bedjs/lib/region.js

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

//Parse a region
module.exports.Parse = function(region)
{
  //Split the regions by comma
  regions = regions.split(',');

  //Output array
  var out = [];

  //Read all the regions
  for(var i = 0; i <regions.length; i++)
  {
    //Split the region by ':'
    var str = regions[i].split(':');

    //Generate the region object
    var region = {};

    //Save the chromosome
    region.chromosome = str[0];

    //Save the start
    region.start = str[1].split('-')[0];

    //Save the end
    region.end = str[1].split('-')[1];

    //Check for strand
    if(str.length > 2)
    {
      //Save the strand
      region.strand = (str[2] === '-1' || str[2] === '-') ? '-' : '+';

      //Save the score
      region.score = 0;

      //Save the region name
      region.name = 'REGION' + i;
    }

    //Check for undefined end
    if(typeof region.end === 'undefined'){ region.end = region.start; }

    //Parse the start position
    region.start = parseInt(region.start);

    //Parse the end position
    region.end = parseInt(region.end);

    //Check the start and end position
    if(region.start > region.end)
    {
      //Create the aux variable
      var aux = region.start;

      //Save the start
      region.start = region.end;

      //Save the end
      region.end = aux;
    }

    //Add the region
    out.push(region);
  }

  //Return the list
  return out;
};

//Convert a region object to string
module.exports.toString = function(regions, opt)
{
  //Check for array
  if(Array.isArray(regions) === false){ regions = [ regions ]; }

  //Check the options
  if(typeof opt === 'undefined'){ var opt = {}; }

  //Check the add strand option
  if(typeof opt.addStrand === 'undefined'){ opt.addStrand = true; }

  //Output list
  var out = [];

  //Read all the regions
  for(var i = 0; i < regions.length; i++)
  {
    //Get the region
    var region = regions[i];

    //Generate the string
    var str = region.chromosome + ':' + region.start + '-' + region.end;

    //Check the strand
    if(typeof region.strand !== 'undefined' && opt.addStrand === true)
    {
      //Add the strand
      str = str + ':' + ((region.strand === '-') ? '-1' : '1');
    }

    //Save the region in string format
    out.push(str);
  }

  //Return the region
  return out;
};