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author | Andreas Maunz <andreas@maunz.de> | 2011-06-27 14:16:41 +0200 |
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committer | Andreas Maunz <andreas@maunz.de> | 2011-06-27 14:16:41 +0200 |
commit | 18d44225d0f5258348db3278a87628f74bd36744 (patch) | |
tree | d8f560cedfb5a3b9b2317ab65814135efb0dca30 | |
parent | 5c3bc078eae55ed3e55fac5328e296348c10b646 (diff) |
Using Hit counts (LAST-PM)
-rw-r--r-- | fminer.rb | 17 |
1 files changed, 13 insertions, 4 deletions
@@ -264,7 +264,11 @@ post '/fminer/bbrc/?' do id_arrs.each { |id_count_hash| id=id_count_hash.keys[0].to_i count=id_count_hash.values[0].to_i - feature_dataset.add(compounds[id], feature_uri, true) + if params[:nr_hits] + feature_dataset.add(compounds[id], feature_uri, count) + else + feature_dataset.add(compounds[id], feature_uri, true) + end } end end @@ -409,9 +413,10 @@ post '/fminer/last/?' do lu = LU.new # AM LAST: uses last-utils here dom=lu.read(xml) # AM LAST: parse GraphML smarts=lu.smarts_rb(dom,'nls') # AM LAST: converts patterns to LAST-SMARTS using msa variant (see last-pm.maunz.de) - instances=lu.match_rb(smi,smarts) # AM LAST: creates instantiations + params[:nr_hits].nil? ? nr_hits=true : nr_hits=false + matches,counts=lu.match_rb(smi,smarts,nr_hits) # AM LAST: creates instantiations - instances.each do |smarts, ids| + matches.each do |smarts, ids| feat_hash = Hash[*(all_activities.select { |k,v| ids.include?(k) }.flatten)] # AM LAST: get activities of feature occurrences; see http://www.softiesonrails.com/2007/9/18/ruby-201-weird-hash-syntax if @@last.GetRegression() p_value = @@last.KSTest(all_activities.values, feat_hash.values).to_f # AM LAST: use internal function for test @@ -436,7 +441,11 @@ post '/fminer/last/?' do } feature_dataset.add_feature feature_uri, metadata end - ids.each { |id| feature_dataset.add(compounds[id], feature_uri, true)} + if params[:nr_hits] + ids.each { |id| feature_dataset.add(compounds[id], feature_uri, true)} + else + ids.each_with_index { |id,i| feature_dataset.add(compounds[id], feature_uri, counts[id][i])} + end end feature_dataset.save(@subjectid) feature_dataset.uri |