code_ruby/test/maasha/seq/test_backtrack.rb

   1 #!/usr/bin/env ruby
   2 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
   3
   4 # Copyright (C) 2007-2011 Martin A. Hansen.
   5
   6 # This program is free software; you can redistribute it and/or
   7 # modify it under the terms of the GNU General Public License
   8 # as published by the Free Software Foundation; either version 2
   9 # of the License, or (at your option) any later version.
  10
  11 # This program is distributed in the hope that it will be useful,
  12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14 # GNU General Public License for more details.
  15
  16 # You should have received a copy of the GNU General Public License
  17 # along with this program; if not, write to the Free Software
  18 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
  19
  20 # http://www.gnu.org/copyleft/gpl.html
  21
  22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
  23
  24 # This software is part of the Biopieces framework (www.biopieces.org).
  25
  26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
  27
  28 require 'test/unit'
  29 require 'maasha/seq'
  30
  31 class BackTrackTest < Test::Unit::TestCase
  32   def setup
  33     #                       0         1
  34     #                       01234567890123456789
  35     @seq = Seq.new("test", "tacgatgctagcatgcacgg")
  36   end
  37
  38   def test_BackTrack_patscan_with_bad_pattern_raises
  39     ["", "X", "1"].each { |pattern|
  40       assert_raise(BackTrackError) { @seq.patscan(pattern) }
  41     }
  42   end
  43
  44   def test_BackTrack_patscan_with_OK_pattern_dont_raise
  45     ["N", "atcg"].each { |pattern|
  46       assert_nothing_raised { @seq.patscan(pattern) }
  47     }
  48   end
  49
  50   def test_BackTrack_patscan_with_bad_pos_raises
  51     [-1, 20].each { |pos|
  52       assert_raise(BackTrackError) { @seq.patscan("N", pos) }
  53     }
  54   end
  55
  56   def test_BackTrack_patscan_with_OK_pos_dont_raise
  57     [0, 19].each { |pos|
  58       assert_nothing_raised { @seq.patscan("N", pos) }
  59     }
  60   end
  61
  62   def test_BackTrack_patscan_with_bad_mis_raises
  63     [-1, 6].each { |mis|
  64       assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
  65     }
  66   end
  67
  68   def test_BackTrack_patscan_with_OK_mis_dont_raise
  69     [0, 5].each { |mis|
  70       assert_nothing_raised { @seq.patscan("N", 0, mis) }
  71     }
  72   end
  73
  74   def test_BackTrack_patscan_with_bad_ins_raises
  75     [-1, 6].each { |ins|
  76       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
  77     }
  78   end
  79
  80   def test_BackTrack_patscan_with_OK_ins_dont_raise
  81     [0, 5].each { |ins|
  82       assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
  83     }
  84   end
  85
  86   def test_BackTrack_patscan_with_bad_del_raises
  87     [-1, 6].each { |del|
  88       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
  89     }
  90   end
  91
  92   def test_BackTrack_patscan_with_OK_del_dont_raise
  93     [0, 5].each { |del|
  94       assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
  95     }
  96   end
  97
  98   def test_BackTrack_patscan_perfect_left_is_ok
  99     assert_equal("0:7:0:0:0:tacgatg", @seq.patscan("TACGATG").first.to_s)
 100   end
 101
 102   def test_BackTrack_patscan_perfect_right_is_ok
 103     assert_equal("13:7:0:0:0:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
 104   end
 105
 106   def test_BackTrack_patscan_ambiguity_is_ok
 107     assert_equal("13:7:0:0:0:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
 108   end
 109
 110   def test_BackTrack_patscan_pos_is_ok
 111     assert_equal("10:1:0:0:0:g", @seq.patscan("N", 10).first.to_s)
 112     assert_equal("19:1:0:0:0:g", @seq.patscan("N", 10).last.to_s)
 113   end
 114
 115   def test_BackTrack_patscan_mis_left_is_ok
 116     assert_equal("0:7:1:0:0:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
 117   end
 118
 119   def test_BackTrack_patscan_mis_right_is_ok
 120     assert_equal("13:7:1:0:0:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
 121   end
 122
 123   def test_BackTrack_patscan_ins_left_is_ok
 124     assert_equal("0:7:0:1:0:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
 125   end
 126
 127   def test_BackTrack_patscan_ins_right_is_ok
 128     assert_equal("13:7:0:1:0:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
 129   end
 130
 131   def test_BackTrack_patscan_del_left_is_ok
 132     assert_equal("0:7:0:0:1:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
 133   end
 134
 135   def test_BackTrack_patscan_del_right_is_ok
 136     assert_equal("12:8:0:0:1:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
 137   end
 138
 139   def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
 140     assert_equal("0:20:1:1:1:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
 141   end
 142 end
 143