generic-sequence-panel/esm/fetchTranscripts.js

read feature and sequence data and produce highlighted fasta

import { RemoteFile } from "generic-filehandle2";
import NCList from "@gmod/nclist";
// 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, }) {
    var _a;
    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) => new RemoteFile(url).readFile(),
    });
    for await (const feature of store.getFeatures({
        refName: refseq,
        start: start,
        end: end,
    })) {
        const f = feature;
        if (f.get("name") === gene) {
            return (_a = f.get("subfeatures")) !== null && _a !== void 0 ? _a : [];
        }
    }
    return [];
}