unprepare_seqs.js

// usage:
// download this file to a file unprepare_seqs.js
// then run:
// node unprepare_seqs.js /path/to/seq/dir output_file.fa
// after that, fold the lines to a constant line length with:
// fold output_file.fa > output_file2.fa
const fs = require('fs')
const path = require('path')
const dir = process.argv[2] || '.'
const output = process.argv[3] || 'out.fa'
const obj = {}
fs.readdirSync(dir, { recursive: true }).forEach(d => {
  const ret = d.lastIndexOf('/')
  if (d.indexOf('-') !== -1) {
    const [chr] = d.slice(ret + 1).split('-')
    if (!obj[chr]) {
      obj[chr] = []
    }
    obj[chr].push(d)
  }
})
let ret = ''
Object.entries(obj).forEach(([chr, files]) => {
  let arg = ''
  for (const file of files) {
    arg += fs.readFileSync(path.join(dir, file), 'utf8')
  }
  ret += `>${chr}\n${arg}\n`
})
fs.writeFileSync(output, ret)