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:

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

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

```rust use bioseqderive::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) } ```