diff options
Diffstat (limited to 'Rakefile')
| -rw-r--r-- | Rakefile | 165 |
1 files changed, 0 insertions, 165 deletions
diff --git a/Rakefile b/Rakefile deleted file mode 100644 index 42ab363..0000000 --- a/Rakefile +++ /dev/null @@ -1,165 +0,0 @@ -#!/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::LazarClassification.find t.prerequisites[0] - dataset = Dataset.find t.prerequisites[1] - prediction = model.predict dataset - f.puts prediction.id - end -end |