gc_count.exs

defmodule ATGCCount do
  def count(sequence), do: cnt(String.to_char_list(sequence),0,0)
  def cnt([65|t],at,gc), do: cnt(t,at+1,gc)
  def cnt([84|t],at,gc), do: cnt(t,at+1,gc)
  def cnt([71|t],at,gc), do: cnt(t,at,gc+1)
  def cnt([67|t],at,gc), do: cnt(t,at,gc+1)
  def cnt([62|_],at,gc), do: {at,gc}
  def cnt([],at,gc), do: {at,gc}
  def cnt(_,0,0), do: {0,0}
  def cnt([_|t], at, gc), do: cnt(t,at,gc)
end
 
defmodule GCCount do
  def process do
    filename = "chry.fa"
    if File.exists?(filename) do
      stream = File.stream!(filename, [:read_ahead, :raw], :line)
      Enum.reduce stream, {0, 0}, fn(line, {at_acc, gc_acc}) ->
        {at, gc} = ATGCCount.count(line)
        {at_acc + at, gc_acc + gc}
      end
    end 
  end
  def gc_ratio do
    {at, gc} = process
    case {gc, at} do
      {0, 0} -> 0
      {at, gc} -> gc/(gc+at)
      {_,_} -> 0
    end
  end
end

@behe Cool! In my experiment on saml.rilspace.org/moar-languagez-gc-content-in-python-d-fpc-c-and-c I put on the restriction to only read one line at a time (except for the second test in the end). Would be very interesting to see what performance we get without that optimization!

All: For reference, the data file used here is available at: http://bit.ly/ychromo
Also see the discussion about these tests on the meetup page: http://www.meetup.com/stockholm-elixir/events/203279212/