fasta/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 __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.selectFasta = exports.asyncReadSmallFasta = exports.asyncReadFasta = void 0;
const child_process_1 = require("child_process");
const fs_1 = __importDefault(require("fs"));
const zlib = require('zlib');
const readline = require('readline');
const Papa = require('papaparse');
const async_exec = (prog, args, onData) => {
    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 => onData(data.toString().trim()));
        child.on('error', err => reject(err));
        child.on('exit', code => resolve(code));
    });
};
// Read fasta/fa/fna
const asyncReadSmallFasta = (path) => {
    return new Promise((resolve, reject) => {
        const rs = fs_1.default.createReadStream(path);
        const rl = readline.createInterface({
            input: rs, crlfDelay: Infinity
        });
        rs.once('error', err => reject(err));
        let tmpObj = {};
        let results = [];
        rl.on('line', (line) => {
            if (line.match(/>/g)) {
                if (tmpObj === null || tmpObj === void 0 ? void 0 : tmpObj.name)
                    results.push(tmpObj);
                tmpObj = { name: line, sequence: '' };
            }
            else {
                tmpObj.sequence += line;
            }
        });
        rl.on('close', (_) => {
            results.push(tmpObj);
            resolve(results);
        });
    });
};
exports.asyncReadSmallFasta = asyncReadSmallFasta;
// https://www.biostars.org/p/98885/
const async_save_fai = (fasta_path) => {
    console.log('Creating new fai from : ', fasta_path);
    return new Promise((resolve, reject) => {
        const child = (0, child_process_1.spawn)('samtools', ['faidx', fasta_path], {
            shell: true,
        });
        let result = '';
        child.stdout.on('data', (data) => {
            result += data.toString();
        });
        child.on('error', (err) => {
            reject(err.toString('utf8'));
        });
        child.on('exit', () => {
            resolve(result);
        });
    });
};
const async_paparse = (path, opt) => {
    return new Promise((resolve, reject) => {
        const output = [];
        const parseStream = Papa.parse(Papa.NODE_STREAM_INPUT, opt);
        let rs = fs_1.default.createReadStream(path);
        if ((new RegExp(/\.gz$/)).test(path)) {
            rs = rs.pipe(zlib.createGunzip());
        }
        rs.pipe(parseStream)
            .on('error', (error) => reject(error))
            .on('data', (row) => { output.push(row); })
            .on('finish', () => resolve(output));
    });
};
const async_read_bytes = (path, start, length) => {
    length = length - 1;
    return new Promise((resolve, reject) => {
        let data = Buffer.alloc(0);
        fs_1.default.createReadStream(path, { start: start, end: start + length })
            .on('error', error => reject(error))
            .on('data', (d) => {
            data = Buffer.concat([data, d]);
        })
            .on('end', () => resolve(data.toString()));
    });
};
// Create fai if not present return sequences names and if provided return : obj {name, sequence}
const asyncReadFasta = (path, sequences) => {
    sequences = Array.isArray(sequences) ? sequences : [sequences];
    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
        const path_fai = (new RegExp('fai$')).test(path) ? path : path + '.fai';
        if (!fs_1.default.existsSync(path_fai)) {
            try {
                yield async_save_fai(path);
            }
            catch (e) {
                reject(e);
            }
        }
        try {
            const fai = yield async_paparse(path_fai, { header: false, dynamicTyping: true });
            if (sequences.length === 0) {
                if (Array.isArray(fai))
                    resolve(fai.map((it) => it[0]));
            }
            else {
                let results = [];
                for (let index = 0; index < sequences.length; index++) {
                    const seqName = sequences[index];
                    const tmpFai = Array.isArray(fai) ? fai.filter((it) => it[0] === seqName)[0] : [];
                    const sequence = yield async_read_bytes(path, tmpFai[2], (Math.trunc(tmpFai[1] / tmpFai[3]) * tmpFai[4]) + (tmpFai[1] % tmpFai[3])); // fu, but better use samtools faidx !
                    results.push({ name: tmpFai[0], sequence });
                }
                resolve(results);
            }
        }
        catch (e) {
            reject(e);
        }
    }));
};
exports.asyncReadFasta = asyncReadFasta;
const selectFasta = (path, name, out) => {
    return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
        if (!Array.isArray(name))
            name = [name];
        yield async_exec('samtools', ['faidx', path, ...name, '>', out], console.log);
    }));
};
exports.selectFasta = selectFasta;