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:

[dependencies]
base_sequence_compression = "1.0.0"

Example

Here's an example of how to use the library:

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.

pub fn compress_sequence(sequence: &str) -> Vec<u8>

• Input: &str - The DNA sequence to be compressed.
• Output: Vec<u8> - The compressed binary data.

decompress_sequence

Decompresses binary data back into the original DNA sequence.

pub fn decompress_sequence(compressed: &[u8], sequence_length: usize) -> io::Result<String>

• Input: &[u8] - The compressed binary data.
• Input: usize - The length of the original DNA sequence.
• Output: io::Result<String> - The decompressed DNA sequence.

compress_fasta

Compresses a FASTA file containing DNA sequences.

pub fn compress_fasta(content: &str) -> Vec<u8>

• Input: &str - The content of the FASTA file.
• Output: Vec<u8> - The compressed binary data.

decompress_fasta

Decompresses binary data back into the original FASTA file content.

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:

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:

#[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

Feel free to reach out for any questions or suggestions regarding the library.