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.
```rust let mut kappacaseinfragmentsalignment = Alignment::withsequences( &[ b"PAPISKWQSMP".tovec(), b"HAQIPQRQYLP".tovec(), b"PAQILQWQVLS".to_vec(), ], )?;
// Let's extract a column of this alignment asserteq!( kappacaseinfragmentsalignment.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 kappacaseinfragmentsalignment.add( b"EHQRP--YVLP".tovec(), )?;
// the new aligned sequence has a gap at the 6th position asserteq!( kappacaseinfragmentsalignment.nth_position(6).unwrap(), [&b'W', &b'R', &b'W', &b'-'] );
// We can also loop over each position of the alignment for aas in kappacaseinfragmentsalignment.iterpositions() { 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().
This crate is currently in early stage development. I wouldn't recommend using it in production but I am interested in possible ideas to further the developemt of this project. Quite some work needs toi be done to improve the API and make it easy to use in other project.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.