uniprotParser/fillInteractDB.js

"use strict";
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());
    });
};
var __asyncValues = (this && this.__asyncValues) || function (o) {
    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
    var m = o[Symbol.asyncIterator], i;
    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
};
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const _1 = require(".");
const fs_1 = __importDefault(require("fs"));
const readline_1 = __importDefault(require("readline"));
const { Database, aql } = require("arangojs");
const fast_xml_parser_1 = require("fast-xml-parser");
const db = new Database({
    url: "http://localhost:8529",
    databaseName: "test",
    auth: { username: "root", password: "test123" },
});
const line$ = (path) => readline_1.default.createInterface({
    input: fs_1.default.createReadStream(path),
    crlfDelay: Infinity
});
const parser = new fast_xml_parser_1.XMLParser({
    ignoreAttributes: false,
    alwaysCreateTextNode: false,
    attributeNamePrefix: "",
    textNodeName: "value",
    allowBooleanAttributes: true,
});
(() => __awaiter(void 0, void 0, void 0, function* () {
    var e_1, _a;
    const uniprotDB = '/home/thomas/NGS/ref/UNIPROT/uniprot_sprot_human.xml';
    try {
        for (var _b = __asyncValues(line$(uniprotDB + '.jsi')), _c; _c = yield _b.next(), !_c.done;) {
            const line = _c.value;
            const acc = /;/.test(line) ? line.split(';')[0] : line.split(/\t/)[0];
            const [from, to] = [line.split(/\t/)[1], line.split(/\t/)[2]];
            const tmp = parser.parse(yield (0, _1.readOffset)(uniprotDB, Number(from), Number(to)));
            if (Object.keys(tmp).length === 0) {
                break;
            }
            else {
                try {
                    const inter = yield (0, _1.getInteractionsFromEntry)(tmp);
                }
                catch (error) {
                    console.log(error);
                    console.log(acc);
                    console.log(tmp.entry.gene);
                    console.log(tmp);
                    break;
                }
            }
        }
    }
    catch (e_1_1) { e_1 = { error: e_1_1 }; }
    finally {
        try {
            if (_c && !_c.done && (_a = _b.return)) yield _a.call(_b);
        }
        finally { if (e_1) throw e_1.error; }
    }
}))();