annonars 0.14.1

Rust template repository
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

//! Reading `clinvar-tsv` sequence variant files.

use std::{fmt::Display, str::FromStr};

use serde::{Deserialize, Serialize};

use crate::clinvar_minimal::pbs;

/// Enumeration for ClinVar pathogenicity for (de)serialization.
#[derive(Debug, Clone, PartialEq, Eq, PartialOrd, Ord)]
pub enum Pathogenicity {
    /// Pathogenic.
    Pathogenic,
    /// Likely pathogenic.
    LikelyPathogenic,
    /// Uncertain significance.
    UncertainSignificance,
    /// Likely benign.
    LikelyBenign,
    /// Benign.
    Benign,
}

impl Display for Pathogenicity {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        match self {
            Pathogenicity::Pathogenic => write!(f, "pathogenic"),
            Pathogenicity::LikelyPathogenic => write!(f, "likely pathogenic"),
            Pathogenicity::UncertainSignificance => write!(f, "uncertain significance"),
            Pathogenicity::LikelyBenign => write!(f, "likely benign"),
            Pathogenicity::Benign => write!(f, "benign"),
        }
    }
}

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

    fn from_str(s: &str) -> Result<Self, Self::Err> {
        match s {
            "pathogenic" => Ok(Pathogenicity::Pathogenic),
            "likely pathogenic" => Ok(Pathogenicity::LikelyPathogenic),
            "uncertain significance" => Ok(Pathogenicity::UncertainSignificance),
            "likely benign" => Ok(Pathogenicity::LikelyBenign),
            "benign" => Ok(Pathogenicity::Benign),
            _ => anyhow::bail!("Unknown pathogenicity: {}", s),
        }
    }
}

impl Serialize for Pathogenicity {
    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
    where
        S: serde::Serializer,
    {
        serializer.serialize_str(&self.to_string())
    }
}

impl<'de> Deserialize<'de> for Pathogenicity {
    fn deserialize<D>(d: D) -> Result<Self, D::Error>
    where
        D: serde::Deserializer<'de>,
    {
        let s = String::deserialize(d)?;
        Self::from_str(&s).map_err(serde::de::Error::custom)
    }
}

impl From<Pathogenicity> for pbs::Pathogenicity {
    fn from(value: Pathogenicity) -> Self {
        match value {
            Pathogenicity::Pathogenic => pbs::Pathogenicity::Pathogenic,
            Pathogenicity::LikelyPathogenic => pbs::Pathogenicity::LikelyPathogenic,
            Pathogenicity::UncertainSignificance => pbs::Pathogenicity::UncertainSignificance,
            Pathogenicity::LikelyBenign => pbs::Pathogenicity::LikelyBenign,
            Pathogenicity::Benign => pbs::Pathogenicity::Benign,
        }
    }
}

impl From<i32> for Pathogenicity {
    fn from(value: i32) -> Self {
        match value {
            0 => Pathogenicity::Pathogenic,
            1 => Pathogenicity::LikelyPathogenic,
            2 => Pathogenicity::UncertainSignificance,
            3 => Pathogenicity::LikelyBenign,
            4 => Pathogenicity::Benign,
            _ => unreachable!(),
        }
    }
}

/// Representation of a record from the `clinvar-tsv` output.
///
/// Note that the pathogenicity and review status are available in two fashions.  The first is
/// "ClinVar style" and attempts to follow the ClinVar approach.  Here, variant assessments
/// with a higher star rating override those a lowe rone.  This is what most users want.
/// The assessment "paranoid" uses all assessments, including those without a star rating,
/// on the same level.
#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
pub struct Record {
    /// Genome release.
    pub release: String,
    /// Chromosome name.
    pub chromosome: String,
    /// 1-based start position.
    pub start: u32,
    /// 1-based end position.
    pub end: u32,
    /// Reference allele bases in VCF notation.
    pub reference: String,
    /// Alternative allele bases in VCF notation.
    pub alternative: String,
    /// VCV accession identifier.
    pub vcv: String,
    /// Pathogenicity summary for the variant (ClinVar style).
    #[serde(deserialize_with = "deserialize_pathogenicity")]
    pub summary_clinvar_pathogenicity: Vec<Pathogenicity>,
    /// Pathogenicity gold stars (ClinVar style).
    pub summary_clinvar_gold_stars: u32,
    /// Pathogenicity summary for the variant ("paranoid" style).
    #[serde(deserialize_with = "deserialize_pathogenicity")]
    pub summary_paranoid_pathogenicity: Vec<Pathogenicity>,
    /// Pathogenicity gold stars ("paranoid" style).
    pub summary_paranoid_gold_stars: u32,
}

fn deserialize_pathogenicity<'de, D>(deserializer: D) -> Result<Vec<Pathogenicity>, D::Error>
where
    D: serde::Deserializer<'de>,
{
    let s: &str = Deserialize::deserialize(deserializer)?;
    let s = s.replace('{', "[").replace('}', "]");
    serde_json::from_str(&s).map_err(serde::de::Error::custom)
}