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#
# test/unit/bio/util/test_contingency_table.rb - Unit test for Bio::ContingencyTable
#
# Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: test_contingency_table.rb,v 1.2 2005/11/23 11:55:17 nakao Exp $
#
require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/util/contingency_table'
module Bio
class TestContingencyTable < Test::Unit::TestCase
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_equal('2.4', results[0][2].to_s)
assert_equal('0.534522483824849', results[0][3].to_s)
assert_equal('12.0', results[5][2].to_s)
assert_equal('0.816496580927726', results[5][3].to_s)
assert_equal('2.4', results[9][2].to_s)
assert_equal('0.534522483824849', results[9][3].to_s)
ctable = Bio::ContingencyTable.new
ctable.table['a']['t'] = 4
ctable.table['a']['g'] = 2
ctable.table['g']['t'] = 3
assert_equal('1.28571428571429', ctable.chi_square.to_s)
assert_equal(ctable.column_sum_all, ctable.row_sum_all)
assert_equal(ctable.column_sum_all, ctable.table_sum_all)
end
end
end
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