RnaAlphabet

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

IUPAC nucleotide codes for RNA: A/C/G/U plus the standard ambiguity codes (R,Y,S,W,K,M,B,D,H,V,N). ‘T’ is deliberately excluded (that’s DnaAlphabet). Also allows ‘-’ and ‘.’ as alignment gap/missing-data characters, since a Sequence doubles as an alignment row. Case-insensitive.

string (minLength 1, pattern ^[ACGURYSWKMBDHVNacguryswkmbdhvn.-]*$)

Valid examples¶

"ACGURYSWKMBDHVNacguryswkmbdhvn.-"

Invalid examples¶

"ACGT"

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://schemas.wur.nl/betula/core/rna-alphabet/0.6.0/schema.json",
  "title": "RnaAlphabet",
  "description": "IUPAC nucleotide codes for RNA: A/C/G/U plus the standard ambiguity codes (R,Y,S,W,K,M,B,D,H,V,N). 'T' is deliberately excluded (that's DnaAlphabet). Also allows '-' and '.' as alignment gap/missing-data characters, since a Sequence doubles as an alignment row. Case-insensitive.",
  "type": "string",
  "minLength": 1,
  "pattern": "^[ACGURYSWKMBDHVNacguryswkmbdhvn.-]*$"
}

Usage¶

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

from betula_schema import RnaAlphabet, parse_json

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

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

const rnaAlphabet: RnaAlphabet = parseJson("RnaAlphabet", readFileSync("rna-alphabet.json", "utf8"));
console.log(rnaAlphabet);

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