denovoAssemblage/index.js

"use strict";
/*
 * Require in path : zgrep, grep
 */
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 __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.denovoAssemblage = void 0;
const child_process_1 = require("child_process");
const os_1 = __importDefault(require("os"));
const path_1 = __importDefault(require("path"));
const fs_1 = __importDefault(require("fs"));
const async_exec = (prog, args, onData, onErr) => {
    return new Promise((resolve, reject) => {
        const child = (0, child_process_1.spawn)(prog, args, { shell: true });
        child.stdout.on('data', data => onData(data.toString().trim()));
        child.stderr.on('data', data => onErr(data.toString().trim()));
        child.on('error', err => reject(err));
        child.on('exit', code => resolve(code));
    });
};
const rmList = (list) => {
    return Promise.all(list.map(e => fs_1.default.promises.rm(e, { recursive: true })));
};
const isDone = (rsltDir) => {
    let done = false;
    if (fs_1.default.existsSync(path_1.default.join(rsltDir, 'contigs.fasta'))) {
        if (fs_1.default.statSync(path_1.default.join(rsltDir, 'contigs.fasta')).size > 1) {
            done = true;
        }
    }
    return done;
};
const denovoAssemblage = (reads, rnames, spadesPath, log) => {
    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
        let readsIn = [];
        let isPairedEnd = false;
        const threads = String(os_1.default.cpus().length);
        if (Array.isArray(reads)) {
            if (reads.length > 2) {
                reject('Only R1 and R2 path are required');
            }
            else {
                console.log('Assuming paired end reads');
                isPairedEnd = true;
                readsIn = reads;
            }
        }
        else {
            readsIn = [reads];
        }
        // Prepare the fastq files for spades inputs
        const rnamesSel = '\'' + rnames.join('\\|') + '\'';
        const tmpSubReads = [];
        let isfq = [];
        for (const R of readsIn) {
            const parsedPath = path_1.default.parse(R);
            const greper = parsedPath.ext === '.gz' ? 'zgrep' : 'grep';
            isfq.push(R.match(/\.fq/) ? true : false);
            const tmp = path_1.default.join(os_1.default.tmpdir(), (+new Date) + '_' + parsedPath.name + (isfq[isfq.length - 1] ? '.fq' : '.fa'));
            tmpSubReads.push(tmp);
            yield async_exec(greper, [rnamesSel, R, '-A3', '--no-group-separator', '>', tmp], log, log);
        }
        const correction = (isfq.filter(e => e).length !== isfq.length || isfq.filter(e => e).length === 0) ? '--only-assembler' : '';
        const args = isPairedEnd ? ['-1', tmpSubReads[0], '-2', tmpSubReads[1]] : ['-s', tmpSubReads[0]];
        const rsltDir = path_1.default.join(os_1.default.tmpdir(), (+new Date) + '_spades');
        yield async_exec(spadesPath, ['-t', threads, '--isolate', correction, ...args, '-o', rsltDir], log, log);
        if (!isDone(rsltDir) && isPairedEnd) {
            yield rmList([rsltDir]);
            console.log('Trying meta');
            yield async_exec(spadesPath, ['-t', threads, '--meta', correction, ...args, '-o', rsltDir], log, log);
            if (!isDone(rsltDir)) {
                yield rmList([rsltDir, ...tmpSubReads]);
                reject('No convergence');
            }
            else {
                yield rmList(tmpSubReads);
                resolve(rsltDir);
            }
        }
        else if (!isDone(rsltDir) && !isPairedEnd) {
            yield rmList([rsltDir, ...tmpSubReads]);
            reject('No convergence');
        }
        else if (isDone(rsltDir)) {
            yield rmList(tmpSubReads);
            resolve(rsltDir);
        }
    }));
};
exports.denovoAssemblage = denovoAssemblage;
/*
(async()=>{
    const spadesPath = '/home/thomas/NGS/tools/SPAdes-3.15.0-Linux/bin/spades.py'
    const reads2 = ['/home/thomas/Documents/Programmes/ttest/R1r.fq', '/home/thomas/Documents/Programmes/ttest/R2r.fq']
    const rnames = [
        'A00680:166:HYCYGDMXX:1:1212:20528:10520_1',
        'A00680:166:HYCYGDMXX:2:2184:24442:19680_2',
        'A00680:166:HYCYGDMXX:1:1419:9344:19586_1',
        'A00680:166:HYCYGDMXX:1:1306:14479:14387_1',
        'A00680:166:HYCYGDMXX:2:2184:24442:19680_1',
        'A00680:166:HYCYGDMXX:2:2148:4779:14653',
        'A00680:166:HYCYGDMXX:2:2148:4860:14826',
        'A00680:166:HYCYGDMXX:2:2148:4924:14935',
        'A00680:166:HYCYGDMXX:2:2148:4933:14920',
        'A00680:166:HYCYGDMXX:2:1205:29559:23249_2',
        'A00680:166:HYCYGDMXX:2:1205:29559:23249',
        'A00680:166:HYCYGDMXX:1:1209:1497:28354',
        'A00680:166:HYCYGDMXX:2:2177:24171:24189_1',
        'A00680:166:HYCYGDMXX:2:2221:30635:15875',
        'A00680:166:HYCYGDMXX:2:1336:8034:35916_2',
        'A00680:166:HYCYGDMXX:2:1336:8052:35916_2',
        'A00680:166:HYCYGDMXX:2:1336:8034:35916',
        'A00680:166:HYCYGDMXX:2:1336:8052:35916',
        'A00680:166:HYCYGDMXX:2:1355:24758:35759',
        'A00680:166:HYCYGDMXX:2:1356:27398:2879',
        'A00680:166:HYCYGDMXX:2:1360:31955:31187_2',
        'A00680:166:HYCYGDMXX:1:2342:28999:6715_2',
        'A00680:166:HYCYGDMXX:1:2342:28999:6715',
        'A00680:166:HYCYGDMXX:1:2213:1072:3818_2',
        'A00680:166:HYCYGDMXX:1:2213:1072:3818',
        'A00680:166:HYCYGDMXX:1:2310:10764:5572_2',
        'A00680:166:HYCYGDMXX:1:2442:17671:31407_2',
        'A00680:166:HYCYGDMXX:2:1409:10122:17613_2',
        'A00680:166:HYCYGDMXX:2:1409:10981:19977_2',
        'A00680:166:HYCYGDMXX:2:2414:23764:19038_2',
        'A00680:166:HYCYGDMXX:1:1262:3323:12164',
        'A00680:166:HYCYGDMXX:2:2414:23764:19038',
        'A00680:166:HYCYGDMXX:1:1467:31105:14215',
        'A00680:166:HYCYGDMXX:2:2212:10926:6417',
        'A00680:166:HYCYGDMXX:1:1262:3323:12164_1',
        'A00680:166:HYCYGDMXX:1:1157:13214:20932_2',
        'A00680:166:HYCYGDMXX:1:1157:13223:20948_2',
        'A00680:166:HYCYGDMXX:1:1157:14145:20040_2',
        'A00680:166:HYCYGDMXX:2:1360:2356:14465',
        'A00680:166:HYCYGDMXX:2:1360:2356:14465_1',
        'A00680:166:HYCYGDMXX:1:1220:28492:17237',
        'A00680:166:HYCYGDMXX:1:2220:28782:13573',
        'A00680:166:HYCYGDMXX:2:1448:26024:25958',
        'A00680:166:HYCYGDMXX:2:2420:7175:19774',
        'A00680:166:HYCYGDMXX:2:1317:17372:23437',
        'A00680:166:HYCYGDMXX:2:2420:10673:32002_2',
        'A00680:166:HYCYGDMXX:2:2420:10673:32002',
        'A00680:166:HYCYGDMXX:2:2420:10999:32847_2',
        'A00680:166:HYCYGDMXX:2:2420:10999:32847',
        'A00680:166:HYCYGDMXX:2:2420:9697:32628_2',
        'A00680:166:HYCYGDMXX:2:2420:9697:32628',
        'A00680:166:HYCYGDMXX:2:2229:25012:10582_2',
        'A00680:166:HYCYGDMXX:2:2229:25012:10582',
        'A00680:166:HYCYGDMXX:2:2229:25165:9846_2',
        'A00680:166:HYCYGDMXX:2:2229:25165:9846',
        'A00680:166:HYCYGDMXX:2:2229:25328:10128_2',
        'A00680:166:HYCYGDMXX:2:2229:25328:10128',
        'A00680:166:HYCYGDMXX:2:2229:25165:9846_1',
        'A00680:166:HYCYGDMXX:2:1317:17372:23437_1',
        'A00680:166:HYCYGDMXX:1:2176:11071:20697_2',
        'A00680:166:HYCYGDMXX:1:2176:11071:20697',
        'A00680:166:HYCYGDMXX:2:2132:9534:32064',
        'A00680:166:HYCYGDMXX:1:2105:13187:20165_2',
        'A00680:166:HYCYGDMXX:1:2105:13187:20165',
        'A00680:166:HYCYGDMXX:1:2105:15365:20713',
        'A00680:166:HYCYGDMXX:1:2105:16559:20462',
        'A00680:166:HYCYGDMXX:1:2463:16152:4883_2',
        'A00680:166:HYCYGDMXX:1:2463:18656:8844_2',
        'A00680:166:HYCYGDMXX:2:2318:21694:26224',
        'A00680:166:HYCYGDMXX:2:2318:22209:27993',
        'A00680:166:HYCYGDMXX:2:1319:15908:27320_2',
        'A00680:166:HYCYGDMXX:1:1462:5665:12774_1',
        'A00680:166:HYCYGDMXX:1:2144:14796:8547_1',
        'A00680:166:HYCYGDMXX:1:2144:14796:8547',
        'A00680:166:HYCYGDMXX:1:1149:20139:3270',
        'A00680:166:HYCYGDMXX:1:1149:24343:11490',
        'A00680:166:HYCYGDMXX:1:1458:12228:29434_2',
        'A00680:166:HYCYGDMXX:1:1458:12228:29434',
        'A00680:166:HYCYGDMXX:1:1462:5665:12774',
        'A00680:166:HYCYGDMXX:1:2105:15365:20713_2',
        'A00680:166:HYCYGDMXX:1:2105:16559:20462_2',
        'A00680:166:HYCYGDMXX:1:2144:14796:8547_2',
        'A00680:166:HYCYGDMXX:2:1367:20166:33974_2',
        'A00680:166:HYCYGDMXX:2:2301:7066:16141',
        'A00680:166:HYCYGDMXX:2:2258:4227:16892',
        'A00680:166:HYCYGDMXX:2:2229:25012:10582_1',
        'A00680:166:HYCYGDMXX:2:1228:29939:33176',
        'A00680:166:HYCYGDMXX:1:1425:24975:12587',
        'A00680:166:HYCYGDMXX:1:2450:13874:8265',
        'A00680:166:HYCYGDMXX:2:1367:20166:33974'
    ]
    const uniq_reads = [...new Set(rnames.map(e => e.split(/_[1-2]$/)[0]))];
    console.log(await denovoAssemblage(reads2, uniq_reads, spadesPath, console.log));
})()*/