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     @seq.extend(BackTrack)
  37   end
  38
  39   def test_BackTrack_patscan_with_bad_pattern_raises
  40     ["", "X", "1"].each { |pattern|
  41       assert_raise(BackTrackError) { @seq.patscan(pattern) }
  42     }
  43   end
  44
  45   def test_BackTrack_patscan_with_OK_pattern_dont_raise
  46     ["N", "atcg"].each { |pattern|
  47       assert_nothing_raised { @seq.patscan(pattern) }
  48     }
  49   end
  50
  51   def test_BackTrack_patscan_with_bad_start_raises
  52     [-1, 20].each { |start|
  53       assert_raise(BackTrackError) { @seq.patscan("N", start) }
  54     }
  55   end
  56
  57   def test_BackTrack_patscan_with_OK_start_dont_raise
  58     [0, 19].each { |start|
  59       assert_nothing_raised { @seq.patscan("N", start) }
  60     }
  61   end
  62
  63   def test_BackTrack_patscan_with_bad_stop_raises
  64     [-1, 20].each { |stop|
  65       assert_raise(BackTrackError) { @seq.patscan("N", [0, stop]) }
  66     }
  67   end
  68
  69   def test_BackTrack_patscan_with_OK_stop_dont_raise
  70     [0, 19].each { |stop|
  71       assert_nothing_raised { @seq.patscan("N", [0, stop]) }
  72     }
  73   end
  74
  75   def test_BackTrack_patscan_with_stop_returns_correctly
  76     assert_nil(@seq.patmatch("G", [0, 2]))
  77     assert_equal("3:1:g", @seq.patmatch("G", [0, 3]).to_s)
  78   end
  79
  80   def test_BackTrack_patscan_with_bad_mis_raises
  81     [-1, 6].each { |mis|
  82       assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
  83     }
  84   end
  85
  86   def test_BackTrack_patscan_with_OK_mis_dont_raise
  87     [0, 5].each { |mis|
  88       assert_nothing_raised { @seq.patscan("N", 0, mis) }
  89     }
  90   end
  91
  92   def test_BackTrack_patscan_with_bad_ins_raises
  93     [-1, 6].each { |ins|
  94       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
  95     }
  96   end
  97
  98   def test_BackTrack_patscan_with_OK_ins_dont_raise
  99     [0, 5].each { |ins|
 100       assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
 101     }
 102   end
 103
 104   def test_BackTrack_patscan_with_bad_del_raises
 105     [-1, 6].each { |del|
 106       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
 107     }
 108   end
 109
 110   def test_BackTrack_patscan_with_OK_del_dont_raise
 111     [0, 5].each { |del|
 112       assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
 113     }
 114   end
 115
 116   def test_BackTrack_patscan_perfect_left_is_ok
 117     assert_equal("0:7:tacgatg", @seq.patscan("TACGATG").first.to_s)
 118   end
 119
 120   def test_BackTrack_patscan_perfect_right_is_ok
 121     assert_equal("13:7:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
 122   end
 123
 124   def test_BackTrack_patscan_ambiguity_is_ok
 125     assert_equal("13:7:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
 126   end
 127
 128   def test_BackTrack_patscan_start_is_ok
 129     assert_equal("10:1:g", @seq.patscan("N", 10).first.to_s)
 130     assert_equal("19:1:g", @seq.patscan("N", 10).last.to_s)
 131   end
 132
 133   def test_BackTrack_patscan_mis_left_is_ok
 134     assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
 135   end
 136
 137   def test_BackTrack_patscan_mis_right_is_ok
 138     assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
 139   end
 140
 141   def test_BackTrack_patscan_ins_left_is_ok
 142     assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
 143   end
 144
 145   def test_BackTrack_patscan_ins_right_is_ok
 146     assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
 147   end
 148
 149   def test_BackTrack_patscan_del_left_is_ok
 150     assert_equal("0:7:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
 151   end
 152
 153   def test_BackTrack_patscan_del_right_is_ok
 154     assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
 155   end
 156
 157   def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
 158     assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
 159   end
 160 end
 161