SequenceReference

https://schemas.wur.nl/betula/core/sequence-reference/0.6.0/schema.json

A pointer to a Sequence by identifier, without embedding the sequence itself. Not yet consumed by another betula schema (every current producer embeds full Sequence objects, e.g. in alignment); this exists as the reusable primitive for when a by-reference link is needed, e.g. a hit record pointing at a locally-known query sequence instead of repeating it.

Field	Type	Required	Description
`identifier`	Identifier	required

No properties beyond those listed are allowed.

Valid examples¶

simple.json

{
  "identifier": "seq1"
}

Invalid examples¶

missing-identifier.json

{}

sequence-reference.schema.json

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://schemas.wur.nl/betula/core/sequence-reference/0.6.0/schema.json",
  "title": "SequenceReference",
  "description": "A pointer to a Sequence by identifier, without embedding the sequence itself. Not yet consumed by another betula schema (every current producer embeds full Sequence objects, e.g. in alignment); this exists as the reusable primitive for when a by-reference link is needed, e.g. a hit record pointing at a locally-known query sequence instead of repeating it.",
  "type": "object",
  "properties": {
    "identifier": { "$ref": "https://schemas.wur.nl/betula/core/identifier/0.6.0/schema.json" }
  },
  "required": ["identifier"],
  "additionalProperties": false
}

Usage¶

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

Python

TypeScript

Rust

sequence-reference.py

from betula_schema import SequenceReference, parse_json

with open("sequence-reference.json") as f:
    sequence_reference = parse_json(SequenceReference, f.read())
print(sequence_reference)

sequence-reference.ts

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

const sequenceReference: SequenceReference = parseJson("SequenceReference", readFileSync("sequence-reference.json", "utf8"));
console.log(sequenceReference);

sequence-reference.rs

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let text = std::fs::read_to_string("sequence-reference.json")?;
    let sequence_reference: betula_schema::SequenceReference = betula_schema::parse_str(&text)?;
    println!("{sequence_reference:?}");
    Ok(())
}