2 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
4 # Copyright (C) 2007-2010 Martin A. Hansen.
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.
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.
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.
20 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # This software is part of the Biopieces framework (www.biopieces.org).
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 class TestPatternMatcher < Test::Unit::TestCase
34 @p = Seq.new("test", "atcg")
37 def test_PatternMatcher_no_match_returns_nil
38 assert_nil(@p.match("gggg"))
41 def test_PatternMatcher_match_perfect_returns_correctly
43 assert_equal(0, m.pos)
44 assert_equal("atcg", m.match)
45 assert_equal(4, m.matches)
46 assert_equal(0, m.mismatches)
47 assert_equal(0, m.insertions)
48 assert_equal(0, m.deletions)
49 assert_equal(4, m.length)
52 def test_PatternMatcher_match_perfect_with_ambiguity_codes_returns_correctly
54 assert_equal(0, m.pos)
55 assert_equal("atcg", m.match)
56 assert_equal(4, m.matches)
57 assert_equal(0, m.mismatches)
58 assert_equal(0, m.insertions)
59 assert_equal(0, m.deletions)
60 assert_equal(4, m.length)
63 def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_zero_returns_nil
64 assert_nil(@p.match("aCcg"))
67 def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_one_returns_correctly
68 m = @p.match("aCcg", 0, 1)
69 assert_equal(0, m.pos)
70 assert_equal("atcg", m.match)
71 assert_equal(3, m.matches)
72 assert_equal(1, m.mismatches)
73 assert_equal(0, m.insertions)
74 assert_equal(0, m.deletions)
75 assert_equal(4, m.length)
78 def test_PatternMatcher_match_with_two_mismatch_and_edit_dist_one_returns_nil
79 assert_nil(@p.match("aGcA", 0, 1))
82 def test_PatternMatcher_match_with_one_insertion_and_edit_dist_zero_returns_nil
83 assert_nil(@p.match("atGcg"))
86 def test_PatternMatcher_match_with_one_insertion_and_edit_dist_one_returns_correctly
87 m = @p.match("atGcg", 0, 1)
88 assert_equal(0, m.pos)
89 assert_equal("atcg", m.match)
90 assert_equal(4, m.matches)
91 assert_equal(0, m.mismatches)
92 assert_equal(1, m.insertions)
93 assert_equal(0, m.deletions)
94 assert_equal(4, m.length)
97 def test_PatternMatcher_match_with_two_insertions_and_edit_dist_one_returns_nil
98 assert_nil(@p.match("atGcTg", 0, 1))
101 def test_PatternMatcher_match_with_two_insertions_and_edit_dist_two_returns_correctly
102 m = @p.match("atGcTg", 0, 2)
103 assert_equal(0, m.pos)
104 assert_equal("atcg", m.match)
105 assert_equal(4, m.matches)
106 assert_equal(0, m.mismatches)
107 assert_equal(2, m.insertions)
108 assert_equal(0, m.deletions)
109 assert_equal(4, m.length)
112 def test_PatternMatcher_match_with_one_deletion_and_edit_distance_zero_returns_nil
113 assert_nil(@p.match("acg"))
116 def test_PatternMatcher_match_with_one_deletion_and_edit_distance_one_returns_correctly
117 m = @p.match("acg", 0, 1)
118 assert_equal(0, m.pos)
119 assert_equal("atcg", m.match)
120 assert_equal(3, m.matches)
121 assert_equal(0, m.mismatches)
122 assert_equal(0, m.insertions)
123 assert_equal(1, m.deletions)
124 assert_equal(4, m.length)
127 def test_PatternMatcher_scan_locates_three_patterns_ok
128 p = Seq.new("test", "ataacgagctagctagctagctgactac")
129 assert_equal(3, p.scan("tag").count)
132 def test_PatternMatcher_scan_with_pos_locates_two_patterns_ok
133 p = Seq.new("test", "ataacgagctagctagctagctgactac")
134 assert_equal(2, p.scan("tag", 10).count)