# `bio-seq` ### Bit packed and well-typed biological sequences

```rust use bio_seq::*;

let seq = dna!("ACTGCTAGCA");

for kmer in seq.kmers::<8>() { println!("{}", kmer); } ```

bio_seq::Dna: DNA use the lexicographically ordered 2-bit representation
bio_seq::Iupac: IUPAC nucleotide ambiguity codes are represented with 4 bits

``` A C G T

S 0 1 1 0
- 0 0 0 0 C 0 1 0 0 N 1 1 1 1 B 0 1 1 1 ... etc. ``` This supports membership resolution with bitwise operations:
rust assert_eq!( format!("{}", iupac!("AS-GYTNA") | iupac!("ANTGCAT-")), "ANTGYWNA" ); assert_eq!( format!("{}", iupac!("ACGTSWKM") & iupac!("WKMSTNNA")), "A----WKA" ); The Iupac struct implements From<Dna>
bio_seq::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. TODO: deal with alternate (e.g. mamalian mitochondrial) translation codes

Kmers

Kmers are sequences with a fixed size. These are implemented with const generics.

K * Codec::WIDTH must fit in a usize (i.e. 64). For larger Kmers use bigk::Kmer: (TODO)

The 2-bit representation of DNA sequences is lexicographically ordered:

rust // find the lexicographically minimum 8-mer fn minimise(seq: Seq<Dna>) -> Option<Kmer::<8>> { seq.kmers::<8>().min() }

Derived codecs

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

```rust

pub enum Dna { A = 0b00, C = 0b01, G = 0b10, T = 0b11, } ```

The width attribute specifies how many bits the encoding requires per symbol.

Kmers are represented stored as usizes with the least significant bit first.

rust dna!("C") == 0b01 // not 0b0100_0000 dna!("CT") == 0b11_01

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

Amino from Kmer<3>; Seq<Amino> from Seq<Dna> (TODO) * 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)

TODO: find out if Kmer<Dna, K> -> Kmer<Amino, K/3> is possible

meant to replace Text/TextSlice