Merge pull request #6 from P2GX/write-hpoa

Support writing HPO annotations into HPOA format

Author: ielis

.gitignore

@@ -20,4 +20,5 @@ Cargo.lock
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-.vscode/
+.vscode/
+.idea/

Cargo.toml

@@ -18,7 +18,7 @@ authors = [
 [dependencies]
 clap = { version = "4.5", features = ["derive"], optional = true }
 flate2 = { version = "1.0", optional = true }
-ontolius = { version = "0.7", default-features = false }
+ontolius = { version = "0.7.1", default-features = false }
 regex = "1.11.1"
 serde = { version = "1.0.197", features = ["derive"], optional = true }
 serde_json = { version = "1.0.140", optional = true }

src/format.rs

@@ -0,0 +1,7 @@
+//! The data formats of ontology annotations.
+
+/// Human Phenotype Ontology annotation format.
+pub struct Hpoa;
+
+/// Gene Ontology annotation format.
+pub struct Gaf;

src/go.rs

@@ -1,15 +1,14 @@
 //! Parse Gene Ontology annotations.
-//!
-//! Use [`GoGafAnnotationLoader`] to parse GAF file into [`GoAnnotations`].
+
+use crate::format::Gaf;
+use crate::io::{AnnotationLoadError, AnnotationLoader, ValidationIssue};
 use ontolius::TermId;
 #[cfg(feature = "serde")]
 use serde::{Deserialize, Serialize};
 use std::fmt::{Display, Formatter};
 use std::io::BufRead;
 use std::str::FromStr;
 
-use crate::io::{AnnotationLoadError, AnnotationLoader, ValidationIssue};
-
 /// The number of columns in GO GAF file.
 const GOA_EXPECTED_FIELDS: usize = 17;
 
@@ -223,10 +222,8 @@ pub struct GoAnnotations {
     pub negated_annotation_count: usize,
 }
 
-pub struct GoGafAnnotationLoader;
-
-impl AnnotationLoader<GoAnnotations> for GoGafAnnotationLoader {
-    fn load_from_buf_read<R>(&self, read: R) -> Result<GoAnnotations, AnnotationLoadError>
+impl AnnotationLoader<Gaf> for GoAnnotations {
+    fn load_from_buf_read<R>(read: R) -> Result<GoAnnotations, AnnotationLoadError>
     where
         R: BufRead,
     {
@@ -377,7 +374,6 @@ pub mod stats {
 
 #[cfg(test)]
 mod tests {
-
     use super::*;
 
     #[test]