1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
|
#
# test/unit/bio/util/test_contingency_table.rb - Unit test for Bio::ContingencyTable
#
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/util/contingency_table'
module Bio #:nodoc:
class TestContingencyTable < Test::Unit::TestCase #:nodoc:
def lite_example(sequences, max_length, characters)
output = []
0.upto(max_length - 1) do |i|
(i+1).upto(max_length - 1) do |j|
ctable = Bio::ContingencyTable.new( characters )
sequences.each do |seq|
i_char = seq[i].chr
j_char = seq[j].chr
ctable.table[i_char][j_char] += 1
end
chi_square = ctable.chi_square
contingency_coefficient = ctable.contingency_coefficient
output << [(i+1), (j+1), chi_square, contingency_coefficient]
end
end
return output
end
def test_lite_example
ctable = Bio::ContingencyTable
allowed_letters = 'abcdefghijk'.split('')
seqs = Array.new
seqs << 'abcde'
seqs << 'abcde'
seqs << 'kacje'
seqs << 'aacae'
seqs << 'akcfa'
seqs << 'akcfe'
length_of_every_sequence = seqs[0].size # 5 letters long
results = lite_example(seqs, length_of_every_sequence, allowed_letters)
=begin
i j chi_square contingency_coefficient
1 2 2.4 0.534522483824849
1 3 0.0 0.0
1 4 6.0 0.707106781186548
1 5 0.24 0.196116135138184
2 3 0.0 0.0
2 4 12.0 0.816496580927726
2 5 2.4 0.534522483824849
3 4 0.0 0.0
3 5 0.0 0.0
4 5 2.4 0.534522483824849
=end
#assert_equal(2.4, results[0][2])
assert_in_delta(2.4, results[0][2], 1e-13)
assert_in_delta(0.534522483824849, results[0][3], 1e-15)
assert_in_delta(12.0, results[5][2], 1e-13)
assert_in_delta(0.816496580927726, results[5][3], 1e-15)
assert_in_delta(2.4, results[9][2], 1e-13)
assert_in_delta(0.534522483824849, results[9][3], 1e-15)
ctable = Bio::ContingencyTable.new
ctable.table['a']['t'] = 4
ctable.table['a']['g'] = 2
ctable.table['g']['t'] = 3
assert_in_delta(1.28571428571429, ctable.chi_square, 1e-14)
assert_equal(ctable.column_sum_all, ctable.row_sum_all)
assert_equal(ctable.column_sum_all, ctable.table_sum_all)
end
end
end
|
