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:

$ 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

#[macro_use]
extern crate jean;

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

fn main() -> Result<(), Box<dyn std::error::Error>> {
  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

#[macro_use]
extern crate jean;

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

fn main() -> Result<(), Box<dyn std::error::Error>> {
  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(())
}