Method: Bio::Alignment::Output#output_fasta

Defined in:
lib/bio/alignment.rb

#output_fasta(options = {}) ⇒ Object

Generates fasta format text and returns a string.



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# File 'lib/bio/alignment.rb', line 1059

def output_fasta(options={})
  #(original)
  width = (options[:width] or 70)
  if options[:avoid_same_name] then
    na = __clustal_avoid_same_name(self.sequence_names, 30)
  else
    na = self.sequence_names.collect do |k|
      k.to_s.gsub(/[\r\n\x00]/, ' ')
    end
  end
  if width and width > 0 then
    w_reg = Regexp.new(".{1,#{width}}")
    self.collect do |s|
      ">#{na.shift}\n" + s.to_s.gsub(w_reg, "\\0\n")
    end.join('')
  else
    self.collect do |s|
      ">#{na.shift}\n" + s.to_s + "\n"
    end.join('')
  end
end