nucs

This is a personal experiment with an API for working with nucleotide and amino acid sequences. Its design is based off of my experience using and helping maintain https://github.com/SecureDNA/quickdna. My goals were to make an API that...

• ...is solely focused on Rust.
• ...integrates with the Rust std library (e.g. representing codons as [Nuc; 3] allows the std library to understand that codons can be cheaply flattened into nucleotides).
• ...is (largely) collection-agnostic.
• ...tries to be consistent with Zipf's law of abbreviation when naming things.

use nucs::{Dna, DnaSlice, NCBI1, Nuc, Peptide};

let mut dna: Dna = "ACACACATATCTTACGCTTAGGAAATCTGACCCGAA"
    .parse().unwrap();

let codons = dna[4..].as_codons_mut();
// Selects this: v-------------------------------------v
//       ACAC    ACA TAT CTT ACG CTT AGG AAA TCT GAC CCG    AA

codons[3..8].revcomp();
// Reverse complements this: v-----------------v
//       ACAC    ACA TAT CTT ACG CTT AGG AAA TCT GAC CCG    AA
// Changing it to:           AGA TTT CCT AAG CGT

dna.extend(const { Nuc::lit(b"CCAACCATTGATGAG") });

let peptide: Peptide = dna.translate(NCBI1).collect();
assert_eq!(peptide.to_string(), "THIS*IS*A*PEPTIDE");

Non-Vec containers are supported too, and it's possible to work with DNA non-destructively via iterators:

use std::collections::VecDeque;
use nucs::{DnaIter, NCBI1, Nuc, Peptide, Seq};

let mut dna: Seq<VecDeque<Nuc>> =
    "ACTCTATCACCTACTCAGAGCGCTCCACCGCGCGTGT".parse().unwrap();
// Prepend things to the `VecDeque`;
// it's no longer stored contiguously.
for _ in 0..4 {
    dna.push_front(Nuc::C);
}

let immutable_dna = dna;
// Apply reverse compliment and NCBI1 non-destructively.
let peptide: Peptide = immutable_dna
    .iter()
    .revcomped()
    .translate(NCBI1)
    .collect();
assert_eq!(peptide.to_string(), "TRAVERSE*VIEW");

Ambiguous nucleotides and amino acids are supported:

use nucs::{AmbiAmino, AmbiNuc, AmbiPeptide, DnaSlice, NCBI1};
use AmbiNuc::{A, C};

let mut dna = AmbiNuc::lit(b"TTAGCGGACGATTAT");

// Because `dna` contains ambiguous nucleotides,
// translating it produces an ambiguous peptide
let peptide: AmbiPeptide = dna.translate(NCBI1).collect();
assert_eq!(peptide.to_string(), "LADDY");

dna[0] |= A | C;
dna[6] |= A;
dna[9] |= A;
assert_eq!(dna.display().to_string(), "HTAGCGRACRATTAT");
let peptide: AmbiPeptide = dna.translate(NCBI1).collect();
assert_eq!(peptide.to_string(), "JABBY");

Planned functionality

• Packing
• FASTA parsing
• Expansion of ambiguous k-mers into concrete k-mers
• Base canonicalization
• Unsafe casts for Vec and Arc
• Better efficiency

Incompatibility with quickdna

Note that while nucs is heavily inspired by https://github.com/SecureDNA/quickdna, there are subtle-yet-important incompatibilities with the order and representation of nucleotides and amino acids. In particular nucleotides are ordered alphabetically in nucs, to keep the ordering identical to strings as well as (hopefully) making future bit-packing work easier.

License

Licensed under either of

• Apache License, Version 2.0 (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
• MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.