Class: Bio::Krona

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-krona/krona.rb

Class Method Summary collapse

Class Method Details

.collapse(count_hash, max_level) ⇒ Object

Take a count_hash (hash of Array => Numeric), and collapse the array down to some maximum number of levels. In krona, the collapsed output would now have less (max_level) rings.

Returns the collapsed count_hash



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# File 'lib/bio-krona/krona.rb', line 53

def self.collapse(count_hash, max_level)
  raise unless max_level.kind_of?(Integer) and max_level > 0
  new_count_hash = {}
  count_hash.each do |array, count|
    raise unless array.kind_of?(Array)
    raise unless count.kind_of?(Numeric)

    new_count_hash[array[0...max_level]] ||= 0
    new_count_hash[array[0...max_level]] += count
  end
  return new_count_hash
end

.html(count_hash, options = {}) ⇒ Object

Given a count_hash, return the html generated by krona

  • count_hash: hash of Array => Numeric, where the array is a list of descriptors (e.g. [Eukaryota, Metazoa, Chordata]), and the Numeric is a count for the number of observations of that description

  • options:

** :krona_path: path to the ktImportText script in the krona directory (default ‘ktImportText’ i.e. assuming it is already in the PATH) ** :resources_url: URL of krona resources (i.e. the -u option of ktImportText)



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# File 'lib/bio-krona/krona.rb', line 11

def self.html(count_hash, options={})
  raise unless count_hash.kind_of?(Hash)
  options[:krona_path] ||= %(ktImportText)

  Tempfile.open('krona') do |tempfile|
    count_hash.each do |array, count|
      raise unless array.kind_of?(Array)
      raise unless count.kind_of?(Numeric)

      tempfile.puts [
        count,
        array
      ].flatten.join("\t")
    end
    tempfile.close

    Tempfile.open('krona_out') do |output|
      output.close

      command = [
        options[:krona_path],
        '-o',
        output.path,
        tempfile.path,
      ].flatten
      if options[:resources_url]
        command.push '-u'
        command.push options[:resources_url]
      end
      Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
        err = stderr.read
        raise err unless err==''
      end

      return File.open(output.path).read
    end
  end
end