generic-sequence-panel/esm/accessFasta.js

read feature and sequence data and produce highlighted fasta

import { RemoteFile } from "generic-filehandle2";
import { BgzipIndexedFasta } from "@gmod/indexedfasta";
export async function accessFasta(refseq, start, end, fastaURL, upDownBp) {
    const fastaFilehandle = new RemoteFile(fastaURL);
    const faiFilehandle = new RemoteFile(fastaURL + ".fai");
    const gziFilehandle = new RemoteFile(fastaURL + ".gzi");
    const t = new BgzipIndexedFasta({
        fasta: fastaFilehandle,
        fai: faiFilehandle,
        gzi: gziFilehandle,
    });
    const upstreamstart = Math.max(0, start - upDownBp);
    const downstreamend = end + upDownBp;
    const seq = await t.getSequence(refseq, start, end);
    const upstream = await t.getSequence(refseq, upstreamstart, start);
    const downstream = await t.getSequence(refseq, end, downstreamend);
    return {
        seq: seq !== null && seq !== void 0 ? seq : "",
        upstream: upstream !== null && upstream !== void 0 ? upstream : "",
        downstream: downstream !== null && downstream !== void 0 ? downstream : "",
    };
}