feat: implement parsing of HGVS variants (#2) (#3)

.gitignore

@@ -1,2 +1,5 @@
 /target
 /Cargo.lock
+
+*~
+.*.sw?

Cargo.toml

@@ -4,3 +4,6 @@ version = "0.1.0"
 edition = "2021"
 
 [dependencies]
+anyhow = "1.0.69"
+nom = "7.1.3"
+pretty_assertions = "1.3.0"

README.md

@@ -1,3 +1,6 @@
+[![CI](https://github.com/bihealth/hgvs-rs/actions/workflows/rust.yml/badge.svg)](https://github.com/bihealth/hgvs-rs/actions/workflows/rust.yml)
+[![codecov](https://codecov.io/gh/bihealth/hgvs-rs/branch/main/graph/badge.svg?token=aZchhLWdzt)](https://codecov.io/gh/bihealth/hgvs-rs)
+
 # hgvs-rs
 
 This is a port of [biocommons/hgvs](https://github.com/biocommons/hgvs) to the Rust programming language.

src/lib.rs

@@ -1,3 +1,5 @@
+pub mod parser;
+
 pub fn add(left: usize, right: usize) -> usize {
     left + right
 }

src/parser/ds.rs

@@ -0,0 +1,291 @@
+//! Data structures for representing HGVS variant descriptions.
+
+/// Expression of "maybe uncertain".
+#[derive(Clone, Debug, PartialEq)]
+pub enum Mu<T> {
+    /// Certain variant of `T`.
+    Certain(T),
+    /// Uncertain variant of `T`.
+    Uncertain(T),
+}
+
+/// Representation of gene symbol, e.g., `TTN` or `Ttn`.
+#[derive(Clone, Debug, PartialEq)]
+pub struct GeneSymbol {
+    pub value: String,
+}
+
+/// Edit of nucleic acids.
+#[derive(Clone, Debug, PartialEq)]
+pub enum NaEdit {
+    /// A substitution where both reference and alternative allele are nucleic acid strings
+    /// (or empty).
+    RefAlt {
+        reference: String,
+        alternative: String,
+    },
+    /// A substitution where the reference is a number and alternative is a count.
+    NumAlt { count: i32, alternative: String },
+    /// Deletion of one or more nucleic acid characters.
+    Del { reference: String },
+    /// Insertion of one or more nucleic acid characters.
+    Ins { alternative: String },
+    /// Duplication of nucleic acid reference sequence.
+    Dup { reference: String },
+    /// Inversion of a (potentially empty) nucleic acid reference sequence.
+    InvRef { reference: String },
+    /// Inversion of a stretch given by its length.
+    InvNum { count: i32 },
+}
+
+/// Uncertain change through extension.
+#[derive(Clone, Debug, PartialEq)]
+pub enum UncertainLengthChange {
+    None,
+    Unknown,
+    Known(i32),
+}
+
+/// Representation of accession, e.g., `NM_01234.5`.
+#[derive(Clone, Debug, PartialEq)]
+pub struct Accession {
+    pub value: String,
+}
+
+/// Protein edit with interval end edit.
+#[derive(Clone, Debug, PartialEq)]
+pub enum ProteinEdit {
+    Fs {
+        alternative: Option<String>,
+        terminal: Option<String>,
+        length: UncertainLengthChange,
+    },
+    Ext {
+        /// Amino acid before "ext"
+        aa_ext: Option<String>,
+        /// Amino acid after "ext", terminal if shift is positive.
+        ext_aa: Option<String>,
+        /// Change in protein length.
+        change: UncertainLengthChange,
+    },
+    Subst {
+        alternative: String,
+    },
+    /// `delins`
+    DelIns {
+        alternative: String,
+    },
+    /// `ins`
+    Ins {
+        alternative: String,
+    },
+    /// `del`
+    Del,
+    /// `dup`
+    Dup,
+    /// `=`
+    Ident,
+}
+
+/// A HGVS variant specification.
+#[derive(Clone, Debug, PartialEq)]
+pub enum HgvsVariant {
+    /// Variant specification with `c.` location.
+    CdsVariant {
+        accession: Accession,
+        gene_symbol: Option<GeneSymbol>,
+        loc_edit: CdsLocEdit,
+    },
+    /// Variant specification with `g.` location.
+    GenomeVariant {
+        accession: Accession,
+        gene_symbol: Option<GeneSymbol>,
+        loc_edit: GenomeLocEdit,
+    },
+    /// Variant specification with `m.` location.
+    MtVariant {
+        accession: Accession,
+        gene_symbol: Option<GeneSymbol>,
+        loc_edit: MtLocEdit,
+    },
+    /// Variant specification with `n.` location.
+    TxVariant {
+        accession: Accession,
+        gene_symbol: Option<GeneSymbol>,
+        loc_edit: TxLocEdit,
+    },
+    /// Variant specification with `p.` location.
+    ProtVariant {
+        accession: Accession,
+        gene_symbol: Option<GeneSymbol>,
+        loc_edit: ProtLocEdit,
+    },
+    /// Variant specification with `r.` location.
+    RnaVariant {
+        accession: Accession,
+        gene_symbol: Option<GeneSymbol>,
+        loc_edit: RnaLocEdit,
+    },
+}
+
+/// Coding sequence location with edit.
+#[derive(Clone, Debug, PartialEq)]
+pub struct CdsLocEdit {
+    /// Location on the CDS.
+    pub loc: Mu<CdsInterval>,
+    /// DNA change description.
+    pub edit: Mu<NaEdit>,
+}
+
+/// CDS position interval.
+#[derive(Clone, Debug, PartialEq)]
+pub struct CdsInterval {
+    /// Start position
+    pub begin: CdsPos,
+    /// End position
+    pub end: CdsPos,
+}
+
+/// Specifies whether the CDS position is relative to the CDS start or
+/// CDS end.
+#[derive(Clone, Debug, PartialEq)]
+pub enum CdsFrom {
+    Start,
+    End,
+}
+
+/// CDS position.
+#[derive(Clone, Debug, PartialEq)]
+pub struct CdsPos {
+    /// Base position.
+    pub base: i32,
+    /// Optional offset.
+    pub offset: Option<i32>,
+    /// Whether starts at CDS start or end.
+    pub cds_from: CdsFrom,
+}
+
+/// Genome sequence location with edit.
+#[derive(Clone, Debug, PartialEq)]
+pub struct GenomeLocEdit {
+    /// Location on the genome.
+    pub loc: Mu<GenomeInterval>,
+    /// DNA change description.
+    pub edit: Mu<NaEdit>,
+}
+
+/// Genome position interval.
+#[derive(Clone, Debug, PartialEq)]
+pub struct GenomeInterval {
+    /// Start position
+    pub begin: Option<i32>,
+    /// End position
+    pub end: Option<i32>,
+}
+
+/// Mitochondrial sequence location with edit.
+#[derive(Clone, Debug, PartialEq)]
+pub struct MtLocEdit {
+    /// Location on the mitochondrium.
+    pub loc: Mu<MtInterval>,
+    /// DNA change description.
+    pub edit: Mu<NaEdit>,
+}
+
+/// Mitochondrial position interval.
+#[derive(Clone, Debug, PartialEq)]
+pub struct MtInterval {
+    /// Start position
+    pub begin: Option<i32>,
+    /// End position
+    pub end: Option<i32>,
+}
+
+/// Transcript sequence location with edit.
+#[derive(Clone, Debug, PartialEq)]
+pub struct TxLocEdit {
+    /// Loction on a transcript.
+    pub loc: Mu<TxInterval>,
+    /// DNA change description.
+    pub edit: Mu<NaEdit>,
+}
+
+/// Transcript position interval.
+#[derive(Clone, Debug, PartialEq)]
+pub struct TxInterval {
+    /// Start position
+    pub begin: TxPos,
+    /// End position
+    pub end: TxPos,
+}
+
+/// Transcript position.
+#[derive(Clone, Debug, PartialEq)]
+pub struct TxPos {
+    /// Base position.
+    pub base: i32,
+    /// Optional offset.
+    pub offset: Option<i32>,
+}
+
+/// RNA sequence location with edit.
+#[derive(Clone, Debug, PartialEq)]
+pub struct RnaLocEdit {
+    /// Location on a transcript.
+    pub loc: Mu<RnaInterval>,
+    /// RNA change description.
+    pub edit: Mu<NaEdit>,
+}
+
+/// RNA position interval.
+#[derive(Clone, Debug, PartialEq)]
+pub struct RnaInterval {
+    /// Start position
+    pub begin: RnaPos,
+    /// End position
+    pub end: RnaPos,
+}
+
+/// RNA position.
+#[derive(Clone, Debug, PartialEq)]
+pub struct RnaPos {
+    /// Base position.
+    pub base: i32,
+    /// Optional offset.
+    pub offset: Option<i32>,
+}
+
+/// Protein sequence location with edit or special.
+#[derive(Clone, Debug, PartialEq)]
+pub enum ProtLocEdit {
+    Ordinary {
+        loc: Mu<ProtInterval>,
+        edit: Mu<ProteinEdit>,
+    },
+    /// `=`
+    NoChange,
+    /// `(=)`
+    NoChangeUncertain,
+    /// `0`
+    NoProtein,
+    /// `0?`
+    NoProteinUncertain,
+}
+
+/// Protein position interval.
+#[derive(Clone, Debug, PartialEq)]
+pub struct ProtInterval {
+    /// Start position
+    pub begin: ProtPos,
+    /// End position
+    pub end: ProtPos,
+}
+
+/// Protein position.
+#[derive(Clone, Debug, PartialEq)]
+pub struct ProtPos {
+    /// Amino acid value.
+    pub aa: String,
+    /// Number of `aa`.
+    pub number: i32,
+}