Slices and merges bigWig files into a single bedGraph file

slice-and-merge.js

#!/usr/bin/env node
/*
 * slice-and-merge - slices and merges bigWig files into a single bedGraph
 *
 * Usage:
 * 	slice-and-merge [OPTIONS] file1.bw file2.bw .. fileN.bw
 *
 * Options:
 * 	-o, --output <FILE>                   output file (default: out.bedGraph)
 * 	-b, --bin <DIR>                       defines the bin directory for utils (default: ./bin)
 * 	-p, --position <CHROM>:<START>-<END>  position to slice, e.g. chr1:1-100000
 * 	-v, --verbose                         print more details
 * 	-h, --help                            print this message
 */

const fs = require('fs')
const path = require('path')
const child_process = require('child_process')
const { promisify } = require('util')
const exec = promisify(child_process.exec)
const writeFile = promisify(fs.writeFile)

const basename = filename => path.basename(filename, path.extname(filename))
const changeExtname = (filename, ext) => path.join(path.dirname(filename), basename(filename) + ext)


const args = process.argv.slice(2)

const options = {
  verbose: false,
  bin: './bin',
  output: 'out.bedGraph'
}
const files = []

if (args.length === 0)
  printUsage()

// Parse arguments
for (let i = 0; i < args.length; i++) {
  const arg = args[i]
  const next = args[i + 1]

  if (['-p', '--position'].some(o => o === arg)) {
    const [ chromosome, position ] = next.split(':')
    const [ start, end ] = position ? position.split('-') : []

    options.chromosome = chromosome
    options.start = start
    options.end = end

    i += 1
  } else if (['-o', '--output'].some(o => o === arg)) {
    options.output = next
    i += 1
  } else if (['-b', '--bin'].some(o => o === arg)) {
    options.bin = next
    i += 1
  } else if (['-v', '--verbose'].some(o => o === arg)) {
    options.verbose = true
  } else if (['-h', '--help'].some(o => o === arg)) {
    printUsage()
  } else {
    files.push(arg)
  }
}

// Command generation

const toWigCommand = file => ({
    output: changeExtname(file, '.wig'),
    command: [
      path.join(options.bin, `bigWigToWig`),
      `${ options.chromosome ? '-chrom=' + options.chromosome : '' }`,
      `${ options.start ? '-start=' + options.start : '' }`,
      `${ options.end ? '-end=' + options.end : '' }`,
      file,
      changeExtname(file, '.wig')
    ].join(' ')
  })

const toBigWigCommand = file => ({
    output: changeExtname(file, '.out.bw'),
    command: [
      path.join(options.bin, `wigToBigWig`),
      file,
      'chrom.sizes',
      changeExtname(file, '.out.bw')
    ].join(' ')
  })

const mergeCommand = files => ({
    output: options.output,
    command: [
      path.join(options.bin, `bigWigMerge`),
      files.join(' '),
      options.output
    ].join(' ')
  })


log(options, '\n')

log('bigWigToWig -------------------------------------------------------')
Promise.all( // bigWigToWig
  files.map(file => {

    const to = toWigCommand(file)
    log(' Running:', to.command)

    return exec(to.command).then(() => to.output)
  })
  .concat(writeFile('chrom.sizes', [options.chromosome, options.end].join(' ')))
)
.then((files) => { // wigToBigWig
  log('wigToBigWig -----------------------------------------------------')
  return Promise.all(
    files.filter(f => f !== undefined).map(file => {

      const to = toBigWigCommand(file)
      log(' Running:', to.command)

      return exec(to.command).then(() => to.output)
    })
  )
})
.then((files) => { // bigWigMerge
  log('bigWigMerge -----------------------------------------------------')

  const merge = mergeCommand(files)
  log(' Running:', merge.command)

  return exec(merge.command).then(() => merge.output)
})
.then((output) => {
  log('Done ------------------------------------------------------------')
  console.log(' Output written at', output)
})
.catch(err =>
  console.error('Error:', err))

function log(...args) {
  if (!options.verbose)
    return
  console.log(...args)
}

function printUsage() {
  console.log('slice-and-merge - slices and merges bigWig files into a single bedGraph')
  console.log('')
  console.log('Usage:')
  console.log('\tslice-and-merge [OPTIONS] file1.bw file2.bw .. fileN.bw')
  console.log('')
  console.log('Options:')
  console.log('\t-o, --output <FILE>                   output file (default: out.bedGraph)')
  console.log('\t-b, --bin <DIR>                       defines the bin directory for utils (default: ./bin)')
  console.log('\t-p, --position <CHROM>:<START>-<END>  position to slice, e.g. chr1:1-100000')
  console.log('\t-v, --verbose                         print more details')
  console.log('\t-h, --help                            print this message')
  process.exit(0)
}