generic-sequence-panel/src/fetchTranscripts.ts

read feature and sequence data and produce highlighted fasta

import { RemoteFile } from "generic-filehandle2";
import NCList from "@gmod/nclist";
import { Feature } from "@jbrowse/core/util";

// Create transcriptList function this function is called by the SeqPanel
// component when it needs to fetch a list of transcripts for a given gene it
// should return an array of transcript names (see @gmod/nclist for more info)
//
// it is called with five arguments:
// - nclistbaseurl: the base URL of the NCList file
// - urltemplate: the URL template for the NCList file
// - refseq: the reference sequence (name, like "chr1")
// - start: the start of the range (in interbase coordinates)
// - end: the end of the range (in interbase coordinates)
// - gene: the name of the gene
export default async function fetchTranscripts({
  nclistbaseurl,
  urltemplate,
  refseq,
  start,
  end,
  gene,
}: {
  nclistbaseurl: string;
  urltemplate: string;
  refseq: string;
  start: number;
  end: number;
  gene: string;
}): Promise<Feature[]> {
  if (refseq == "NC_045512.2") {
    throw new Error(
      "Unfortunately, Sequence Details doesn't yet support fetching viral sequences; sorry.",
    );
  }

  const store = new NCList({
    urlTemplate: urltemplate,
    baseUrl: nclistbaseurl,
    readFile: (url: string) => new RemoteFile(url).readFile(),
  });

  for await (const feature of store.getFeatures({
    refName: refseq,
    start: start,
    end: end,
  })) {
    const f = feature as Feature;
    if (f.get("name") === gene) {
      return f.get("subfeatures") ?? [];
    }
  }
  return [];
}