biolic 0.1.0

A modular bioinformatics toolkit in Rust for long-read sequence processing
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

//! Integration tests for the biolic CLI.
//!
//! These run the compiled binary against `tests/data/small.fastq` (5 reads,
//! 206 total bases). Note: `assert_cmd` pipes stdout, so the default output
//! format is TSV (not human-readable), per biolic's TTY-detection convention.

use assert_cmd::Command;
use predicates::prelude::*;
use std::fs;

const FASTQ: &str = "tests/data/small.fastq";
const FASTQ_GZ: &str = "tests/data/small.fastq.gz";
const FASTA: &str = "tests/data/small.fasta";

#[test]
fn stats_default_output_is_tsv_when_piped() {
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["stats", FASTQ])
        .assert()
        .success()
        .stdout(predicate::str::starts_with("file\t"))
        .stdout(predicate::str::contains("n50"));
}

#[test]
fn stats_json_reports_five_reads() {
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["stats", FASTQ, "--json"])
        .assert()
        .success()
        .stdout(predicate::str::contains("\"read_count\": 5"))
        .stdout(predicate::str::contains("\"total_bases\": 206"))
        .stdout(predicate::str::contains("\"n50\""));
}

#[test]
fn count_json_reports_five_reads() {
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["count", FASTQ, "--json"])
        .assert()
        .success()
        .stdout(predicate::str::contains("\"reads\": 5"))
        .stdout(predicate::str::contains("\"bases\": 206"));
}

#[test]
fn stats_reads_gzip_input() {
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["stats", FASTQ_GZ, "--json"])
        .assert()
        .success()
        .stdout(predicate::str::contains("\"read_count\": 5"))
        .stdout(predicate::str::contains("\"total_bases\": 206"));
}

#[test]
fn stats_reads_from_stdin() {
    let data = fs::read(FASTQ).unwrap();
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["stats", "-", "--json"])
        .write_stdin(data)
        .assert()
        .success()
        .stdout(predicate::str::contains("\"read_count\": 5"));
}

#[test]
fn stats_reads_gzip_from_stdin() {
    let data = fs::read(FASTQ_GZ).unwrap();
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["stats", "-", "--json"])
        .write_stdin(data)
        .assert()
        .success()
        .stdout(predicate::str::contains("\"read_count\": 5"));
}

#[test]
fn stats_reads_fasta() {
    // FASTA: 3 sequences, 12 + 16 + 12 = 40 bases, no quality.
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["stats", FASTA, "--json"])
        .assert()
        .success()
        .stdout(predicate::str::contains("\"read_count\": 3"))
        .stdout(predicate::str::contains("\"total_bases\": 40"));
}

#[test]
fn count_reads_fasta() {
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["count", FASTA, "--json"])
        .assert()
        .success()
        .stdout(predicate::str::contains("\"reads\": 3"))
        .stdout(predicate::str::contains("\"bases\": 40"));
}

#[test]
fn help_works() {
    Command::cargo_bin("biolic")
        .unwrap()
        .arg("--help")
        .assert()
        .success()
        .stdout(predicate::str::contains("biolic"));
}

#[test]
fn unimplemented_module_errors_cleanly() {
    Command::cargo_bin("biolic")
        .unwrap()
        .args(["filter", FASTQ])
        .assert()
        .failure();
}