https://github.com/marshallku/base-sequence-compression
Rust library for compressing and decompressing DNA sequences
https://github.com/marshallku/base-sequence-compression
dna-sequences rust-lang
Last synced: about 2 months ago
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Rust library for compressing and decompressing DNA sequences
- Host: GitHub
- URL: https://github.com/marshallku/base-sequence-compression
- Owner: marshallku
- License: mit
- Created: 2024-06-18T09:43:08.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2024-07-31T22:36:56.000Z (about 1 year ago)
- Last Synced: 2024-12-07T20:53:33.832Z (10 months ago)
- Topics: dna-sequences, rust-lang
- Language: Rust
- Homepage: https://crates.io/crates/base_sequence_compression
- Size: 12.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Base Sequence Compression
Base Sequence Compression is a Rust library for compressing and decompressing DNA sequences. This library efficiently encodes DNA sequences, reducing storage space while preserving the integrity of the original data. The DNA bases (A, C, T, G) are encoded using 2 bits each, allowing for significant compression.
## Features
- **Compression and Decompression**: Compress DNA sequences into a binary format and decompress them back to their original form.
- **Error Handling**: Handles invalid DNA sequences by panicking, ensuring data integrity.
- **Compression Rate Calculation**: Calculate the compression rate to evaluate the efficiency of the compression.
- **FASTA File Compression**: Compress and decompress FASTA files containing multiple DNA sequences.
- **WASM Support**: The library can be compiled to WebAssembly for use in web applications.
## Usage
### Adding the Library to Your Project
Add the following to your `Cargo.toml`:
```toml
[dependencies]
base_sequence_compression = "1.0.0"
```
### Example
Here's an example of how to use the library:
```rust
use base_sequence_compression::{compress_sequence, decompress_sequence};
fn main() {
let dna_sequence = "ACGTACGTACGT";
let compressed = compress_sequence(dna_sequence);
let sequence_length = dna_sequence.len();
let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
assert_eq!(dna_sequence, decompressed);
println!("Compression successful!");
}
```
## API
### `compress_sequence`
Compresses a DNA sequence into a binary format.
```rust
pub fn compress_sequence(sequence: &str) -> Vec
```
- **Input**: `&str` - The DNA sequence to be compressed.
- **Output**: `Vec` - The compressed binary data.
### `decompress_sequence`
Decompresses binary data back into the original DNA sequence.
```rust
pub fn decompress_sequence(compressed: &[u8], sequence_length: usize) -> io::Result
```
- **Input**: `&[u8]` - The compressed binary data.
- **Input**: `usize` - The length of the original DNA sequence.
- **Output**: `io::Result` - The decompressed DNA sequence.
### `compress_fasta`
Compresses a FASTA file containing DNA sequences.
```rust
pub fn compress_fasta(content: &str) -> Vec
```
- **Input**: `&str` - The content of the FASTA file.
- **Output**: `Vec` - The compressed binary data.
### `decompress_fasta`
Decompresses binary data back into the original FASTA file content.
```rust
pub fn decompress_fasta(data: &[u8]) -> String
```
- **Input**: `&[u8]` - The compressed binary data.
- **Output**: `String` - The decompressed FASTA file content.
## Tests
The library includes a comprehensive set of tests to ensure the correctness of the compression and decompression functions. To run the tests, use the following command:
```sh
cargo test
```
### Test Cases
- **Compression and Decompression**: Tests compressing and decompressing various sequences, including edge cases.
- **Invalid Sequence Handling**: Ensures that invalid sequences are handled appropriately by panicking.
- **Compression Rate**: Evaluates the efficiency of the compression algorithm.
## Example Test
Here's an example test that checks the compression and decompression of a DNA sequence:
```rust
#[test]
fn test_compress_decompress() {
let dna_sequence = "ACGTACGTACGT";
let compressed = compress_sequence(dna_sequence);
let sequence_length = dna_sequence.len();
let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
assert_eq!(dna_sequence, decompressed);
}
```
## License
This project is licensed under the MIT License. See the `LICENSE` file for more details.
## Contributing
Contributions are welcome! Please open an issue or submit a pull request if you have any improvements or bug fixes.
## Acknowledgements
Thanks to the contributors and the open-source community for their invaluable feedback and support.
---
**Repository**: [Base Sequence Compression](https://github.com/yourusername/base-sequence-compression)
Feel free to reach out for any questions or suggestions regarding the library.