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 include BackTrack
  32
  33 class BackTrackTest < Test::Unit::TestCase
  34   def setup
  35     #                       0         1
  36     #                       01234567890123456789
  37     @seq = Seq.new("test", "tacgatgctagcatgcacgg")
  38   end
  39
  40   def test_BackTrack_patscan_with_bad_pattern_raises
  41     ["", "X", "1"].each { |pattern|
  42       assert_raise(BackTrackError) { @seq.patscan(pattern) }
  43     }
  44   end
  45
  46   def test_BackTrack_patscan_with_OK_pattern_dont_raise
  47     ["N", "atcg"].each { |pattern|
  48       assert_nothing_raised { @seq.patscan(pattern) }
  49     }
  50   end
  51
  52   def test_BackTrack_patscan_with_bad_pos_raises
  53     [-1, 20].each { |pos|
  54       assert_raise(BackTrackError) { @seq.patscan("N", pos) }
  55     }
  56   end
  57
  58   def test_BackTrack_patscan_with_OK_pos_dont_raise
  59     [0, 19].each { |pos|
  60       assert_nothing_raised { @seq.patscan("N", pos) }
  61     }
  62   end
  63
  64   def test_BackTrack_patscan_with_bad_mis_raises
  65     [-1, 6].each { |mis|
  66       assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
  67     }
  68   end
  69
  70   def test_BackTrack_patscan_with_OK_mis_dont_raise
  71     [0, 5].each { |mis|
  72       assert_nothing_raised { @seq.patscan("N", 0, mis) }
  73     }
  74   end
  75
  76   def test_BackTrack_patscan_with_bad_ins_raises
  77     [-1, 6].each { |ins|
  78       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
  79     }
  80   end
  81
  82   def test_BackTrack_patscan_with_OK_ins_dont_raise
  83     [0, 5].each { |ins|
  84       assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
  85     }
  86   end
  87
  88   def test_BackTrack_patscan_with_bad_del_raises
  89     [-1, 6].each { |del|
  90       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
  91     }
  92   end
  93
  94   def test_BackTrack_patscan_with_OK_del_dont_raise
  95     [0, 5].each { |del|
  96       assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
  97     }
  98   end
  99
 100   def test_BackTrack_patscan_perfect_left_is_ok
 101     assert_equal("0:7:0:0:0:tacgatg", @seq.patscan("TACGATG").first.to_s)
 102   end
 103
 104   def test_BackTrack_patscan_perfect_right_is_ok
 105     assert_equal("13:7:0:0:0:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
 106   end
 107
 108   def test_BackTrack_patscan_ambiguity_is_ok
 109     assert_equal("13:7:0:0:0:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
 110   end
 111
 112   def test_BackTrack_patscan_pos_is_ok
 113     assert_equal("10:1:0:0:0:g", @seq.patscan("N", 10).first.to_s)
 114     assert_equal("19:1:0:0:0:g", @seq.patscan("N", 10).last.to_s)
 115   end
 116
 117   def test_BackTrack_patscan_mis_left_is_ok
 118     assert_equal("0:7:1:0:0:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
 119   end
 120
 121   def test_BackTrack_patscan_mis_right_is_ok
 122     assert_equal("13:7:1:0:0:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
 123   end
 124
 125   def test_BackTrack_patscan_ins_left_is_ok
 126     assert_equal("0:7:0:1:0:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
 127   end
 128
 129   def test_BackTrack_patscan_ins_right_is_ok
 130     assert_equal("13:7:0:1:0:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
 131   end
 132
 133   def test_BackTrack_patscan_del_left_is_ok
 134     assert_equal("0:7:0:0:1:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
 135   end
 136
 137   def test_BackTrack_patscan_del_right_is_ok
 138     assert_equal("12:8:0:0:1:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
 139   end
 140
 141   def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
 142     assert_equal("0:20:1:1:1:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
 143   end
 144 end
 145