• ¶

    bionode-sra

    A Node.js wrapper for SRA Toolkit.

    doi: ? author: Bruno Vieira email: mail@bmpvieira.com license: MIT

  • ¶

    Usage

    This module can be used in Node.js as described further below, or as a command line tool. Examples:

    $ npm install -g bionode-sra

# bionode-sra [command] [arguments...]
$ bionode-sra fastq-dump SRR1509835.sra
$ bionode-sra fastq-dump SRR1509835.sra fastqOutputDirectory

    
var path = require('path')
var spawn = require('child_process').spawn
var through = require('through2')

module.exports = exports = SRA
  • ¶

    SRA

    Takes a SRA toolkit command and returns a Stream that accepts arguments for it. For example, for fastq-dump, arguments can be an array with [srcSRA, destDir], a string like 'srcSRA destDir'. If destDir is omitted, the current directory will be used.

    var sra = require('bionode-sra')
var fastqDump = sra('fastq-dump')()
fastqDump.on('data', console.log)
fastqDump.write(['SRR1509835.sra', 'fastqOutDir'])
=> { srcFile: 'SRR1509835.sra',
     command: 'fastq-dump',
     destDir: 'fastqOutDir' }

    A callback style can also be used:

    var fastqDump = sra('fastq-dump')
fastqDump('SRR1509835.sra fastqOutDir', function(err, data) {
  console.log(data)
})

    Or pipes, for example, from a file with just a list of SRA file names:

    var split = require('split')
var fastqDump = sra('fastq-dump')()
fs.createReadStream('sraFilesList.txt')
.pipe(split())
.pipe(fastqDump)

    function SRA(command) {
  var command = command || 'fastq-dump'

  return sraStream

  function sraStream(srcFileDestDir, callback) {
    var stream = through.obj(transform)
    if (srcFileDestDir) { stream.write(srcFileDestDir); stream.end() }
    if (callback) {
      stream.on('data', function(data) {
        callback(null, data)
      })
      stream.on('error', callback)
    }
    return stream

    function transform(obj, enc, next) {
      var self = this

      if (typeof obj === 'string') { obj = obj.split(' ') }

      if (obj.length > 2) { self.emit('error', new Error('Too many arguments')); next() }

      if (obj.length === 1) { obj.push('.') }

      var sraPath = path.join(__dirname, '../sra/bin/'+command)
      var srcFile = obj[0]
      var destDir = obj[1]
      var options
      if (destDir === '.') {
        options = [srcFile]
      }
      else {
        var options = [srcFile, '-O', destDir]
      }
      var sra = spawn(sraPath, options)

      sra.stderr.on('data', function(data) {
        self.emit('error', new Error(data.toString()))
        next()
      })

      sra.on('close', function(code) {
        if (code) {
          self.emit('error', new Error('Unknown error, check that "'+obj[0]+'" exists'))
        }
        else {
          self.push({srcFile: obj[0], command: command, destDir: obj[1]})
          next()
        }
      })
    }
  }
}