$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
$: << File.expand_path('.')
path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')

#puts path
require path
require "test/unit"

class TestBlast < Test::Unit::TestCase
  Query  = File.dirname(__FILE__) + '/data/' + "BS00068396_51.fa"
  Target = File.dirname(__FILE__) + '/data/' + "BS00068396_51_contigs.fa"
  Blast_file = File.dirname(__FILE__) + '/data/' + "BS00068396_51_blast.tab"
  #Set up the paths
  def setup
    File.expand_path(File.dirname(__FILE__) + '/data/')
  end
  
  
  
  def test_blast_to_exo
    lines = File.readlines(Blast_file)
    expected = [
    "BS00068396_51 0 101 + 2AS_5222932 3015 2914 - 99",
    "BS00068396_51 0 101 + 2DS_5334799 6812 6913 + 99",
    "BS00068396_51 0 101 + 2BS_5245544 4549 4651 + 87",
    "BS00068396_51 101 0 - 2BS_5163353 7425 7323 - 87"]

    expected_v = [
      "M 101 101", 
      "M 101 101",
      "M 69 69 G 0 1 M 32 32",
      "M 69 69 G 1 0 M 32 32"]

    lines.each_with_index do |line , i|
      tmp =  Bio::DB::Blast.to_sugar(line)
      assert_equal(tmp, expected[i], "Error in line #{i} of the SUGAR")
      tmp =   Bio::DB::Blast.to_vulgar(line)
      assert_equal(tmp, expected_v[i], "Error in line #{i} of the Vulgar")

      tmp =   Bio::DB::Blast.to_exo(line)
      puts tmp
    
    end
    
  end
  
end