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 require 'maasha/seq/backtrack'
  31
  32 class Seq
  33   include BackTrack
  34 end
  35
  36 class BackTrackTest < Test::Unit::TestCase
  37   def setup
  38     #                       0         1
  39     #                       01234567890123456789
  40     @seq = Seq.new("test", "tacgatgctagcatgcacgg")
  41   end
  42
  43   def test_BackTrack_patscan_with_bad_pattern_raises
  44     ["", "X", "1"].each { |pattern|
  45       assert_raise(BackTrackError) { @seq.patscan(pattern) }
  46     }
  47   end
  48
  49   def test_BackTrack_patscan_with_OK_pattern_dont_raise
  50     ["N", "atcg"].each { |pattern|
  51       assert_nothing_raised { @seq.patscan(pattern) }
  52     }
  53   end
  54
  55   def test_BackTrack_patscan_with_bad_pos_raises
  56     [-1, 20].each { |pos|
  57       assert_raise(BackTrackError) { @seq.patscan("N", pos) }
  58     }
  59   end
  60
  61   def test_BackTrack_patscan_with_OK_pos_dont_raise
  62     [0, 19].each { |pos|
  63       assert_nothing_raised { @seq.patscan("N", pos) }
  64     }
  65   end
  66
  67   def test_BackTrack_patscan_with_bad_mis_raises
  68     [-1, 6].each { |mis|
  69       assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
  70     }
  71   end
  72
  73   def test_BackTrack_patscan_with_OK_mis_dont_raise
  74     [0, 5].each { |mis|
  75       assert_nothing_raised { @seq.patscan("N", 0, mis) }
  76     }
  77   end
  78
  79   def test_BackTrack_patscan_with_bad_ins_raises
  80     [-1, 6].each { |ins|
  81       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
  82     }
  83   end
  84
  85   def test_BackTrack_patscan_with_OK_ins_dont_raise
  86     [0, 5].each { |ins|
  87       assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
  88     }
  89   end
  90
  91   def test_BackTrack_patscan_with_bad_del_raises
  92     [-1, 6].each { |del|
  93       assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
  94     }
  95   end
  96
  97   def test_BackTrack_patscan_with_OK_del_dont_raise
  98     [0, 5].each { |del|
  99       assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
 100     }
 101   end
 102
 103   def test_BackTrack_patscan_perfect_left_is_ok
 104     assert_equal("0:7:tacgatg", @seq.patscan("TACGATG").first.to_s)
 105   end
 106
 107   def test_BackTrack_patscan_perfect_right_is_ok
 108     assert_equal("13:7:tgcacgg", @seq.patscan("TGCACGG").first.to_s)
 109   end
 110
 111   def test_BackTrack_patscan_ambiguity_is_ok
 112     assert_equal("13:7:tgcacgg", @seq.patscan("TGCACNN").first.to_s)
 113   end
 114
 115   def test_BackTrack_patscan_pos_is_ok
 116     assert_equal("10:1:g", @seq.patscan("N", 10).first.to_s)
 117     assert_equal("19:1:g", @seq.patscan("N", 10).last.to_s)
 118   end
 119
 120   def test_BackTrack_patscan_mis_left_is_ok
 121     assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
 122   end
 123
 124   def test_BackTrack_patscan_mis_right_is_ok
 125     assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
 126   end
 127
 128   def test_BackTrack_patscan_ins_left_is_ok
 129     assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
 130   end
 131
 132   def test_BackTrack_patscan_ins_right_is_ok
 133     assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
 134   end
 135
 136   def test_BackTrack_patscan_del_left_is_ok
 137     assert_equal("0:7:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
 138   end
 139
 140   def test_BackTrack_patscan_del_right_is_ok
 141     assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
 142   end
 143
 144   def test_BackTrack_patscan_ambiguity_mis_ins_del_all_ok
 145     assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
 146   end
 147 end
 148