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#!/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
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