diff options
Diffstat (limited to 'fminer.rb')
| -rw-r--r-- | fminer.rb | 31 |
1 files changed, 30 insertions, 1 deletions
@@ -200,6 +200,8 @@ post '/fminer/bbrc/?' do step_width = 80 / @@bbrc.GetNoRootNodes().to_f features = Set.new + feature_count = {} + # run @@bbrc (0 .. @@bbrc.GetNoRootNodes()-1).each do |j| results = @@bbrc.MineRoot(j) @@ -245,6 +247,9 @@ post '/fminer/bbrc/?' do } feature_dataset.add_feature feature_uri, metadata #feature_dataset.add_feature_parameters feature_uri, feature_dataset.parameters + + feature_count[feature_uri] = 0 + end id_arrs.each { |id_count_hash| id=id_count_hash.keys[0].to_i @@ -253,6 +258,7 @@ post '/fminer/bbrc/?' do feature_dataset.add(fminer.compounds[id], feature_uri, count) else feature_dataset.add(fminer.compounds[id], feature_uri, 1) + feature_count[feature_uri] = feature_count[feature_uri]+1 end } @@ -261,7 +267,30 @@ post '/fminer/bbrc/?' do # AM: add feature values for non-present features # feature_dataset.complete_data_entries - + + if (params[:max_num_features] && feature_dataset.features.size>params[:max_num_features].to_i) + LOGGER.debug "removing features, found: #{feature_dataset.features.size}, max-num: #{params[:max_num_features]}" + + feature_p_count = [] + feature_dataset.features.each do |f_uri,m| + feature_p_count << [f_uri, m[OT.pValue], feature_count[f_uri]] + end + # sort by p-value, tie breaking by number of compounds that match this feature + sorted = feature_p_count.sort do |a,b| + if b[1] == a[1] + b[2] <=> a[2] + else + b[1] <=> a[1] + end + end + (params[:max_num_features].to_i..(sorted.size-1)).each do |i| + feature_dataset.features.delete(sorted[i][0]) + feature_dataset.compounds.each do |c| + feature_dataset.data_entries[c].delete(sorted[i][0]) + end + end + end + feature_dataset.save(@subjectid) feature_dataset.uri end |