omics_variation/
lib.rs

1//! Genomic variation.
2
3use std::str::FromStr;
4
5use omics_molecule::compound::Nucleotide;
6use thiserror::Error;
7
8pub mod snv;
9
10/// An error related to a [`Variant`].
11#[derive(Error, Debug)]
12pub enum Error {
13    /// Unsuccessfully attempted to parse a [`Variant`] from a string.
14    #[error("unable to parse a variant from `{0}`")]
15    ParseError(String),
16}
17
18/// A variant.
19#[derive(Debug)]
20pub enum Variant<N: Nucleotide> {
21    /// A single nucleotide substitution.
22    SingleNucleotideVariation(snv::Variant<N>),
23}
24
25impl<N: Nucleotide> std::str::FromStr for Variant<N>
26where
27    <N as FromStr>::Err: std::fmt::Debug + std::fmt::Display,
28{
29    type Err = Error;
30
31    fn from_str(s: &str) -> Result<Self, Self::Err> {
32        if let Ok(snv) = s.parse::<snv::Variant<N>>() {
33            return Ok(Variant::SingleNucleotideVariation(snv));
34        }
35
36        Err(Error::ParseError(s.to_string()))
37    }
38}
39
40impl<N: Nucleotide> std::fmt::Display for Variant<N>
41where
42    <N as FromStr>::Err: std::fmt::Debug + std::fmt::Display,
43{
44    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
45        match self {
46            Variant::SingleNucleotideVariation(variant) => write!(f, "{variant}"),
47        }
48    }
49}
50
51#[cfg(test)]
52mod tests {
53    use omics_coordinate::Strand;
54    use omics_molecule::polymer::dna;
55
56    use super::*;
57
58    #[test]
59    fn it_parses_dna_snvs_correctly() -> Result<(), Box<dyn std::error::Error>> {
60        let variant = "seq0:+:1:A:C".parse::<Variant<dna::Nucleotide>>()?;
61        assert!(matches!(variant, Variant::SingleNucleotideVariation(_)));
62
63        match variant {
64            Variant::SingleNucleotideVariation(snv) => {
65                assert_eq!(snv.coordinate().contig().as_str(), "seq0");
66                assert_eq!(snv.coordinate().strand(), Strand::Positive);
67                assert_eq!(snv.coordinate().position().get(), 1);
68                assert_eq!(snv.reference(), dna::Nucleotide::A);
69                assert_eq!(snv.alternate(), dna::Nucleotide::C);
70            }
71        }
72
73        Ok(())
74    }
75
76    #[test]
77    fn it_errors_when_attempting_to_parse_invalid_variants()
78    -> Result<(), Box<dyn std::error::Error>> {
79        let err = "seq0:1:A".parse::<Variant<dna::Nucleotide>>().unwrap_err();
80        assert_eq!(err.to_string(), "unable to parse a variant from `seq0:1:A`");
81
82        let err = "seq0:1:A:".parse::<Variant<dna::Nucleotide>>().unwrap_err();
83        assert_eq!(
84            err.to_string(),
85            "unable to parse a variant from `seq0:1:A:`"
86        );
87
88        let err = "seq0:A:C:1"
89            .parse::<Variant<dna::Nucleotide>>()
90            .unwrap_err();
91        assert_eq!(
92            err.to_string(),
93            "unable to parse a variant from `seq0:A:C:1`"
94        );
95
96        Ok(())
97    }
98
99    #[test]
100    fn it_serializes_correctly() -> Result<(), Box<dyn std::error::Error>> {
101        let variant = "seq0:+:1:A:C".parse::<Variant<dna::Nucleotide>>()?;
102        assert_eq!(variant.to_string(), "seq0:+:1:A:C");
103
104        let variant = "seq0:+:1:A:C".parse::<Variant<dna::Nucleotide>>()?;
105        assert_eq!(variant.to_string(), "seq0:+:1:A:C");
106
107        Ok(())
108    }
109}
omics_variation/lib.rs

omics_variation/
lib.rs
