GOparser/index.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 });
exports.getGOterms = exports.getSymbol = void 0;
const fs_1 = __importDefault(require("fs"));
const readline_1 = __importDefault(require("readline"));
const line$ = (path) => readline_1.default.createInterface({
    input: fs_1.default.createReadStream(path),
    crlfDelay: Infinity
});
// http://geneontology.org/docs/guide-go-evidence-codes/
// http://wiki.geneontology.org/index.php/Category:Evidence_Codes
const getSymbol = (symbol, goaPath, oboPath) => __awaiter(void 0, void 0, void 0, function* () {
    var e_1, _a;
    var _b;
    const header = [
        'database', 'ID', 'Symbol', 'Qualifier',
        'GO_Term', 'Evidence', 'Evidence_Code',
        'With', 'From', 'Name', 'Alternative_symbols',
        'Class', 'Taxon', 'Date', 'Origin'
    ];
    const tester = new RegExp('\t' + symbol + '\t');
    const separator = new RegExp('\\|');
    const results = [];
    try {
        for (var _c = __asyncValues(line$(goaPath)), _d; _d = yield _c.next(), !_d.done;) {
            const line = _d.value;
            if (tester.test(line))
                results.push(line.split('\t').reduce((p, c, i) => (Object.assign(Object.assign({}, p), { [header[i]]: separator.test(c) ? c.split('|') : c })), {}));
        }
    }
    catch (e_1_1) { e_1 = { error: e_1_1 }; }
    finally {
        try {
            if (_d && !_d.done && (_a = _c.return)) yield _a.call(_c);
        }
        finally { if (e_1) throw e_1.error; }
    }
    const subTerms = results.map(e => e === null || e === void 0 ? void 0 : e.GO_Term);
    const cacheTerms = yield getGOterms(subTerms, oboPath);
    for (let index = 0; index < results.length; index++) {
        const goTerm = (_b = results[index]) === null || _b === void 0 ? void 0 : _b.GO_Term;
        results[index]['GO_Term'] = cacheTerms.filter(e => e.id === goTerm)[0];
    }
    return results;
});
exports.getSymbol = getSymbol;
const getGOterms = (terms, oboPath) => __awaiter(void 0, void 0, void 0, function* () {
    var e_2, _e;
    const testerList = terms.map(e => new RegExp('id: ' + e));
    let delim = false;
    const results = [];
    let result = {};
    try {
        for (var _f = __asyncValues(line$(oboPath)), _g; _g = yield _f.next(), !_g.done;) {
            const line = _g.value;
            if (testerList.some(rx => rx.test(line)))
                delim = true;
            if (line === '' && delim) {
                delim = false;
                results.push(result);
                result = {};
            }
            if (delim)
                result[line.split(': ')[0]] = line.split(': ')[1];
        }
    }
    catch (e_2_1) { e_2 = { error: e_2_1 }; }
    finally {
        try {
            if (_g && !_g.done && (_e = _f.return)) yield _e.call(_f);
        }
        finally { if (e_2) throw e_2.error; }
    }
    return results;
});
exports.getGOterms = getGOterms;