finch_cli 0.5.0

An implementation of min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation.
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

use std::io::{BufReader, Cursor};
use std::process::Command;

use assert_cmd::prelude::*;
use predicates::prelude::predicate;

use finch::serialization::{read_finch_file, read_mash_file, Sketch};

#[test]
fn file_doesnt_exist() -> Result<(), Box<dyn std::error::Error>> {
    let mut cmd = Command::cargo_bin("finch")?;
    cmd.arg("sketch").arg("test/file/doesnt/exist");
    cmd.assert()
        .failure()
        .stderr(predicate::str::contains("No such file or directory"));

    Ok(())
}

#[test]
fn finch_sketch() -> Result<(), Box<dyn std::error::Error>> {
    let mut cmd = Command::cargo_bin("finch")?;
    cmd.arg("sketch")
        .args(&["--n-hashes", "10"])
        .args(&["-O"])
        .arg("tests/data/query.fa");
    cmd.assert().success();

    let output = Cursor::new(cmd.output().unwrap().stdout);
    let sketch: serde_json::Value = serde_json::from_reader(output)?;
    assert_eq!(sketch["kmer"], 21);
    assert_eq!(sketch["alphabet"], "ACGT");
    assert_eq!(sketch["sketchSize"], 10);
    assert_eq!(sketch["hashSeed"], 0);

    Ok(())
}

#[test]
fn finch_sketch_bin() -> Result<(), Box<dyn std::error::Error>> {
    let mut cmd = Command::cargo_bin("finch")?;
    cmd.arg("sketch")
        .args(&["--n-hashes", "10"])
        .arg("-b")
        .arg("-O")
        .arg("tests/data/query.fa");
    cmd.assert().success();

    let output = Cursor::new(cmd.output().unwrap().stdout);
    let mut buf_reader = BufReader::new(output);
    let sketch: Vec<Sketch> = read_finch_file(&mut buf_reader)?;
    assert_eq!(sketch.len(), 1);
    assert_eq!(sketch[0].sketch_params.k(), 21);
    assert_eq!(sketch[0].sketch_params.expected_size(), 10);
    assert_eq!(sketch[0].hashes.len(), 10);
    Ok(())
}

#[test]
fn finch_sketch_msh() -> Result<(), Box<dyn std::error::Error>> {
    let mut cmd = Command::cargo_bin("finch")?;
    cmd.arg("sketch")
        .args(&["--n-hashes", "10"])
        .arg("-B")
        .arg("-O")
        .arg("tests/data/query.fa");
    cmd.assert().success();

    let output = Cursor::new(cmd.output().unwrap().stdout);
    let mut buf_reader = BufReader::new(output);
    let sketch: Vec<Sketch> = read_mash_file(&mut buf_reader)?;
    assert_eq!(sketch.len(), 1);
    assert_eq!(sketch[0].sketch_params.k(), 21);
    // mash doesn't set an expected size?
    // assert_eq!(sketch[0].sketch_params.expected_size(), 10);
    assert_eq!(sketch[0].hashes.len(), 10);
    Ok(())
}

#[test]
fn finch_sketch_scaled() -> Result<(), Box<dyn std::error::Error>> {
    let mut cmd = Command::cargo_bin("finch")?;
    cmd.arg("sketch")
        .args(&["--n-hashes", "10"])
        .args(&["--sketch-type", "scaled"])
        .args(&["--scale", ".001"])
        .arg("tests/data/query.fa")
        .arg("-O");
    cmd.assert().success();

    let output = Cursor::new(cmd.output().unwrap().stdout);
    let sketch: serde_json::Value = serde_json::from_reader(output)?;
    assert_eq!(sketch["kmer"], 21);
    assert_eq!(sketch["alphabet"], "ACGT");
    assert_eq!(sketch["sketchSize"], 10);
    //assert_eq!(sketch["max_hash"], usize::max_value() / 1000);
    assert_eq!(sketch["hashSeed"], 0);

    Ok(())
}