predictosaurus 0.3.2

Uncertainty aware haplotype based genomic variant effect prediction
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

use anyhow::{anyhow, Result};
use colored::Colorize;
use serde::{Deserialize, Serialize};
use std::fmt;
use std::str::FromStr;

#[derive(Debug, PartialEq, Eq, Ord, PartialOrd, Clone, Copy, Serialize, Deserialize)]
pub(crate) enum Impact {
    None,
    Modifier,
    Low,
    Moderate,
    High,
}

impl FromStr for Impact {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> Result<Self> {
        match s.to_lowercase().as_str() {
            "none" => Ok(Impact::None),
            "modifier" => Ok(Impact::Modifier),
            "low" => Ok(Impact::Low),
            "moderate" => Ok(Impact::Moderate),
            "high" => Ok(Impact::High),
            _ => Err(anyhow!("'{}' is not a valid Impact variant", s)),
        }
    }
}

impl fmt::Display for Impact {
    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
        let colored_str = match *self {
            Impact::None => "None".green(),
            Impact::Modifier => "Modifier".green(),
            Impact::Low => "Low".yellow(),
            Impact::Moderate => "Moderate".red(),
            Impact::High => "High".purple(),
        };
        write!(f, "{}", colored_str)
    }
}

impl Impact {
    /// Serializes the Impact variant to a string without color
    pub(crate) fn to_raw_string(self) -> &'static str {
        match self {
            Impact::None => "None",
            Impact::Modifier => "Modifier",
            Impact::Low => "Low",
            Impact::Moderate => "Moderate",
            Impact::High => "High",
        }
    }
}

#[cfg(test)]
mod impact_enum_tests {
    use super::Impact;
    use colored::Colorize;

    #[test]
    fn test_impact_order() {
        assert!(Impact::High > Impact::Moderate);
        assert!(Impact::High > Impact::Low);
        assert!(Impact::High > Impact::Modifier);
        assert!(Impact::High > Impact::None);
        assert!(Impact::Moderate > Impact::Low);
        assert!(Impact::Moderate > Impact::Modifier);
        assert!(Impact::Moderate > Impact::None);
        assert!(Impact::Low > Impact::Modifier);
        assert!(Impact::Low > Impact::None);
        assert!(Impact::Modifier > Impact::None);
    }

    #[test]
    fn display_none_impact() {
        let impact = Impact::None;
        assert_eq!(format!("{}", impact), "None".green().to_string());
    }

    #[test]
    fn display_modifier_impact() {
        let impact = Impact::Modifier;
        assert_eq!(format!("{}", impact), "Modifier".green().to_string());
    }

    #[test]
    fn display_low_impact() {
        let impact = Impact::Low;
        assert_eq!(format!("{}", impact), "Low".yellow().to_string());
    }

    #[test]
    fn display_moderate_impact() {
        let impact = Impact::Moderate;
        assert_eq!(format!("{}", impact), "Moderate".red().to_string());
    }

    #[test]
    fn display_high_impact() {
        let impact = Impact::High;
        assert_eq!(format!("{}", impact), "High".purple().to_string());
    }

    #[test]
    fn from_str_none() {
        let impact = "none".parse::<Impact>().unwrap();
        assert_eq!(impact, Impact::None);
    }

    #[test]
    fn from_str_modifier() {
        let impact = "modifier".parse::<Impact>().unwrap();
        assert_eq!(impact, Impact::Modifier);
    }

    #[test]
    fn from_str_low() {
        let impact = "low".parse::<Impact>().unwrap();
        assert_eq!(impact, Impact::Low);
    }

    #[test]
    fn from_str_moderate() {
        let impact = "moderate".parse::<Impact>().unwrap();
        assert_eq!(impact, Impact::Moderate);
    }

    #[test]
    fn from_str_high() {
        let impact = "high".parse::<Impact>().unwrap();
        assert_eq!(impact, Impact::High);
    }

    #[test]
    fn from_str_invalid() {
        let impact = "invalid".parse::<Impact>();
        assert!(impact.is_err());
    }
}