crispr_screen 0.1.14

A fast and configurable differential expression analysis tool for CRISPR screens
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

mod compute_aggregation;
mod results;
mod utils;

use clap::ValueEnum;
pub use compute_aggregation::compute_aggregation;
pub use results::AggregationResult;

/// Enum describing aggregation procedure selection
#[derive(ValueEnum, Clone, Debug, PartialEq)]
#[allow(clippy::upper_case_acronyms)]
pub enum GeneAggregationSelection {
    /// Alpha Robust Rank Algorithm (αRRA)
    RRA,

    /// INC Method, i.e. Mann-Whitney U-Test
    Inc,
}

/// Enum describing the different gene aggregation procedures and their associated configurations.
#[derive(Debug)]
pub enum GeneAggregation<'a> {
    AlpaRRA {
        alpha: f64,
        npermutations: usize,
        adjust_alpha: bool,
    },
    Inc {
        token: &'a str,
        fdr: f64,
        group_size: usize,
    },
}

#[cfg(test)]
mod testing {
    use super::{GeneAggregation, GeneAggregationSelection};
    use clap::ValueEnum;

    #[test]
    fn test_enum() {
        let rra = GeneAggregationSelection::RRA;
        let inc = GeneAggregationSelection::Inc;

        assert_eq!(
            GeneAggregationSelection::from_str("RRA", true).unwrap(),
            rra
        );
        assert_eq!(
            GeneAggregationSelection::from_str("Inc", true).unwrap(),
            inc
        );
    }

    #[test]
    fn test_enum_case_insensitive() {
        let rra = GeneAggregationSelection::RRA;
        let inc = GeneAggregationSelection::Inc;

        assert_eq!(
            GeneAggregationSelection::from_str("rra", true).unwrap(),
            rra
        );
        assert_eq!(
            GeneAggregationSelection::from_str("inc", true).unwrap(),
            inc
        );
    }

    #[test]
    fn test_enum_invalid() {
        assert!(GeneAggregationSelection::from_str("invalid", true).is_err());
    }

    #[test]
    fn test_enum_rra_string() {
        let rra = GeneAggregationSelection::RRA;
        assert_eq!(format!("{:?}", rra), "RRA");
    }

    #[test]
    fn test_enum_inc_string() {
        let inc = GeneAggregationSelection::Inc;
        assert_eq!(format!("{:?}", inc), "Inc");
    }

    #[test]
    fn test_enum_gene_aggregation_rra() {
        let agg = GeneAggregation::AlpaRRA {
            alpha: 0.5,
            npermutations: 100,
            adjust_alpha: true,
        };
        assert_eq!(
            format!("{:?}", agg),
            "AlpaRRA { alpha: 0.5, npermutations: 100, adjust_alpha: true }"
        );
    }

    #[test]
    fn test_enum_gene_aggregation_inc() {
        let agg = GeneAggregation::Inc {
            token: "non-targeting",
            fdr: 0.05,
            group_size: 3,
        };
        assert_eq!(
            format!("{:?}", agg),
            "Inc { token: \"non-targeting\", fdr: 0.05, group_size: 3 }"
        );
    }
}