Crate disambiseq 

disambiseq

Background

I’ve rewritten this functionality a few times for different use cases and put it into a standalone crate since it might be useful to others.

This is used to generate unambiguous one-off mismatch libraries for a set of DNA sequences.

Usage

Creating a new unambiguous set

use disambiseq::Disambiseq;

let sequences = vec![
    "ACT".to_string(),
    "AGT".to_string()
];
let dsq = Disambiseq::from_slice(&sequences);
println!("{:#?}", dsq);

Visualizing the set

Disambiseq {
    unambiguous: {
        "TCT": "ACT",
        "ACA": "ACT",
        "CCT": "ACT",
        "ACC": "ACT",
        "CGT": "AGT",
        "GGT": "AGT",
        "AGA": "AGT",
        "GCT": "ACT",
        "ACG": "ACT",
        "TGT": "AGT",
        "AGC": "AGT",
        "AGT": "ACT",
        "AGG": "AGT",
    },
    parents: {
        "AGT",
        "ACT",
    },
    ambiguous: {
        "ATT",
        "AAT",
    },
}

Querying the Set

use disambiseq::Disambiseq;

let sequences = vec![
    "ACT".to_string(),
    "AGT".to_string()
];
let dsq = Disambiseq::from_slice(&sequences);

// retrieve a parental sequence
assert_eq!(dsq.get_parent("ACT").unwrap().sequence(), "ACT");

// retrieve a mutation sequence's parent
assert_eq!(dsq.get_parent("TCT").unwrap().sequence(), "ACT");

// exclude sequences with ambiguous parents
assert_eq!(dsq.get_parent("AAT"), None);
assert_eq!(dsq.get_parent("ATT"), None);

Structs

ByteWrapper

Disambibyte

Disambiseq

SeqWrapper

Sequence