bio-seq-derive 2.0.2

Derive macros for the bio-seq crate
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78

# 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](https://github.com/jeff-k/bio-seq) 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 = "2.0"
```

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

```rust
use bio_seq_derive::Codec;
```

Note that codec enums require a `#[repr(u8)]` annotation.

```rust
#[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)
}
```