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
|
require_relative "setup.rb"
class FminerTest < MiniTest::Test
def test_fminer_bbrc
dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
refute_nil dataset.id
feature_dataset = OpenTox::Algorithm::Fminer.bbrc :dataset => dataset
assert_equal dataset.compounds.size, feature_dataset.compounds.size
assert_equal 54, feature_dataset.features.size
assert_equal "C-C-C=C", feature_dataset.features.first.smarts
compounds = feature_dataset.compounds
smarts = feature_dataset.features.collect{|f| f.smarts}
match = OpenTox::Algorithm::Descriptor.smarts_count compounds, smarts
p smarts
compounds.each_with_index do |c,i|
p c.smiles
p match[i]
p feature_dataset.feature_values(c)
smarts.each_with_index do |s,j|
#unless match[i][j] == DataEntry.where(:dataset_id => feature_dataset.id, :compound_id => c.id, :feature_id => feature_dataset.features[j]).distinct(:value).first
#p c
#p s
#p feature_dataset.features[j]
#p match[i][j]
#p DataEntry.where(:dataset_id => feature_dataset.id, :compound_id => c.id, :feature_id => feature_dataset.features[j]).distinct(:value)
#end
#assert_equal match[i][j], feature_dataset[c,feature_dataset.features[j]]
end
end
dataset.delete
feature_dataset.delete
end
def test_fminer_last
dataset = OpenTox::Dataset.new
dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
feature_dataset = OpenTox::Algorithm::Fminer.last :dataset => dataset
assert_equal dataset.compounds.size, feature_dataset.compounds.size
assert_equal 21, feature_dataset.features.size
assert_equal '[#6&A]-[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]', feature_dataset.features.first.smarts
compounds = feature_dataset.compounds
smarts = feature_dataset.features.collect{|f| f.smarts}
match = OpenTox::Algorithm::Descriptor.smarts_match compounds, smarts
compounds.each_with_index do |c,i|
smarts.each_with_index do |s,j|
assert_equal match[i][j], feature_dataset.data_entries[i][j].to_i
end
end
dataset.delete
feature_dataset.delete
end
end
|
