gistfile1.rb

def process_command
    File.open(@o_file, 'w') do |of|
      File.open(@i_file).each_line do |l|
        of.puts affy_to_csv(l.split)
      end
    end
  end

private

  def affy_to_csv(affy_line)
    AffyLine.new(affy_line).to_csv
  end

  # Encapsulate a line of an Affy file. And help us 
  # perform conversions to csv.
  class AffyLine
    attr_accessor :chrm, :pos, :id, :var, :ref, :seq

    def initialize(args)
      @chrm, @pos, @id, @var, @ref, @seq = args
    end

    # chromosome, position, SNPid, fiveP, threeP, reference, variant
    def to_csv
      t = "\t"
      @chrm + t + @pos + t + @id + t + split_seq + t + split_var
    end

    private

    # AAANCCC -> AAA CCC
    def split_seq
      @seq.split('N').join("\t")
    end

    # A/C -> A C
    def split_var
      @ref.split('/').join("\t")
    end
  end
end