diff options
Diffstat (limited to 'fminer.rb')
| -rw-r--r-- | fminer.rb | 42 |
1 files changed, 33 insertions, 9 deletions
@@ -98,16 +98,38 @@ post '/fminer/:method/match?' do f_dataset.features.each do |f,m| res_dataset.add_feature(f,m) end - c_dataset.compounds.each do |c| - res_dataset.add_compound(c) - comp = OpenTox::Compound.new(c) - f_dataset.features.each do |f,m| - if params[:nr_hits] == "true" + + step_width = 100 / c_dataset.compounds.size.to_f + count = 0 + + if params[:nr_hits] == "true" + c_dataset.compounds.each do |c| + res_dataset.add_compound(c) + comp = OpenTox::Compound.new(c) + f_dataset.features.each do |f,m| hits = comp.match_hits([m[OT.smarts]]) res_dataset.add(c,f,hits[m[OT.smarts]]) if hits[m[OT.smarts]] - else - res_dataset.add(c,f,1) if comp.match?(m[OT.smarts]) end + count += 1 + task.progress step_width*count + end + else + LOGGER.debug "match #{c_dataset.compounds.size} compounds with #{f_dataset.features.keys.size} features" + + obconversion = OpenBabel::OBConversion.new + obmol = OpenBabel::OBMol.new + obconversion.set_in_format('inchi') + smarts_pattern = OpenBabel::OBSmartsPattern.new + c_dataset.compounds.each do |c| + res_dataset.add_compound(c) + comp = OpenTox::Compound.new(c) + obconversion.read_string(obmol,comp.inchi) + f_dataset.features.each do |f,m| + smarts_pattern.init(m[OT.smarts]) + res_dataset.add(c,f,1) if smarts_pattern.match(obmol) + end + count += 1 + task.progress step_width*count if count%100==0 end end res_dataset.save @subjectid @@ -167,7 +189,8 @@ post '/fminer/bbrc/?' do fminer.smi = [] # AM LAST: needed for matching the patterns back # Add data to fminer - fminer.add_fminer_data(@@bbrc, params, @value_map) + #fminer.add_fminer_data(@@bbrc, params, @value_map) + fminer.add_fminer_data(@@bbrc, @value_map) g_array=fminer.all_activities.values # DV: calculation of global median for effect calculation g_median=g_array.to_scale.median @@ -298,7 +321,8 @@ post '/fminer/last/?' do fminer.smi = [] # AM LAST: needed for matching the patterns back # Add data to fminer - fminer.add_fminer_data(@@last, params, @value_map) + #fminer.add_fminer_data(@@last, params, @value_map) + fminer.add_fminer_data(@@last, @value_map) raise "No compounds in dataset #{fminer.training_dataset.uri}" if fminer.compounds.size==0 |