bio-seq 0.14.8

Bit packed and well-typed biological sequences
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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129

use crate::codec::Codec;
//use crate::{Complement, Maskable, Reverse, ReverseComplement};
use crate::{ComplementMut, Maskable, MaskableMut}; //, ReverseComplementMut, ReverseMut};

/// 5-bit encoding for maskable IUPAC symbols
/// The middle bit is the mask flag and symbols are complemented by reversing the bit pattern
#[derive(Clone, Copy, Debug, PartialEq, Eq, PartialOrd, Ord, Hash, Codec)]
#[bits(5)]
#[repr(u8)]
pub enum Iupac {
    A = 0b10000,
    C = 0b01000,
    G = 0b00010,
    T = 0b00001,

    Y = 0b01001,
    R = 0b10010,
    W = 0b10001,
    S = 0b01010,

    K = 0b00011,
    M = 0b11000,
    D = 0b10011,
    V = 0b11010,

    H = 0b11001,
    B = 0b01011,

    N = 0b11011,
    #[display('-')]
    X = 0b00000,

    #[display('a')]
    AMasked = 0b10100,
    #[display('c')]
    CMasked = 0b01100,
    #[display('g')]
    GMasked = 0b00110,
    #[display('t')]
    TMasked = 0b00101,

    #[display('y')]
    YMasked = 0b01101,
    #[display('r')]
    RMasked = 0b10110,
    #[display('w')]
    WMasked = 0b10101,
    #[display('s')]
    SMasked = 0b01110,

    #[display('k')]
    KMasked = 0b00111,
    #[display('m')]
    MMasked = 0b11100,
    #[display('d')]
    DMasked = 0b10111,
    #[display('v')]
    VMasked = 0b11110,

    #[display('h')]
    HMasked = 0b11101,
    #[display('b')]
    BMasked = 0b01111,

    #[display('n')]
    NMasked = 0b11111,
    #[display('.')]
    XMasked = 0b00100,
}

#[allow(clippy::cast_possible_truncation)]
impl ComplementMut for Iupac {
    /// This representation can be complemented by reversing the bit pattern
    fn comp(&mut self) {
        let bits = self.to_bits();
        *self = Self::unsafe_from_bits(
            ((bits & 0b10000) >> 4)
                | ((bits & 0b01000) >> 2)
                | (bits & 0b00100)
                | ((bits & 0b00010) << 2)
                | ((bits & 0b00001) << 4),
        );
    }
}

impl MaskableMut for Iupac {
    /// Setting the middle bit sets the mask flag
    fn mask(&mut self) {
        let b = *self as u8 | 0b00100;
        *self = Self::unsafe_from_bits(b);
    }

    /// Unsetting the middle bit clears the mask flag
    fn unmask(&mut self) {
        let b = *self as u8 & 0b11011;
        *self = Self::unsafe_from_bits(b);
    }
}

impl Maskable for Iupac {}

#[cfg(test)]
mod tests {
    use crate::codec::masked;
    use crate::prelude::*;

    #[test]
    fn mask_iupac_seq() {
        let mut seq = Seq::<masked::Iupac>::try_from("A.TCGCgtcataN--A").unwrap();

        assert_eq!(seq.to_mask().to_string(), "a.tcgcgtcatan..a".to_string());

        seq.mask();
        assert_eq!(seq.to_unmask().to_string(), "A-TCGCGTCATAN--A".to_string());
        seq.unmask();
        assert_eq!(seq.to_mask().to_string(), "a.tcgcgtcatan..a".to_string());
    }

    #[test]
    fn comp_iupac_seq() {
        let mut seq = Seq::<masked::Iupac>::try_from("A.TCGCgtcataN--A").unwrap();

        assert_ne!(seq.to_comp().to_string(), "A.TCGCgtcataN--A".to_string());
        assert_eq!(seq.to_comp().to_string(), "T.AGCGcagtatN--T".to_string());

        seq.comp();
        assert_eq!(seq.to_comp().to_string(), "A.TCGCgtcataN--A".to_string());
    }
}