomDNA(randomDNA)

    case Left(_) => // Already printed error
  }
}

✅ Output

✅ Valid DNA: ACGTACGT

 Nucleotide Counts:
┌────────────┬───────┐
│ Name       │ Count │
├────────────┼───────┤
│ Adenine    │     2 │
│ Cytosine   │     2 │
│ Guanine    │     2 │
│ Thymine    │     2 │
└────────────┴───────┘

🔹 Random DNA (length: 10):
GCTTAGCATA

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📂 Project Structure

src/
  main/
    scala/
      co/
        helix/
          Nucleotide.scala   # Defines Nucleotide type
          DNA.scala          # DNA class with validation
          Helix.scala        # Core functions (count, random DNA)
          PrettyPrinter.scala# Colorful terminal printing

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🚀 Roadmap

• Add RNA support
• Add complementary strand computation
• Add ASCII double helix visualization
• Publish as a Scala package

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🤝 Contributing

Contributions, issues, and feature requests are welcome! Feel free to fork the repo and submit a PR.

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👨‍💻 Author

Deyan Sirakov 📧 Email: deyan.sirakov2006@abv.bg 🌐 GitHub: Deyan2306

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📜 License

This project is licensed under the MIT License.

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