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