1 files changed, 165 insertions, 0 deletions
diff --git a/Rakefile b/Rakefile
new file mode 100644
index 0000000..5d63b4f
--- /dev/null
+++ b/Rakefile
@@ -0,0 +1,165 @@
+#!/usr/bin/env ruby
+require_relative '../lazar/lib/lazar.rb'
+include OpenTox
+
+#task :default => ["predictions/PA_mutagenicity.id","validations/mutagenicity-merged.id"]
+task :default => ["predictions/PA_mutagenicity.id"]
+
+# summaries
+# predictions
+
+file "predictions/PA_mutagenicity.id" => ["models/mutagenicity-merged.id", "data/PA.id"] do |t| predict t end
+file "predictions/PA_carcinogenicity.id" => ["models/carcinogenicity.id", "data/PA.id"] do |t| predict t end
+
+# validations
+
+file "validations/mutagenicity-merged.id" => "models/mutagenicity-merged.id" do |t| validate_model t end
+file "validations/carcinogenicity.id" => "models/carcinogenicity.id" do |t| validate_model t end
+
+# models
+
+file "models/mutagenicity-merged.id" => "data/mutagenicity-merged.id" do |t| create_model t end
+file "models/carcinogenicity.id" => "data/carcinogenicity.id" do |t| create_model t end
+
+# test data
+
+file "data/PA.id" => "data/PA.sdf" do |t| import_sdf t end
+	
+# training data
+
+file "data/mutagenicity-merged.id" => ["data/hansen.id", "data/kazius.id", "data/efsa.id"] do |t|
+  input = t.prerequisites.collect{|id| Dataset.find(File.read(id).chomp)}
+  source_feature = Feature.where(:name => "Ames test categorisation").first # Kazius
+  target_feature = Feature.where(:name => "Mutagenicity").first
+  merged = Dataset.merge input, {source_feature => target_feature}, {1 => "mutagen", 0 => "nonmutagen"}
+  File.open(t.name,"w+") { |f| f.puts merged.id }
+end
+
+file "data/carcinogenicity.id" do |t|
+  File.open(t.name,"w+") do |f| 
+    d = Dataset.from_pubchem 1205
+    f.puts d.id
+  end
+end
+
+# kazius
+
+file "data/kazius.id" => "data/cas_4337.sdf" do |t| import_sdf t end
+
+file "data/cas_4337.sdf" => "data/cas_4337.zip" do |t|
+	`cd data && unzip cas_4337.zip`
+end
+
+file "data/cas_4337.zip" do
+	`cd data && wget "http://cheminformatics.org/datasets/bursi/cas_4337.zip"`
+end
+
+# efsa
+
+file "data/efsa.id" => "data/efsa.csv" do |t| import_csv t end
+
+file "data/efsa.csv" => "data/GENOTOX_data_and_dictionary.tsv" do |t| efsa2csv t end
+
+file "data/GENOTOX_data_and_dictionary.tsv" => "data/GENOTOX_data_and_dictionary.xls" do |t|
+  `xls2csv -s cp1252 -d utf-8 -x -c "	" #{t.name} > #{t.prerequisites[0]}`
+end
+
+file "data/GENOTOX_data_and_dictionary.xls" do |t|
+  `cd data && wget "https://data.europa.eu/euodp/data/storage/f/2017-07-19T142131/GENOTOX%20data%20and%20dictionary.xls" -o #{t.name}`
+end
+
+# hansen
+
+file "data/hansen.id" => "data/hansen.csv" do |t| import_csv t end
+
+file "data/hansen.csv" => "data/Mutagenicity_N6512.csv" do |t|
+  File.open(t.name,"w+") do |f| 
+    i = 0
+    CSV.foreach(t.prerequisites[0]) do |row|
+      if i == 0
+        f.puts "ID,SMILES,Mutagenicity"
+      else
+        c = OpenTox::Compound.from_smiles(row[5]).smiles
+        f.puts ["hansen_#{row[0]}",c, row[2]].join ","
+      end
+      i += 1
+    end
+  end
+end
+
+file "data/Mutagenicity_N6512.csv" do
+  `cd data && wget "http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv"`
+end
+
+# cleanup
+
+task :clean do `rm data/*id` end
+task :cleanall do `rm data/*` end
+
+# functions
+
+def import_csv t
+  File.open(t.name,"w+") do |f| 
+    d = Dataset.from_csv_file t.prerequisites[0]
+    f.puts d.id
+  end
+end
+
+def import_sdf t
+  File.open(t.name,"w+") do |f| 
+    d = Dataset.from_sdf_file t.prerequisites[0]
+    f.puts d.id
+  end
+end
+
+def efsa2csv t
+  File.open(t.name,"w+") do |f| 
+    i = 0
+    db = {}
+    CSV.foreach(t.prerequisites[0], :encoding => "UTF-8", :col_sep => "\t", :liberal_parsing => true) do |row|
+      if i > 0 and row[11] and !row[11].empty? and row[24].match(/Salmonella/i) and ( row[25].match("TA 98") or row[25].match("TA 100") ) and row[33]
+        begin
+          c = OpenTox::Compound.from_smiles(row[11].gsub('"','')).smiles
+        rescue
+          c = OpenTox::Compound.from_inchi(row[12]).smiles # some smiles (row[11]) contain non-parseable characters
+        end
+        db[c] ||= {}
+        db[c][:id] ||= "efsa_#{row[2]}"
+        if row[33].match(/Positiv/i)
+          db[c][:value] = 1 # at least one positive result in TA 98 or TA 100
+        elsif row[33].match(/Negativ/i)
+          db[c][:value] ||= 0
+        end
+      end
+      i += 1
+    end
+
+    f.puts "ID,SMILES,Mutagenicity"
+    db.each do |s,v|
+      f.puts [v[:id],s,v[:value]].join ","
+    end
+  end
+end
+
+def create_model t
+  File.open(t.name,"w+") do |f| 
+    model = Model::LazarClassification.create(training_dataset: Dataset.find(File.read(t.prerequisites.first).chomp))
+    f.puts model.id
+  end
+end
+
+def validate_model t
+  File.open(t.name,"w+") do |f| 
+    rcv = Validation::RepeatedCrossValidation.create(Model.find(File.read(t.prerequisites.first).chomp))
+    f.puts rcv.id
+  end
+end
+
+def predict t
+  File.open(t.name,"w+") do |f| 
+    model = Model.find t.prerequisites[0]
+    dataset = Dataset.find t.prerequisites[1]
+    prediction = model.predict dataset
+    f.puts prediction.id
+  end
+end