ProteinAlphabet

https://schemas.wur.nl/betula/core/protein-alphabet/0.6.0/schema.json

IUPAC amino acid codes: the standard 20 (A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y) plus the ambiguity/special codes B (Asx), Z (Glx), X (any), J (Leu/Ile), U (selenocysteine), O (pyrrolysine) -- together these cover all 26 letters, so this pattern is effectively any letter. Also allows ‘*’ for a stop codon, and ‘-’/‘.’ as alignment gap/missing-data characters, since a Sequence doubles as an alignment row. Case-insensitive.

string (minLength 1, pattern ^[A-Za-z*.-]*$)

Valid examples¶

"MKBZXJUO*-"

Invalid examples¶

"MK123"

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://schemas.wur.nl/betula/core/protein-alphabet/0.6.0/schema.json",
  "title": "ProteinAlphabet",
  "description": "IUPAC amino acid codes: the standard 20 (A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y) plus the ambiguity/special codes B (Asx), Z (Glx), X (any), J (Leu/Ile), U (selenocysteine), O (pyrrolysine) -- together these cover all 26 letters, so this pattern is effectively any letter. Also allows '*' for a stop codon, and '-'/'.' as alignment gap/missing-data characters, since a Sequence doubles as an alignment row. Case-insensitive.",
  "type": "string",
  "minLength": 1,
  "pattern": "^[A-Za-z*.-]*$"
}

Usage¶

Read a JSON document and parse it as a ProteinAlphabet. CI runs this exact code against the first valid example above; see Getting started to install the bindings.

from betula_schema import ProteinAlphabet, parse_json

with open("protein-alphabet.json") as f:
    protein_alphabet = parse_json(ProteinAlphabet, f.read())
# ProteinAlphabet is a RootModel; protein_alphabet.root is the plain value
print(protein_alphabet)

import { readFileSync } from "node:fs";
import { parseJson, type ProteinAlphabet } from "betula-schema";

const proteinAlphabet: ProteinAlphabet = parseJson("ProteinAlphabet", readFileSync("protein-alphabet.json", "utf8"));
console.log(proteinAlphabet);

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let text = std::fs::read_to_string("protein-alphabet.json")?;
    let protein_alphabet: betula_schema::ProteinAlphabet = betula_schema::parse_str(&text)?;
    // ProteinAlphabet is a newtype; deref it (&*protein_alphabet) for the inner value
    println!("{protein_alphabet:?}");
    Ok(())
}