Module bio_seq::codec::iupac

4-bit IUPAC nucleotide ambiguity codes

IUPAC nucleotide ambiguity codes are represented with 4 bits

	A	C	G	T
A	1	0	0	0
C	0	1	0	0
G	0	0	1	0
T	0	0	0	1
Y	0	1	0	1
R	1	0	1	0
W	1	0	0	1
S	0	1	1	0
K	0	0	1	1
M	1	1	0	0
D	1	0	1	1
V	1	1	1	0
H	1	1	0	1
B	0	1	1	1
N	1	1	1	1
X/-	0	0	0	0

This naturally supports set membership operations:

use bio_seq::prelude::*;

// Set union:
assert_eq!(iupac!("AS-GYTNA") | iupac!("ANTGCAT-"), iupac!("ANTGYWNA"));

// Set intersection:
assert_eq!(iupac!("ACGTSWKM") & iupac!("WKMSTNNA"), iupac!("A----WKA"));

Which can be used to implement pattern matching:

use bio_seq::prelude::*;

let seq = iupac!("AGCTNNCAGTCGACGTATGTA");
let pattern = iupac!("AYG");

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

// ACG matches pattern
// ATG matches pattern

Enums

• Iupac