calculate and plot hydropathy score

hydropathy_plot.rb

require 'gruff'

f = open(ARGV[0])
seq = f.read.delete(" \n").upcase
f.close

hydropathy_index = {
  'A' => 1.8,
  'B' => -3.5,
  'C' => 2.5,
  'D' => -3.5,
  'E' => -3.5,
  'F' => 2.8,
  'G' => -0.4,
  'H' => -3.2,
  'I' => 4.5,
  'K' => -3.9,
  'L' => 3.8,
  'M' => 1.9,
  'N' => -3.5,
  'P' => -1.6,
  'Q' => -3.5,
  'R' => -4.5,
  'S' => -0.8,
  'T' => -0.7,
  'U' => 0.0,
  'V' => 4.2,
  'W' => -0.9,
  'Y' => -1.3,
  'X' => -0.49,
  'Z' => -3.5,
}

scores = Array.new
len = seq.length
3.upto(len-4) do |i|
  score = 0.0
  (i-3).upto(i+3) do |j|
    score += hydropathy_index[seq[j]]
  end
  score /= 7.0
  #puts sprintf("%3.1f", score)
  scores.push(score)
end

hscore = scores.inject(0.0){|sum, s| sum + s} / scores.length
puts "Score: ", hscore

thres = [-0.4] * scores.length
g = Gruff::Line.new
g.title = "Hydropathy"
g.data("Score", scores)
g.data("Threshold", thres)
g.write("hydrophobicity_graph.png")