• ¶

    fasta-parser

    Buffer Stream parser from FASTA to JSON.

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

  • ¶

    Usage

    $ npm install fasta-parser

var parser = require('fasta-parser')

var fastaData = new Buffer ('>sequence1\n\
ATGCACGTCACGTCAGTACTCGTCAGTAC\n\
>sequence2\n\
CAGTCCTACTGCATGCATGCATGCATGCATCGATGCATGTCGACTGCATGCATGC\n')

var parser = fasta()
parser.on('data', function(data) {
  console.log(JSON.parse(data.toString()))
})
parser.write(fastaData)
parser.end()
//   { id: 'sequence1',
//     seq: 'ATGCACGTCACGTCAGTACTCGTCAGTAC' }
//   { id: 'sequence2',
//     seq: 'CAGTCCTACTGCATGCATGCATGCATGCATCGATGCATGTCGACTGCATGCATGC' }

    For a more useful API, check the dependent module:

    bionode-fasta

    var through = require('through2')
var split = require('split')
var pumpify = require('pumpify')

module.exports = function() {
  return pumpify(split(), parser())
}

function parser() {
  var cacheBuf
  var cacheBufLen = 8
  var openID = new Buffer('{"id":"')
  var closeIDOpenSeq = new Buffer('","seq":"')
  var closeSeq = new Buffer('"}\n')
  var stream = through(transform, flush)

  return stream

  function transform(buf, enc, next) {
    if (buf[0] === 62) { // If line starts with '>', this is an ID
      if (cacheBuf) { // If a previous object is in cache, push it
        cacheBuf = Buffer.concat([cacheBuf, closeSeq], cacheBufLen+3)
        this.push(cacheBuf)
      }
      var id = buf.toString().slice(1).trim().replace(/"/g, '\\"')
      cacheBufLen = id.length + 16
      cacheBuf = Buffer.concat([openID, new Buffer(id), closeIDOpenSeq], cacheBufLen)
    }
    else {
      cacheBufLen += buf.length
      cacheBuf = Buffer.concat([cacheBuf, buf], cacheBufLen)
    }
    next()
  }

  function flush() {
    cacheBuf = Buffer.concat([cacheBuf, closeSeq], cacheBufLen+3)
    this.push(cacheBuf)
    this.push(null)
  }
}