use bio_seq::prelude::*;

let seq = dna!("ATACGATCGATCGATCGATCCGT");

// iterate over the 8-mers of the reverse complement
for kmer in seq.revcomp().kmers::<8>() {
    println!("{}", kmer);
}

The IUPAC nucleotide ambiguity codes naturally encode a set of bases for each position:

use bio_seq::prelude::*;

let seq = iupac!("AGCTNNCAGTCGACGTATGTA");
let pattern = Seq::<Iupac>::from_str("AYG").unwrap();

for slice in seq.windows(pattern.len()) {
    if pattern.contains(slice) {
        println!("{} matches pattern", slice);
    }
}

The primary design goal of this crate is to make translating between biological sequence types safe and convenient:

// debruijn sequence of all 3-mers:
let seq: Seq<Dna> =
    dna!("AATTTGTGGGTTCGTCTGCGGCTCCGCCCTTAGTACTATGAGGACGATCAGCACCATAAGAACAAA");
let aminos: Seq<Amino> = Seq::from_iter(seq.kmers().map(|kmer| kmer.into()));
assert_eq!(
    aminos,
    amino!("NIFLCVWGGVFSRVSLCARGALSPRAPPLL*SVYTLYM*ERGDTRDISQSAHTPHI*KRENTQK")
);

Contents

• Codec: Coding/Decoding schemes for the characters of a biological sequence
• Seq: A sequence of encoded characters
• Kmer: A fixed size sequence of length K
• Derivable codecs: This crate offers utilities for defining your own bit-level encodings
• Safe conversion between sequences

Codecs

The Codec trait describes the coding/decoding process for the characters of a biological sequence. This trait can be derived procedurally. There are three built-in codecs:

codec::Dna

Using the lexicographically ordered 2-bit representation

codec::Iupac

IUPAC nucleotide ambiguity codes are represented with 4 bits. This supports membership resolution with bitwise operations. Logical or is the union:

assert_eq!(iupac!("AS-GYTNA") | iupac!("ANTGCAT-"), iupac!("ANTGYWNA"));

Logical and is the intersection of two iupac sequences:

assert_eq!(iupac!("ACGTSWKM") & iupac!("WKMSTNNA"), iupac!("A----WKA"));

codec::Amino

Amino acid sequences are represented with 6 bits. The representation of amino acids is designed to be easy to coerce from sequences of 2-bit encoded DNA.

Sequences

Strings of encoded characters are packed into Seqs. Slicing, chunking, and windowing return SeqSlices. Seq<A: Codec>/&SeqSlice<A: Codec> are analogous to String/&str.

All data is stored little-endian. This effects the order that sequences map to the integers ("colexicographic" order):

for i in 0..=15 {
    println!("{}: {}", i, Kmer::<Dna, 5>::from(i));
}

0: AAAAA
1: CAAAA
2: GAAAA
3: TAAAA
4: ACAAA
5: CCAAA
6: GCAAA
7: TCAAA
8: AGAAA
9: CGAAA
10: GGAAA
11: TGAAA
12: ATAAA
13: CTAAA
14: GTAAA
15: TTAAA

Kmers

kmers are sequences with a fixed size that can fit into a register. these are implemented with const generics.

Dense encodings

For dense encodings, a lookup table can be populated and indexed in constant time with the usize representation:

fn kmer_histogram<C: Codec, const K: usize>(seq: &SeqSlice<C>) -> Vec<usize> {
    // For dna::Dna our histogram will need 4^4
    // bins to count every possible 4-mer.
    let mut histo = vec![0; 1 << (C::WIDTH * K as u8)];

    for kmer in seq.kmers::<K>() {
        histo[usize::from(kmer)] += 1;
    }

    histo
}

This example builds a histogram of kmer occurences

Sketching

Hashing

The Hash trait is implemented for Kmers

Canonical Kmers

Depending on the application, it may be permissible to superimpose the forward and reverse complements of a kmer:

k = kmer!("ACGTGACGT");
let canonical = k ^ k.revcomp(); // TODO: implement ReverseComplement for Kmer

Kmer minimisers

The 2-bit representation of nucleotides is ordered A < C < G < T. Sequences and kmers are stored in little-endian and are ordered "colexicographically". This means that AAAA < CAAA < GAAA < ... < AAAC < ... < TTTT

fn minimise(seq: Seq<Dna>) -> Option<Kmer::<Dna, 8>> {
    seq.kmers().min()
}

Example: Hashing minimiser of canonical Kmers

for ckmer in seq.window(8).map(|kmer| hash(kmer ^ kmer.revcomp())) {
    // TODO: example
    ...
}

Derivable codecs

Sequence coding/decoding is derived from the variant names and discriminants of enum types:

use bio_seq_derive::Codec;
use bio_seq::codec::Codec;

#[derive(Clone, Copy, Debug, PartialEq, Codec)]
#[width = 2]
#[repr(u8)]
pub enum Dna {
    A = 0b00,
    C = 0b01,
    G = 0b10,
    T = 0b11,
}

impl From<Dna> for u8 {
    fn from(dna: Dna) -> Self {
        dna as u8
    }
}

The width attribute specifies how many bits the encoding requires per symbol. The maximum supported is 8. If this attribute isn't specified then the optimal width will be chosen.

Sequence conversions

Iupac from Dna; Seq<Iupac> from Seq<Dna>

Amino from Kmer<3>; Seq<Amino> from Seq<Dna>

• Sequence length not a multiple of 3 is an error

Seq<Iupac> from Amino; Seq<Iupac> from Seq<Amino> (TODO)

Vec<Seq<Dna>> from Seq<Iupac>: A sequence of IUPAC codes can generate a list of DNA sequences of the same length. (TODO)