A crate to manipulate multiple sequences alignments in Rust.
APACHE-2.0 License
A crate to manipulate multiple sequences alignments in Rust.
Instead of storing aligned sequences as multiple strings, multi_seq_align
stores bases or residues in Alignment
using a list of characters, like a matrix. This allows easy access to specific rows and columns of the alignment.
let mut kappa_casein_fragments_alignment = Alignment::with_sequences(
&[
b"PAPISKWQSMP".to_vec(),
b"HAQIPQRQYLP".to_vec(),
b"PAQILQWQVLS".to_vec(),
],
)?;
// Let's extract a column of this alignment
assert_eq!(
kappa_casein_fragments_alignment.nth_position(6).unwrap(),
[&b'W', &b'R', &b'W']
);
// But we also have the aligned sequence for the Platypus
// Let's add it to the original alignment
kappa_casein_fragments_alignment.add(
b"EHQRP--YVLP".to_vec(),
)?;
// the new aligned sequence has a gap at the 6th position
assert_eq!(
kappa_casein_fragments_alignment.nth_position(6).unwrap(),
[&b'W', &b'R', &b'W', &b'-']
);
// We can also loop over each position of the alignment
for aas in kappa_casein_fragments_alignment.iter_positions() {
println!("{:?}", aas);
assert_eq!(aas.len(), 4); // 4 sequences
}
Here I instancied an alignment using u8
, but Alignment
works on generics like numbers, custom or third-party structs.
Alignment
from one or multiple aligned sequences at once (see add()
and create()
).iter_positions()
and iter_sequences(
).My goal is to reduce the footprint of this crate, there is ome work to do to achieve it. The code will eventually be optimised to be faster and to better use memory.
Assuring that all the sequences have the same lengths in a generic way is chalenging and result in some not so nice code.
Please create a new issue on the project repository.
Aa-regex is distributed under the terms of the Apache License (Version 2.0). See LICENSE for details.