gbffParser/cli.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 });
const chalk_1 = __importDefault(require("chalk"));
const _1 = require(".");
const blessed_1 = __importDefault(require("blessed"));
const figlet_1 = __importDefault(require("figlet"));
const fs_1 = __importDefault(require("fs"));
const formatSeq = (seq) => {
    return seq.split('').map(c => {
        let r;
        switch (c) {
            case 'A':
                r = chalk_1.default.green(c);
                break;
            case 'T':
                r = chalk_1.default.red(c);
                break;
            case 'C':
                r = chalk_1.default.blue(c);
                break;
            case 'G':
                r = chalk_1.default.yellow(c);
                break;
            case '.':
                //r = chalk.hex('#FF0000').bgBlue(' ')
                // r = chalk.bgHex('#DEADED').underline(' ')
                // break;
                r = c;
            default:
                r = c;
                break;
        }
        return r;
    }).join('');
};
const combineSTr = (strings, lineN) => {
    const splittedSts = [];
    const r = new RegExp(".{1," + lineN + "}", "g");
    for (const s of strings) {
        const tmpLines = s.match(r) || [];
        const resLines = [];
        for (const line of tmpLines)
            resLines.push(line.length < lineN ? line + ' '.repeat(lineN - line.length) : line);
        splittedSts.push(resLines);
    }
    const firstLines = splittedSts.shift() || [];
    return firstLines.map((e, i) => formatSeq(e.toUpperCase()) + formatSeq(splittedSts.map(ee => ee[i]).join(''))).join('');
};
(() => __awaiter(void 0, void 0, void 0, function* () {
    var _a;
    const arg = process.argv.slice(2);
    console.log(chalk_1.default.blue('Welcome to gbffParser!'));
    if (arg.length === 0 || arg.length > 1) {
        console.log(chalk_1.default.red('Usage : cli.js <Accession>'));
    }
    else {
        const screen = blessed_1.default.screen({
            smartCSR: true,
            dockBorders: true,
            autoPadding: true
        });
        screen.title = 'gbffParser';
        const mainBox = blessed_1.default.box({
            top: '15%',
            left: '10%',
            width: '90%',
            height: '85%',
            content: '',
            tags: true,
            border: {
                type: 'line'
            },
            scrollable: true,
            scrollbar: {
                style: { bg: 'blue' },
            },
            keys: true,
            mouse: false,
            style: {
                fg: 'white',
                border: {
                    fg: '#f0f0f0'
                }
            }
        });
        const topBox = blessed_1.default.box({
            top: 0,
            left: 0,
            width: '100%',
            height: '15%',
            content: 'top',
            tags: true,
            border: {
                type: 'line'
            },
            scrollable: false,
            keys: true,
            mouse: false,
            style: {
                fg: 'white',
                border: {
                    fg: '#f0f0f0'
                }
            }
        });
        const leftBox = blessed_1.default.box({
            top: '15%',
            left: 0,
            width: '10%',
            height: '85%',
            content: 'left',
            tags: true,
            border: {
                type: 'line'
            },
            scrollable: false,
            keys: true,
            mouse: false,
            style: {
                fg: 'white',
                border: {
                    fg: '#f0f0f0'
                }
            }
        });
        screen.append(topBox);
        screen.append(leftBox);
        screen.append(mainBox);
        screen.key(['escape', 'q', 'C-c'], (ch, key) => process.exit(0));
        const dbPath = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10].map(n => '/home/thomas/NGS/ref/ncbi/RNA/human.' + n + '.rna.gbff');
        const result = yield (0, _1.getFromAcc)(arg[0], dbPath);
        if (result) {
            yield fs_1.default.promises.writeFile('tmp.json', JSON.stringify(result));
            const title = ((_a = result.features.filter(feature => feature.type === 'gene')[0]) === null || _a === void 0 ? void 0 : _a.name) || arg[0];
            topBox.setContent(figlet_1.default.textSync(title));
            mainBox.setContent(result.sequence);
            mainBox.focus();
            const lineN = mainBox.getScreenLines()[0].length;
            mainBox.setContent(combineSTr([result.sequence, result.sequence.split('').map(e => '.').join('')], lineN));
            screen.render();
        }
    }
}))();