https://github.com/dangreco/jean

Computational biology utility library for Rust featuring sequence alignment, genome annotation, and I/O of biological files
https://github.com/dangreco/jean

bioinformatics biology computational-biology dna genes genetics protein rna

Last synced: 23 days ago
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Computational biology utility library for Rust featuring sequence alignment, genome annotation, and I/O of biological files

• Host: GitHub
• URL: https://github.com/dangreco/jean
• Owner: dangreco
• License: other
• Created: 2022-11-29T22:48:21.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2022-12-01T22:42:00.000Z (about 2 years ago)
• Last Synced: 2024-12-09T03:40:51.819Z (27 days ago)
• Topics: bioinformatics, biology, computational-biology, dna, genes, genetics, protein, rna
• Language: Rust
• Homepage:
• Size: 1.96 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        

# jean

jean is a computational biology library written in Rust. It offers

computational biology primitives such as sequences (DNA, RNA, and Protein), bases, amino acids, and codons. Optional features extend the 

abilities of jean, such as `io` which allows for reading/writing from/to common biological file formats (e.g. FASTA, GFF3) and `alignment` which allows for aligning sequences. 

## Getting Started

Add `jean` and any needed features to your Rust project:

```sh

$ cargo add jean # --features io,...

```

## Feature Matrix

  

    

      Feature

      Use

      Links

    

    

      io

      I/O of common biological file formats (e.g. FASTA, GFF3)

      

        (Documentation)

      

    

    

      macros

      Macros for creating sequences

      

        (Documentation)

      

    

    

      alignment

      Sequence alignment tools

      

        (Documentation)

      

    

    

      blosum

      BLOSUM substitution matrices

      

        (Documentation)

      

    

  

## Examples

### DNA Sequence Alignment

```rust

#[macro_use]

extern crate jean;

use jean::{alignment::global::NeedlemanWunsch, blosum::NUC_4_2, dna::Dna};

fn main() -> Result<(), Box> {

  let seq1: Dna = dna!("AGACTAGTTAC");

  let seq2: Dna = dna!("CGAGACGT");

  let alignment = NeedlemanWunsch::new()

    .matrix(&NUC_4_2)

    .gap_penalty(|k| -2 * k)

    .align(&seq1, &seq2)?;

  assert_eq!(alignment.score, 16);

  assert_eq!(alignment.a, dna!("--AGACTAGTTAC"));

  assert_eq!(alignment.b, dna!("CGAGAC--G-T--"));

  Ok(())

}

```

### DNA -> RNA -> Protein

```rust

#[macro_use]

extern crate jean;

use jean::{cut::Cut, dna::Dna, prelude::*, protein::Protein, rna::Rna};

fn main() -> Result<(), Box> {

  let cut = Cut::read_file("homo_sapien.cut")?;

  /* DNA -> RNA -> Protein */

  let d: Dna = dna!("AGGCTGGGCACC");

  let r: Rna = d.transcribe();

  let p: Protein = r.translate(&cut);

  assert_eq!(p, protein!("RLGT"));

  /* ...and back again */

  let r_ = p.rev_translate(&cut);

  let d_ = r_.rev_transcribe();

  assert_eq!(d, d_);

  Ok(())

}

```