jeff-k / bio-seq-derive

Procedural macros used by bio-seq

This crate is now hosted as a workspace in the bio-seq repo: https://github.com/jeff-k/bio-seq/bio-seq-derive

This repo will be archived

bio-seq-derive

bio-seq-derive is a procedural macro crate that provides the Codec derive macro for the bio-seq library. It allows users to define custom bit-packed alphabets from an enum. The bit representation of the enum is derived from the discriminants.

Please refer to the bio-seq documentation for a complete guide on defining custom alphabets.

Features

• width attribute: Specify the number of bits required to represent each variant in the custom alphabet. Default is optimal.
• alt attribute: Define alternate bit representations for the same variant.
• display attribute: Set a custom character representation for a variant.

Usage

To use bio-seq-derive, add it as a dependency in your Cargo.toml file:

[dependencies]
bio-seq-derive = "0.1.0"

Then, import the bio_seq_derive::Codec macro in your Rust code:

use bio_seq_derive::Codec;

#[derive(Clone, Copy, Debug, PartialEq, Eq, Hash, Codec)]
#[width = 6]
#[repr(u8)]
pub enum Amino {
    #[alt(0b110110, 0b010110, 0b100110)]
    A = 0b000110, // GCA
    #[alt(0b111011)]
    C = 0b011011, // TGC
    #[alt(0b110010)]
    D = 0b010010, // GAC
    #[alt(0b100010)]
    E = 0b000010, // GAA
    #[alt(0b111111)]
    F = 0b011111, // TTC
    #[alt(0b101010, 0b011010, 0b111010)]
    G = 0b001010, // GGA
    #[alt(0b110001)]
    H = 0b010001, // CAC
    #[alt(0b011100, 0b111100)]
    I = 0b001100, // ATA
    #[alt(0b100000)]
    K = 0b000000, // AAA
    #[alt(0b001111, 0b101111, 0b111101, 0b011101, 0b101101)]
    L = 0b001101, // CTA
    M = 0b101100, // ATG
    #[alt(0b110000)]
    N = 0b010000, // AAC
    #[alt(0b010101, 0b100101, 0b110101)]
    P = 0b000101, // CCA
    #[alt(0b100001)]
    Q = 0b000001, // CAA
    #[alt(0b101000, 0b111001, 0b011001, 0b001001, 0b101001)]
    R = 0b001000, // AGA
    #[alt(0b110111, 0b010111, 0b000111, 0b100111, 0b111000)]
    S = 0b011000, // AGC
    #[alt(0b110100, 0b010100, 0b100100)]
    T = 0b000100, // ACA
    #[alt(0b011110, 0b111110, 0b101110)]
    V = 0b001110, // GTA
    W = 0b101011, // TGG
    #[alt(0b110011)]
    Y = 0b010011, // TAC
    #[display = '*']
    #[alt(0b001011, 0b100011)]
    X = 0b000011, // TAA (stop)
}