diff options
Diffstat (limited to 'lib/bbrc.rb')
| -rw-r--r-- | lib/bbrc.rb | 44 |
1 files changed, 11 insertions, 33 deletions
diff --git a/lib/bbrc.rb b/lib/bbrc.rb index 1c04a6d..cf6fa6c 100644 --- a/lib/bbrc.rb +++ b/lib/bbrc.rb @@ -14,13 +14,13 @@ module OpenTox # - nr_hits Set to "true" to get hit count instead of presence # - get_target Set to "true" to obtain target variable as feature # @return [text/uri-list] Task URI - def self.bbrc params + def self.bbrc dataset, params={} table_of_elements = [ "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Uut", "Fl", "Uup", "Lv", "Uus", "Uuo"] @fminer=OpenTox::Algorithm::Fminer.new - @fminer.check_params(params,5) + @fminer.check_params(dataset,params,5) time = Time.now @@ -41,7 +41,7 @@ module OpenTox @bbrc.SetConsoleOut(false) feature_dataset = FminerDataset.new( - :training_dataset_id => params[:dataset].id, + :training_dataset_id => dataset.id, :training_algorithm => "#{self.to_s}.bbrc", :training_feature_id => params[:prediction_feature].id , :training_parameters => { @@ -51,22 +51,14 @@ module OpenTox } ) - feature_dataset.compounds = params[:dataset].compounds + feature_dataset.compounds = dataset.compounds - @fminer.compounds = [] - @fminer.db_class_sizes = Array.new # AM: effect - @fminer.all_activities = Hash.new # DV: for effect calculation in regression part - @fminer.smi = [] # AM LAST: needed for matching the patterns back - # Add data to fminer @fminer.add_fminer_data(@bbrc, value_map) g_median=@fminer.all_activities.values.to_scale.median #task.progress 10 #step_width = 80 / @bbrc.GetNoRootNodes().to_f - features = [] - feature_ids = [] - matches = {} $logger.debug "Setup: #{Time.now-time}" time = Time.now @@ -81,12 +73,13 @@ module OpenTox rt = Time.now f = YAML.load(result)[0] smarts = f.shift - # convert fminer representation into a more human readable format + # convert fminer SMARTS representation into a more human readable format smarts.gsub!(%r{\[#(\d+)&(\w)\]}) do element = table_of_elements[$1.to_i-1] $2 == "a" ? element.downcase : element end p_value = f.shift + f.flatten! =begin if (!@bbrc.GetRegression) @@ -118,14 +111,13 @@ module OpenTox #"effect" => effect, "dataset_id" => feature_dataset.id }) - feature_dataset.add_feature feature - feature_ids << feature.id.to_s + feature_dataset.feature_ids << feature.id ftime += Time.now - ft it = Time.now - f.first.each do |id_count_hash| + f.each do |id_count_hash| id_count_hash.each do |id,count| - matches[@fminer.compounds[id].id.to_s] = {feature.id.to_s => count} + feature_dataset[id-1, feature_dataset.feature_ids.size-1] = count.to_i end end itime += Time.now - it @@ -136,25 +128,11 @@ module OpenTox $logger.debug "Fminer: #{Time.now-time} (read: #{rtime}, iterate: #{itime}, find/create Features: #{ftime})" time = Time.now - n = 0 - feature_dataset.compound_ids.each do |cid| - cid = cid.to_s - feature_dataset.feature_ids.each_with_index do |fid,i| - fid = fid.to_s - unless matches[cid] and matches[cid][fid]# fminer returns only matches - count = 0 - else - count = matches[cid][fid] - end - feature_dataset.bulk << [cid,fid,count] - n +=1 - end - end + feature_dataset.fill_nil_with 0 $logger.debug "Prepare save: #{Time.now-time}" time = Time.now - feature_dataset.bulk_write - feature_dataset.save + feature_dataset.save_all $logger.debug "Save: #{Time.now-time}" feature_dataset |