gbffParser/cli.ts

import chalk from 'chalk';
import { getFromAcc } from '.'
import blessed from 'blessed'
import figlet from 'figlet'
import fs from 'fs'
const formatSeq = (seq:string) => {
    return seq.split('').map(c => {
        let r
        switch (c) {
            case 'A':
                r = chalk.green(c)
                break;
            case 'T':
                r = chalk.red(c)
                break;
            case 'C':
                r = chalk.blue(c)
                break;
            case 'G':
                r = chalk.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: string[], lineN:number) => {
    const splittedSts: RegExpMatchArray[] = []
    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('')
}

(async()=>{
    const arg = process.argv.slice(2)
    console.log(chalk.blue('Welcome to gbffParser!'))
    if (arg.length === 0 || arg.length > 1) {
        console.log(chalk.red('Usage : cli.js <Accession>'))
    } else {
        const screen = blessed.screen({
            smartCSR: true,
            dockBorders: true,
            autoPadding: true
        })
        screen.title = 'gbffParser'
     
        const mainBox = blessed.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.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.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 = await getFromAcc(arg[0], dbPath)
        
        if (result) {
            await fs.promises.writeFile('tmp.json', JSON.stringify(result))
            const title = result.features.filter(feature => feature.type === 'gene')[0]?.name || arg[0]
            topBox.setContent(figlet.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();
        }
        

    }
})()