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author | Christoph Helma <helma@in-silico.ch> | 2015-10-08 10:43:43 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2015-10-08 10:43:43 +0200 |
commit | 1a56148aadef031c4f487bc23fda43f4ac5b7369 (patch) | |
tree | 3555c5883ed0c292b105c40c185ebba3e5bd4e3e /test/fminer.rb | |
parent | 394d564699756288569169ff3e198d6d7702f092 (diff) | |
parent | e3217075b602a950a0ee995fcfa731d97b5ba3eb (diff) |
new master branch
Diffstat (limited to 'test/fminer.rb')
-rw-r--r-- | test/fminer.rb | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/test/fminer.rb b/test/fminer.rb new file mode 100644 index 0000000..16e1f9e --- /dev/null +++ b/test/fminer.rb @@ -0,0 +1,52 @@ +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 + feature_dataset = Dataset.find feature_dataset.id + assert_equal dataset.compounds.size, feature_dataset.compounds.size + # TODO: fminer calculates 62 instead of 54 features + # it is unclear which commit changed the numbers (occurs with old libraries/mongodb branch too + # modification of Compound to use smiles instead of inchis seems to have no effect + #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 + smarts.each do |smart| + assert smart.p_value.round(2) >= 0.95 + end + match = OpenTox::Algorithm::Descriptor.smarts_match compounds, smarts + feature_dataset.data_entries.each_with_index do |fingerprint,i| + assert_equal match[i], fingerprint + end + + dataset.delete + feature_dataset.delete + end + + def test_fminer_last + skip "last features have to be activated" + 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 |