generic-sequence-panel
Version:
read feature and sequence data and produce highlighted fasta
37 lines (36 loc) • 2.04 kB
JavaScript
;
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
return new (P || (P = Promise))(function (resolve, reject) {
function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
step((generator = generator.apply(thisArg, _arguments || [])).next());
});
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.accessFasta = accessFasta;
const generic_filehandle2_1 = require("generic-filehandle2");
const indexedfasta_1 = require("@gmod/indexedfasta");
function accessFasta(refseq, start, end, fastaURL, upDownBp) {
return __awaiter(this, void 0, void 0, function* () {
const fastaFilehandle = new generic_filehandle2_1.RemoteFile(fastaURL);
const faiFilehandle = new generic_filehandle2_1.RemoteFile(fastaURL + ".fai");
const gziFilehandle = new generic_filehandle2_1.RemoteFile(fastaURL + ".gzi");
const t = new indexedfasta_1.BgzipIndexedFasta({
fasta: fastaFilehandle,
fai: faiFilehandle,
gzi: gziFilehandle,
});
const upstreamstart = Math.max(0, start - upDownBp);
const downstreamend = end + upDownBp;
const seq = yield t.getSequence(refseq, start, end);
const upstream = yield t.getSequence(refseq, upstreamstart, start);
const downstream = yield 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 : "",
};
});
}