molstar/lib/cli/cif2bcif/index.js

A comprehensive macromolecular library.

#!/usr/bin/env node
/**
 * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
import { __awaiter, __generator } from "tslib";
import * as argparse from 'argparse';
import * as util from 'util';
import * as fs from 'fs';
import * as zlib from 'zlib';
import { convert } from './converter';
require('util.promisify').shim();
function process(srcPath, outPath, configPath, filterPath) {
    return __awaiter(this, void 0, void 0, function () {
        var config, filter, res;
        return __generator(this, function (_a) {
            switch (_a.label) {
                case 0:
                    config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
                    filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
                    return [4 /*yield*/, convert(srcPath, false, config, filter)];
                case 1:
                    res = _a.sent();
                    return [4 /*yield*/, write(outPath, res)];
                case 2:
                    _a.sent();
                    return [2 /*return*/];
            }
        });
    });
}
var zipAsync = util.promisify(zlib.gzip);
function write(outPath, res) {
    return __awaiter(this, void 0, void 0, function () {
        var isGz;
        return __generator(this, function (_a) {
            switch (_a.label) {
                case 0:
                    isGz = /\.gz$/i.test(outPath);
                    if (!isGz) return [3 /*break*/, 2];
                    return [4 /*yield*/, zipAsync(res)];
                case 1:
                    res = _a.sent();
                    _a.label = 2;
                case 2:
                    fs.writeFileSync(outPath, res);
                    return [2 /*return*/];
            }
        });
    });
}
function run(args) {
    process(args.src, args.out, args.config, args.filter);
}
var parser = new argparse.ArgumentParser({
    add_help: true,
    description: 'Convert any CIF file to a BCIF file'
});
parser.add_argument('src', {
    help: 'Source CIF path'
});
parser.add_argument('out', {
    help: 'Output BCIF path'
});
parser.add_argument('-c', '--config', {
    help: 'Optional encoding strategy/precision config path',
    required: false
});
parser.add_argument('-f', '--filter', {
    help: 'Optional filter whitelist/blacklist path',
    required: false
});
var args = parser.parse_args();
if (args) {
    run(args);
}
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