Crate rtemis_a3 

rtemis-a3

Rust implementation of the A3 (Amino Acid Annotation) format.

A3 is a structured format for annotating amino acid sequences with site, region, post-translational modification, processing, and variant information.

Quick start

use rtemis_a3::{a3_from_json, a3_to_json};

// `annotations` and `metadata` are optional; both default to empty.
let json = r#"{
  "$schema": "https://schema.rtemis.org/a3/v1/schema.json",
  "a3_version": "1.0.0",
  "sequence": "MAEPRQ"
}"#;

let a3 = a3_from_json(json).unwrap();
assert_eq!(a3.sequence(), "MAEPRQ");

Error handling

Validation is collect-all: a document is checked in four stages, every issue in the earliest failing stage is reported at once, and each issue carries a stable code and an RFC 6901 JSON Pointer.

use rtemis_a3::a3_from_json;

let json = r#"{
  "$schema": "https://schema.rtemis.org/a3/v1/schema.json",
  "a3_version": "1.0.0",
  "sequence": "MAEPRQ",
  "annotations": { "site": { "active": { "index": [3, 99] } } }
}"#;

let err = a3_from_json(json).unwrap_err();
let issues = err.issues();
assert_eq!(issues.len(), 1);
assert_eq!(issues[0].code.code(), "A3E_POS_OUT_OF_BOUNDS");
assert_eq!(issues[0].path, "/annotations/site/active/index/1");
assert_eq!(err.stage(), Some(4));

Codes and paths are contractual and identical across the R, Python, Julia, TypeScript, and Rust implementations. Messages are not — they may be reworded freely. See spec/error-codes.md and spec/error-paths.md.

Module layout

• error — A3Error enum
• issue — A3Issue, A3IssueCode, JSON Pointer construction
• types — data model structs and enums
• normalization — the three normalization rules
• validation — four-stage validation over the raw parsed JSON

Re-exports

pub use error::A3Error;

pub use issue::A3Issue;

pub use issue::A3IssueCode;

pub use types::A3;

pub use types::A3_SCHEMA_URI;

pub use types::A3_VERSION;

pub use types::A3Index;

pub use types::Annotations;

pub use types::FlexEntry;

pub use types::Metadata;

pub use types::RegionEntry;

pub use types::SiteEntry;

pub use types::VariantRecord;

pub use validation::validate;

Modules

error

Error types for the rtemis-a3 library.

issue

Validation issues: stable codes, RFC 6901 paths, and human messages.

normalization

Normalization — the three transformations A3 applies to a valid document.

types

Data model for the A3 format.

validation

Four-stage A3 validation over the raw parsed JSON.

Functions

a3_from_json

Parse and validate an A3 JSON string.

a3_to_json

Serialize a validated A3 to a JSON string.

residue_at

Return the amino acid character at a 1-based position.

variants_at

Return all variant records at a 1-based position.