DNA Cryptography — Binary → DNA → Base64-char Decoder

A small Python utility that decodes a binary string by interpreting it as DNA bases and then translating DNA codons to printable characters.

This repository demonstrates a simple two-stage decoding pipeline often seen in CTFs and steganography puzzles:

Binary (bits) → DNA bases (A, G, C, T) → 6-bit codons → Base64 character

Why this exists

• Educational / puzzle purpose: shows how compact binary data can be reinterpreted as biological codons for fun encodings.
• Useful as a starting point for CTF challenges or demonstrations of non-standard encodings.

Contents

• dnasolver.py — main Python script. Reads dna.txt (or a file you pass), converts binary to DNA bases, then maps codons (3 bases) to characters using a 6-bit conversion into the Base64 alphabet.
• dna.txt — (not modified) your input file containing the binary string to decode.
• sample_dna.txt — a tiny example input you can use to verify the script.

Requirements

• Python 3.8+ (should run on any modern Python 3 interpreter)

Quick start

1. Put your input binary bitstring in dna.txt (or use sample_dna.txt). The file may contain whitespace; only 0 and 1 characters are used.
2. Run the script:

python3 dnasolver.py           # reads dna.txt
python3 dnasolver.py -i sample_dna.txt --output-only

The script prints either a short, human-friendly report or just the decoded output when --output-only is used.

How it works (short)

1. Binary → DNA

   • The script reads dna.txt, keeps only 0 and 1 characters, and processes the string in 2-bit chunks.
   • Mapping used in dnasolver.py:
     • 00 → A
     • 01 → G
     • 10 → C
     • 11 → T

2. DNA → Characters

   • The DNA string is processed in codons (groups of 3 bases).
   • Each codon represents 6 bits (2 bits per base). Those 6 bits are interpreted as a number 0–63 and mapped to the Base64 alphabet (A–Z a–z 0–9 + /).

Notes and tips

• The script is intentionally small and straightforward. It performs basic validation:
  • Non 0/1 characters in the input are ignored.
  • If the input length isn't a multiple of 2, the final bit is truncated.
  • Incomplete final codons (fewer than 3 DNA bases) are ignored.
• Use --ignore-unknown-bases to silently drop codons containing unexpected bases.

Contributing

If you want CLI features, alternate output encodings (e.g. produce raw bytes from the 6-bit stream), or unit tests, open a PR or suggest changes.

License

This project is available under the MIT License (see LICENSE).

Author

• echobash