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
use std::{io::{BufRead, BufReader}, fs::File};
use flate2::read::MultiGzDecoder;
use anyhow::Result;
use super::{
FastxRead,
FastaReader,
FastqReader,
Record
};
fn initialize_generic_buffer(
path: &str,
is_gzip: bool) -> Result<Box<dyn BufRead>>
{
match is_gzip {
true => {
let file = File::open(path)?;
let gzip = MultiGzDecoder::new(file);
let buffer = BufReader::new(gzip);
Ok(Box::new(buffer))
}
false => {
let file = File::open(path)?;
let buffer = BufReader::new(file);
Ok(Box::new(buffer))
}
}
}
fn initialize_generic_reader(
buffer: Box<dyn BufRead>,
is_fasta: bool) -> Box<dyn FastxRead<Item = Record>>
{
match is_fasta {
true => Box::new(FastaReader::new(buffer)),
false => Box::new(FastqReader::new(buffer))
}
}
pub fn initialize_reader(path: &str) -> Result<Box<dyn FastxRead<Item = Record>>>{
let is_gzip = path.ends_with(".gz");
let is_fasta = path.contains(".fa") | path.contains(".fasta");
let buffer = initialize_generic_buffer(path, is_gzip)?;
let reader = initialize_generic_reader(buffer, is_fasta);
Ok(reader)
}
#[cfg(test)]
mod test {
use super::*;
#[test]
fn assign_fasta() {
let path = "example/sequences.fa";
let reader = initialize_reader(path).expect("invalid path");
let num_records = reader
.into_iter()
.map(|x| assert!(!x.empty()))
.count();
assert_eq!(num_records, 10);
}
#[test]
fn assign_gzfasta() {
let path = "example/sequences.fa.gz";
let reader = initialize_reader(path).expect("invalid path");
let num_records = reader
.into_iter()
.map(|x| assert!(!x.empty()))
.count();
assert_eq!(num_records, 10);
}
#[test]
fn assign_fastq() {
let path = "example/sequences.fq";
let reader = initialize_reader(path).expect("invalid path");
let num_records = reader
.into_iter()
.map(|x| assert!(!x.empty()))
.count();
assert_eq!(num_records, 10);
}
#[test]
fn assign_gzfastq() {
let path = "example/sequences.fq.gz";
let reader = initialize_reader(path).expect("invalid path");
let num_records = reader
.into_iter()
.map(|x| assert!(!x.empty()))
.count();
assert_eq!(num_records, 10);
}
}