zoe 0.0.30

A nightly library for viral genomics
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
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153

use crate::assert_fp_eq;

use super::*;

pub(crate) static LONG_READ_1: &[u8] = include_bytes!(concat!(env!("CARGO_MANIFEST_DIR"), "/tests/data/KJ907623.1.txt")); // H5 HA, complete CDS
pub(crate) static LONG_READ_2: &[u8] = include_bytes!(concat!(env!("CARGO_MANIFEST_DIR"), "/tests/data/KJ907631.1.txt")); // H5 HA, complete CDS

static AMBIGUOUS_READ_1: &[u8] = b"ACGTX";
static AMBIGUOUS_READ_2: &[u8] = b"ACGAT";
static SHORT_READ_1: &[u8] = b"ATCGATCGATCG";
static SHORT_READ_2: &[u8] = b"ATCGATCGATCA";
static MID_READ_GAPS_1: &[u8] = include_bytes!(concat!(env!("CARGO_MANIFEST_DIR"), "/tests/data/KP326324.1.txt")); // H5 HA, complete CDS, aligned
static MID_READ_GAPS_2: &[u8] = include_bytes!(concat!(env!("CARGO_MANIFEST_DIR"), "/tests/data/KC684446.1.txt")); // H5 HA, complete CDS, aligned

#[test]
fn test_hamming_from_matrix() {
    let sub_matrix = dna_substitution_matrix(SHORT_READ_1, SHORT_READ_2);
    let hamming = hamming_dist_from_sub_matrix(&sub_matrix);
    assert_eq!(hamming, 1);

    let sub_matrix = dna_substitution_matrix(MID_READ_GAPS_1, MID_READ_GAPS_2);
    let hamming = hamming_dist_from_sub_matrix(&sub_matrix);
    assert_eq!(hamming, 9);

    let sub_matrix = dna_substitution_matrix(LONG_READ_1, LONG_READ_2);
    let hamming = hamming_dist_from_sub_matrix(&sub_matrix);
    assert_eq!(hamming, 148);
}

#[test]
fn test_jc() {
    let data = [
        (SHORT_READ_1, SHORT_READ_2, Some(0.088_337_276_7)),
        (MID_READ_GAPS_1, MID_READ_GAPS_2, Some(0.040_188_184_6)),
        (LONG_READ_1, LONG_READ_2, Some(0.092_309_042_4)),
        (LONG_READ_1, LONG_READ_1, Some(0.0)),
        (LONG_READ_1, b"", None),
        (&LONG_READ_1[0..20], LONG_READ_2, Some(0.051_744_653_615_213_576)),
        (
            AMBIGUOUS_READ_1,
            AMBIGUOUS_READ_2,
            dna_substitution_matrix(b"ACGT", b"ACGA").jc69_distance(),
        ),
    ];

    for (a, b, expected) in data {
        let sm = dna_substitution_matrix(a, b);
        assert_fp_eq!(sm.jc69_distance(), expected);
        assert_fp_eq!(jukes_cantor_69(a, b), expected);
    }
}

#[test]
fn compare_jc_regression() {
    let data: Vec<(&[u8], &[u8])> = vec![
        (b"gug", b"ggg"),
        (b"gggcaaaccacaaaaaaaaaaaaaaaaaaaaaa", b"aaaaaaaaaaaaaaaaaaaaaataatttttttt"),
    ];
    for (a, b) in data.into_iter().skip(1) {
        let sm = dna_substitution_matrix(a, b);
        assert_eq!(sm.jc69_distance(), jukes_cantor_69(a, b));
    }
}

#[test]
fn test_k80() {
    let data = [
        (SHORT_READ_1, SHORT_READ_2, Some(0.091_160_778_3)),
        (MID_READ_GAPS_1, MID_READ_GAPS_2, Some(0.040_576_991_6)),
        (LONG_READ_1, LONG_READ_2, Some(0.093_274_373_1)),
        (LONG_READ_1, LONG_READ_1, Some(0.0)),
        (b"", b"", None),
        (LONG_READ_1, b"", None),
        (AMBIGUOUS_READ_1, AMBIGUOUS_READ_2, kimura_80(b"ACGT", b"ACGA")),
    ];

    for (a, b, expected) in data {
        assert_fp_eq!(kimura_80(a, b), expected);
    }
}

#[test]
fn test_k81() {
    let data = [
        (SHORT_READ_1, SHORT_READ_2, Some(0.091_160_778_396_977_3)),
        (MID_READ_GAPS_1, MID_READ_GAPS_2, Some(0.040_582_502_030_320_3)),
        (LONG_READ_1, LONG_READ_2, Some(0.093_297_615_589_788_4)),
        (LONG_READ_1, LONG_READ_1, Some(0.0)),
        (LONG_READ_1, b"", None),
        (b"", b"", None),
        (AMBIGUOUS_READ_1, AMBIGUOUS_READ_2, kimura_81(b"ACGT", b"ACGA")),
    ];
    for (a, b, expected) in data {
        assert_fp_eq!(kimura_81(a, b), expected);
    }
}

#[test]
fn test_f81() {
    let data = [
        (SHORT_READ_1, SHORT_READ_2, Some(0.088_362_461_866_048_9)),
        (MID_READ_GAPS_1, MID_READ_GAPS_2, Some(0.040_201_884_674_593_0)),
        (LONG_READ_1, LONG_READ_2, Some(0.092_428_092_165_986_7)),
        (LONG_READ_1, LONG_READ_1, Some(0.0)),
        (LONG_READ_1, b"", None),
        (b"", b"", None),
        (AMBIGUOUS_READ_1, AMBIGUOUS_READ_2, felsenstein_81(b"ACGT", b"ACGA")),
    ];

    for (a, b, expected) in data {
        assert_fp_eq!(felsenstein_81(a, b), expected);
    }
}

#[test]
fn test_tn93() {
    let data = [
        (SHORT_READ_1, SHORT_READ_2, Some(0.102_047_809_6)),
        (MID_READ_GAPS_1, MID_READ_GAPS_2, Some(0.040_633_116_7)),
        (LONG_READ_1, LONG_READ_2, Some(0.093_467_734_2)),
        (LONG_READ_1, LONG_READ_1, Some(0.0)),
        (LONG_READ_1, b"", None),
        (b"", b"", None),
        (AMBIGUOUS_READ_1, AMBIGUOUS_READ_2, tamura_nei_93(b"ACGT", b"ACGA")),
    ];

    for (a, b, expected) in data {
        assert_fp_eq!(tamura_nei_93(a, b), expected);
    }
}

#[test]
fn test_p_distance_invalid_long() {
    let mut seq1 = vec![b'A'; 2 * 255 + 2];
    let mut seq2 = vec![b'A'; 2 * 255 + 2];

    seq1[0] = b'N';
    seq1[1] = b'X';

    seq2[0] = b'T';
    seq2[1] = b'T';

    assert_fp_eq!(p_distance_acgt::<2>(&seq1, &seq2), Some(0.0));
}

#[test]
fn test_p_distance_all_invalid_long() {
    let seq1 = vec![b'N'; 2 * 255 + 2];
    let seq2 = vec![b'A'; 2 * 255 + 2];

    let result = p_distance_acgt::<2>(&seq1, &seq2);
    assert_eq!(result, None);
}