dataset merge

1 files changed, 50 insertions, 0 deletions

diff --git a/test/use_cases.rb b/test/use_cases.rb
new file mode 100644
index 0000000..d9ae78b
--- /dev/null
+++ b/test/use_cases.rb
@@ -0,0 +1,50 @@
+require_relative "setup.rb"
+
+class UseCasesTest < MiniTest::Test
+
+  def test_PA
+    kazius = Dataset.from_sdf_file "#{DATA_DIR}/cas_4337.sdf"
+    hansen = Dataset.from_csv_file "#{DATA_DIR}/hansen.csv"
+    efsa = Dataset.from_csv_file "#{DATA_DIR}/efsa.csv"
+    datasets = [kazius,hansen,efsa]
+    training_dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,map,map], keep_original_features: false, remove_duplicates: true
+    model = Model::Validation.create training_dataset: training_dataset, species: "Salmonella typhimurium", endpoint: "Mutagenicity"
+    pa = Dataset.from_sdf_file "#{DATA_DIR}/PA.sdf"
+    prediction_dataset = model.predict pa
+    puts prediction_dataset.to_csv
+    assert_equal 8281, d.compounds.size
+  end
+
+  def test_public_models
+    skip
+=begin
+    #classification
+    aids = [
+      1205, #Rodents (multiple species/sites)
+      1208, # rat carc
+      1199 # mouse
+      # Mutagenicity
+
+
+      1195 #MRDD
+      1188 #FHM
+      1208, # rat carc td50
+      1199 # mouse td50
+    
+    # daphnia
+    # Blood Brain Barrier Penetration
+    # Lowest observed adverse effect level (LOAEL)
+
+      # 1204  estrogen receptor
+      # 1259408, # GENE-TOX
+      # 1159563 HepG2 cytotoxicity assay
+      # 588209 hepatotoxicity
+      # 1259333 cytotoxicity
+      # 1159569 HepG2 cytotoxicity counterscreen Measured in Cell-Based System Using Plate Reader - 2153-03_Inhibitor_Dose_DryPowder_Activity
+      # 2122 HTS Counterscreen for Detection of Compound Cytotoxicity in MIN6 Cells
+      # 116724 Acute toxicity determined after intravenal administration in mice
+      # 1148549 Toxicity in po dosed mouse assessed as mortality after 7 days
+=end
+
+  end
+end