bedjs/lib/fasta.js

Manage BED (Browser Extensible Data) files with Node.JS (Bioinformatics)

//Import dependencies
var fs = require('fs');
var path = require('path');
var pstat = require('pstat');

//Import utils
var GetLine = require('./utils/get-line.js');
var Sequence = require('./utils/sequence.js');

//Import bed functions
var bedRead = require('./read.js');
var bedRegion = require('./region.js');

//Get sequence from a fasta file
module.exports.Get = function(fasta, bed, opt)
{
  //Check the options
  if(typeof opt === 'undefined'){ var opt = {}; }

  //Check the strand specific
  if(typeof opt.strand === 'undefined'){ opt.strand = false; }

  //Generate the index file
  var index = fasta + '.json';

  //Check the fasta file
  if(pstat.isFileSync(fasta) === false)
  {
    //Show error
    console.error('Fasta file ' + fasta + ' doesn\'t exists');

    //Return empty
    return [];
  }

  //Check the index file
  if(pstat.isFileSync(index) === false)
  {
    //Show error
    console.error('Index file for fasta file ' + fasta + ' doesn\'t exists. Have you indexed it?');

    //Return empty
    return [];
  }

  //Bed content
  var bedContent = (typeof bed === 'string') ? bedRead(bed) : bed;

  //Fasta index content
  var indexContent = fs.readFileSync(index, 'utf8');

  //Parse the index file
  indexContent = JSON.parse(indexContent);

  //Open the fasta file
  var fastaFd = fs.openSync(fasta, 'r');

  //Output object
  var out = [];

  //Get all bed regions
  for(var i = 0; i < bedContent.length; i++)
  {
    //Region number
    var rn = i + 1;

    //Get the region
    var region = bedContent[i];

    //Sequence object
    var obj = { head: '', sequence: '' };

    //Add the sequence head
    obj.head = bedRegion.toString(region, { addStrand: false });

    //Get the chromosome info
    var chr = indexContent.chromosomes[region.chromosome];

    //Get the start increments
    var start_inc = Math.floor((region.start - 1)/chr.bases);

    //Calculate the end increments
    var end_inc = Math.floor((region.end - 1)/chr.bases);;

    //Get the start line
    var start = chr.start + region.start + start_inc;

    //Get the end file
    var end = chr.start + region.end + end_inc;

    //Get the strand
    var strand = (typeof region.strand !== 'undefined') ? region.strand : '+';

    //Check the end
    if(chr.end <= end)
    {
      //Show warning
      console.log('WARNING: end of the feature at line ' + rn + ' exceeds the reference length...');

      //Update the end
      end = chr.end - 1;
    }

    //Get the region length
    var length = end - start;

    //Check the length
    if(length === 0)
    {
      //Show warning
      console.log('WARNING: feature at line ' + rn + ' has length 0. Skipping feature.');

      //Save an empty region
      out.push(obj);

      //Next region
      continue;
    }

    //Create the buffer
    var buff = new Buffer(length);

    //Get the line
    var bytesRead = fs.readSync(fastaFd, buff, 0, length, start);

    //Convert the sequence
    obj.sequence = buff.toString('utf8').replace(/\n/g, '');

    //Check the strand
    if(opt.strand === true && strand === '-')
    {
      //Update the sequence head
      obj.head = bedRegion.toString(region, { addStrand: true });

      //Get the complement sequence
      obj.sequence = Sequence.complement(obj.sequence);
    }

    //Save the sequence object
    out.push(obj);
  }

  //Close the fasta file
  fs.closeSync(fastaFd);

  //Return the sequences
  return out;
};


//Index a fasta file
module.exports.Index = function(file)
{
  //Check the file
  if(pstat.isFileSync(file) === false)
  {
    //Show error and exit
    return console.error('Error: file ' + file + ' doesn\'t exists...');
  }

  //Initialize the index file
  var index = { chromosomes: {}, length: 0 };

  //Save the file name
  index.file = path.basename(file);

  //Open the fasta file
  var fileFd = fs.openSync(file, 'r');

  //Initialize the line count
  var count = 0;

  //Initialize the line
  var line = null;

  //Iitialize the line in utf8
  var lineStr = '';

  //Actual position
  var position = 0;

  //Actual chromosome
  var chr = '';

  //First line
  var first = true;

  //Read the full file
  while(true)
  {
    //Get the line
    line = GetLine(fileFd, position);

    //Check for exit
    if(line === false){ break; }

    //Convert the line to utf8
    lineStr = line.toString('utf8');

    //Check for empty line
    if(line.length === 0)
    {
      //Check the actual chromosome
      if(chr !== '')
      {
        //Save the chromosome end
        index.chromosomes[chr].end = position;
      }

      //Reset the chromosome
      chr = '';

      //Check the first line
      first = true;
    }

    //Check the first character
    else if(lineStr.charAt(0) === '>')
    {
      //Check the actual chromosome
      if(chr !== '')
      {
        //Save the chromosome end
        index.chromosomes[chr].end = position;
      }

      //Get the chromosome
      chr = lineStr.split(' ')[0].replace('>', '');

      //Initialize the chromosome object
      index.chromosomes[chr] = { start: 0, bases: 0, end: 0, length: 0, head: '' };

      //Save the head
      index.chromosomes[chr].head = lineStr;

      //Save the start
      index.chromosomes[chr].start = position + line.length + 1;

      //Set first line as true
      first = true;

      //Show in console
      console.log('Indexing chromosome ' + chr.replace('chr', '') + '...');
    }

    //Check the code
    else if(first === true)
    {
      //Save the number of bases per line
      index.chromosomes[chr].bases = line.length;

      //Set first as false
      first = false;
    }

    //Increment the line counter
    count = count + 1;

    //Increment the position
    position = position + line.length + 1;
  }

  //Check the actual chromosome
  if(chr !== '')
  {
    //Save the chromosome end
    index.chromosomes[chr].end = position;
  }

  //Update hte number of lines
  index.length = count;

  //Save the json file
  fs.writeFileSync(file + '.json', JSON.stringify(index, null, '  '), 'utf8');

  //Show in console
  console.log('Done!');
  console.log('Index file saved as "' + file + '.json"');

  //Exit
  return true;
};