Crate bio_seq

Bit-packed and well-typed biological sequences

• [Seq] heap allocated sequences of variable length
• [Kmer] short fixed length sequences
• [Codec] coder/decoder implementations

This crate is designed to facilitate common bioinformatics tasks, incuding amino acid translation, k-mer minimisation and hashing, and nucleotide sequence manipulation.

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);
}

Custom encodings are supported with the help of the bio-seq-derive crate.

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);
    }
}

Re-exports

• pub use error::ParseBioError;

Modules

• codec
  Coding/Decoding trait for bit-packable enums representing biological alphabets
• error
• kmer
• prelude
• seq
• translation
  Genetic Code Translation

Macros

• amino
• dna
• iupac
• kmer