GeneZip 🧬

GeneZip is a Rust command-line tool designed to compress files containing strings of genetic information using Huffman encoding. Huffman encoding is an efficient method for compressing data by assigning variable-length codes to input characters based on their frequencies.

Features

• Compress genetic information files using Huffman encoding and run-length-tokenized encoding(in development!)
• Decompress files compressed with GeneZip
• Simple and intuitive command-line interface

Installation

To install GeneZip, you need to have Rust and Cargo installed on your machine. If you don't have them installed, you can get them from rust-lang.org.

Once Rust and Cargo are installed, you can install GeneZip using the following command:

cargo install genezip

Usage

Note GeneZip is currently in an extremely beta phase. Huffman encoding is currently implemented, but without sequence-based-token encoding and run-based encoding it will always create larger files than before. GeneZip is being continuously updated and will receieve these features soon!

GeneZip provides two main commands: compress and decompress.

Compress

To compress a file, use the compress command followed by the input file and the desired output file:

genezip compress <input_file> <output_file>

Compressing will create your desired compression file, alongside a serialized key that holds the encodings necessary to decompress the genmoe file

Example:

genezip compress sequences.txt sequences.gzp

Decompress

To decompress a file, use the decompress command followed by the compressed file, the generated .gzpky key created from compressing and the desired output file:

genezip decompress <input_file> <key_file> <output_file>

Example:

genezip decompress sequences.gzp sequences.gzpky sequences.txt

Example

Compressing a File

Suppose you have a file genetic_data.txt containing strings of genetic information. To compress this file, run:

genezip compress genetic_data.txt genetic_data.gzp

Decompressing a File

To decompress the previously compressed file genetic_data.gzp, run:

genezip decompress genetic_data.gzp genetic_data.gzp.gzpky genetic_data_decompressed.txt

Contributing

Contributions are welcome! If you have suggestions for improvements or new features, feel free to open an issue or submit a pull request. Please ensure your code adheres to the existing code style and includes appropriate tests.

License

GeneZip is licensed under the MIT License. See the LICENSE file for more information.