1 files changed, 58 insertions, 0 deletions
diff --git a/5x_cv/5x_crossvalidation.rb b/5x_cv/5x_crossvalidation.rb
new file mode 100644
index 0000000..bdde2dc
--- /dev/null
+++ b/5x_cv/5x_crossvalidation.rb
@@ -0,0 +1,58 @@
+# Do a five times 10-fold crossvalidation
+# # Author: Andreas Maunz, David Vorgrimmler
+# # @params: CSV-File, Method (LAST, BBRC), Minimum Frequency
+
+require 'rubygems'
+require 'opentox-ruby'
+require 'lib/cv_am.rb'
+
+subjectid = nil
+
+if ARGV.size != 1
+  puts
+  puts "Error! Arguments: <algorithm_params> in the form p1=v1;p2=v2;...;pn=vn"
+  exit 1
+end
+
+# Arguments for lib/cv.rb: file_or_dataset_uri feature_generation min_frequency min_chisq_significance backbone stratified random_seed prediction_algorithm local_svm_kernel nr_hits conf_stdev
+position_mapper={
+  "dataset_uri" => 0, 
+  "feature_generation_uri" => 1,
+  "min_frequency" => 2,
+  "min_chisq_significance" => 3,
+  "backbone" => 4,
+  "stratified" => 5,
+  "random_seed" => 6,
+  "prediction_algorithm" => 7,
+  "local_svm_kernel" => 8,
+  "nr_hits" => 9,
+  "conf_stdev" => 10
+}
+
+param_str=$ARGV[0]
+puts param_str
+params = Array.new(position_mapper.size,"")
+param_str.split(";").each { |param|
+  k,v = param.split("=")
+  params[position_mapper[k]] = v
+}
+params[5]="false" # stratified 
+
+exception_config = YAML.load_file("exceptions_config.yaml")
+if ! exception_config[params[0]].nil?
+  exception_config[params[0]].each { |k,v|
+    puts "Setting exception: #{k} => #{v}"
+    params[position_mapper[k]] = v
+  }
+end
+
+for i in 1..5
+  begin
+    puts
+    puts "Round #{i.to_s}."
+    params[6]=i # random seed
+    cv(params)
+  rescue Exception => e
+    puts "Error in 5xCV: #{e.message}: #{e.backtrace}"
+  end
+end