Rakefile fix, directories added/fixed

5 files changed, 0 insertions, 100 deletions

diff --git a/scripts/export-sdf.rb b/scripts/export-sdf.rb
deleted file mode 100755
index c2e75e7..0000000
--- a/scripts/export-sdf.rb
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env ruby
-require_relative '../../lazar/lib/lazar'
-include OpenTox
-
-dataset = Dataset.find File.read(ARGV[0]).chomp
-dataset.to_sdf
diff --git a/scripts/hansen2csv.rb b/scripts/hansen2csv.rb
deleted file mode 100755
index 3c8c3e1..0000000
--- a/scripts/hansen2csv.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env ruby
-require 'csv'
-require_relative '../../lazar/lib/lazar.rb'
-
-i = 0
-CSV.foreach(ARGV[0]) do |row|
-  if i > 0
-    c = OpenTox::Compound.from_smiles(row[5]).smiles
-    puts ["hansen_#{row[0]}",c, row[2]].join ","
-  end
-  i += 1
-end
diff --git a/scripts/kazius2csv.rb b/scripts/kazius2csv.rb
deleted file mode 100755
index 52b78c1..0000000
--- a/scripts/kazius2csv.rb
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env ruby
-require_relative '../../lazar/lib/lazar.rb'
-
-sdfs = []
-results = []
-read_result = false
-@sdf = ""
-File.readlines(ARGV[0]).each do |line|
-  if line.match %r{\$\$\$\$}
-    @sdf << line
-    sdfs << @sdf
-    @sdf = ""
-  elsif line.match ">  <Ames test categorisation>"
-    read_result = true
-  else
-      #p line
-    if read_result
-      if line.chomp == "mutagen"
-        results << 1
-      elsif line.chomp == "nonmutagen"
-        results << 0
-      else
-        results << line.chomp
-      end
-      read_result = false
-    else
-      @sdf << line
-    end
-  end
-end
-
-obconversion = OpenBabel::OBConversion.new
-obconversion.set_in_and_out_formats "sdf","can"
-obmol = OpenBabel::OBMol.new
-
-sdfs.each_with_index do |sdf,i|
-  cas = sdf.split("\n").first.chomp
-  obconversion.read_string obmol,sdf
-  s = obconversion.write_string(obmol).split.first
-  puts ["kazius_#{cas}",s,results[i]].join ","
-end
- 
diff --git a/scripts/merge-mutagenicity.rb b/scripts/merge-mutagenicity.rb
deleted file mode 100755
index 2de7d1c..0000000
--- a/scripts/merge-mutagenicity.rb
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env ruby
-require 'csv'
-require 'json'
-
-acts = {}
-ids = {}
-ARGV.each do |csv|
-  CSV.foreach(csv) do |row|
-    acts[row[1]] ||= []
-    acts[row[1]] << row[2]
-    ids[row[1]] ||= []
-    ids[row[1]] << row[0]
-  end
-end
-
-contradictions = {}
-puts ["SMILES","Mutagenicity"].join(",")
-acts.each do |s,a|
-  if a.uniq.size > 1
-    contradictions[s] ||= {}
-    a.each_with_index do |act,i|
-      contradictions[s][ids[s][i]] = act
-      puts [s,act].join ","
-    end
-  else
-    puts [s,a.first].join ","
-  end
-end
-
-File.open(File.join(File.dirname(__FILE__),"..","data","contradictions.json"),"w+") { |cont| cont.puts contradictions.to_json }
diff --git a/scripts/repeated_crossvalidation.rb b/scripts/repeated_crossvalidation.rb
deleted file mode 100755
index 8631245..0000000
--- a/scripts/repeated_crossvalidation.rb
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env ruby
-require_relative '../../lazar/lib/lazar'
-include OpenTox
-
-dataset = Dataset.from_csv_file ARGV[0]
-
-model = Model::LazarClassification.create(training_dataset: dataset)
-
-rcv = Validation::RepeatedCrossValidation.create(model)
-puts "#{rcv.id}"