nafcodec 0.3.1

Rust coder/decoder for Nucleotide Archive Format (NAF) files.
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
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175

extern crate nafcodec;

use std::borrow::Cow;
use std::io::Cursor;

use nafcodec::Decoder;
use nafcodec::EncoderBuilder;
use nafcodec::Flag;
use nafcodec::Record;
use nafcodec::SequenceType::Dna;

fn test_records() -> Vec<Record<'static>> {
    vec![
        Record {
            id: Some(Cow::from("r1")),
            comment: Some(Cow::from("record 1")),
            sequence: Some(Cow::from("NGCTCTTAAACCTGCTA")),
            quality: Some(Cow::from("#8CCCGGGGGGGGGGGG")),
            length: Some(17),
        },
        Record {
            id: Some(Cow::from("r2")),
            comment: Some(Cow::from("record 2")),
            sequence: Some(Cow::from("NTAATAAGCAATGACGGCAGC")),
            quality: Some(Cow::from("#8AACCFF<FFGGFGE@@@@@")),
            length: Some(21),
        },
    ]
}

#[test]
pub fn encode_id() {
    let mut encoder = EncoderBuilder::from_flags(Dna, Flag::Id)
        .with_memory()
        .unwrap();

    let records = test_records();
    encoder.push(&records[0]).unwrap();
    encoder.push(&records[1]).unwrap();

    let mut buffer = Vec::new();
    encoder.write(&mut buffer).unwrap();

    let mut decoder = Decoder::new(Cursor::new(buffer)).unwrap();
    assert!(decoder.header().flags().test(Flag::Id));
    assert!(!decoder.header().flags().test(Flag::Comment));
    assert!(!decoder.header().flags().test(Flag::Sequence));
    assert!(!decoder.header().flags().test(Flag::Quality));

    let r1 = decoder.next().unwrap().unwrap();
    assert_eq!(r1.id, Some(Cow::from("r1")));
    assert!(r1.comment.is_none());
    assert!(r1.sequence.is_none());
    assert!(r1.quality.is_none());
    assert!(r1.length.is_none());

    let r2 = decoder.next().unwrap().unwrap();
    assert_eq!(r2.id, Some(Cow::from("r2")));
    assert!(r2.comment.is_none());
    assert!(r2.sequence.is_none());
    assert!(r2.quality.is_none());
    assert!(r2.length.is_none());
}

#[test]
pub fn encode_id_sequence() {
    let mut encoder = EncoderBuilder::from_flags(Dna, Flag::Id | Flag::Sequence)
        .with_memory()
        .unwrap();

    let records = test_records();
    encoder.push(&records[0]).unwrap();
    encoder.push(&records[1]).unwrap();

    let mut buffer = Vec::new();
    encoder.write(&mut buffer).unwrap();

    let mut decoder = Decoder::new(Cursor::new(buffer)).unwrap();
    assert!(decoder.header().flags().test(Flag::Id));
    assert!(!decoder.header().flags().test(Flag::Comment));
    assert!(decoder.header().flags().test(Flag::Sequence));
    assert!(!decoder.header().flags().test(Flag::Quality));

    let r1 = decoder.next().unwrap().unwrap();

    assert_eq!(r1.id, Some(Cow::from("r1")));
    assert!(r1.comment.is_none());
    assert_eq!(r1.sequence, Some(Cow::from("NGCTCTTAAACCTGCTA")));
    assert!(r1.quality.is_none());
    assert!(r1.length.is_some());

    let r2 = decoder.next().unwrap().unwrap();
    assert_eq!(r2.id, Some(Cow::from("r2")));
    assert!(r2.comment.is_none());
    assert_eq!(r2.sequence, Some(Cow::from("NTAATAAGCAATGACGGCAGC")));
    assert!(r2.quality.is_none());
    assert!(r2.length.is_some());
}

#[test]
pub fn encode_quality() {
    let mut encoder = EncoderBuilder::new(Dna)
        .quality(true)
        .sequence(false)
        .id(false)
        .with_memory()
        .unwrap();

    let records = test_records();
    encoder.push(&records[0]).unwrap();
    encoder.push(&records[1]).unwrap();

    let mut buffer = Vec::new();
    encoder.write(&mut buffer).unwrap();

    let mut decoder = Decoder::new(Cursor::new(buffer)).unwrap();
    println!("{:?}", decoder.header());
    assert!(!decoder.header().flags().test(Flag::Id));
    assert!(!decoder.header().flags().test(Flag::Comment));
    assert!(!decoder.header().flags().test(Flag::Sequence));
    assert!(decoder.header().flags().test(Flag::Quality));

    let r1 = decoder.next().unwrap().unwrap();
    assert!(r1.id.is_none());
    assert!(r1.comment.is_none());
    assert!(r1.sequence.is_none());
    assert_eq!(r1.quality, Some(Cow::from("#8CCCGGGGGGGGGGGG")));
    assert!(r1.length.is_some());

    let r2 = decoder.next().unwrap().unwrap();
    assert!(r2.id.is_none());
    assert!(r2.comment.is_none());
    assert!(r2.sequence.is_none());
    assert_eq!(r2.quality, Some(Cow::from("#8AACCFF<FFGGFGE@@@@@")));
    assert!(r2.length.is_some());
}

#[test]
pub fn encode_all() {
    let mut encoder = EncoderBuilder::new(Dna)
        .quality(true)
        .sequence(true)
        .id(true)
        .comment(true)
        .with_memory()
        .unwrap();

    let records = test_records();
    encoder.push(&records[0]).unwrap();
    encoder.push(&records[1]).unwrap();

    let mut buffer = Vec::new();
    encoder.write(&mut buffer).unwrap();

    let mut decoder = Decoder::new(Cursor::new(buffer)).unwrap();
    println!("{:?}", decoder.header());
    assert!(decoder.header().flags().test(Flag::Id));
    assert!(decoder.header().flags().test(Flag::Comment));
    assert!(decoder.header().flags().test(Flag::Sequence));
    assert!(decoder.header().flags().test(Flag::Quality));

    let r1 = decoder.next().unwrap().unwrap();
    assert_eq!(r1.id, Some(Cow::from("r1")));
    assert_eq!(r1.comment, Some(Cow::from("record 1")));
    assert_eq!(r1.sequence, Some(Cow::from("NGCTCTTAAACCTGCTA")));
    assert_eq!(r1.quality, Some(Cow::from("#8CCCGGGGGGGGGGGG")));
    assert!(r1.length.is_some());

    let r2 = decoder.next().unwrap().unwrap();
    assert_eq!(r2.id, Some(Cow::from("r2")));
    assert_eq!(r2.comment, Some(Cow::from("record 2")));
    assert_eq!(r2.sequence, Some(Cow::from("NTAATAAGCAATGACGGCAGC")));
    assert_eq!(r2.quality, Some(Cow::from("#8AACCFF<FFGGFGE@@@@@")));
    assert!(r2.length.is_some());
}