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https://github.com/bradeneverson/genezip
Huffman Tree Genomics Compression Implementation
https://github.com/bradeneverson/genezip
Last synced: about 2 months ago
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Huffman Tree Genomics Compression Implementation
- Host: GitHub
- URL: https://github.com/bradeneverson/genezip
- Owner: BradenEverson
- Created: 2024-06-22T13:38:40.000Z (7 months ago)
- Default Branch: master
- Last Pushed: 2024-06-26T10:56:33.000Z (7 months ago)
- Last Synced: 2024-10-07T11:11:23.137Z (3 months ago)
- Language: Rust
- Size: 21.5 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# GeneZip 🧬
[](https://crates.io/crates/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](https://www.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
```
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
```
**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](LICENSE) file for more information.