Rakefile in rbbt-sources-3.0.20

- old
+ new

@@ -4,38 +4,44 @@
 module NCI
   def self.get_pathways(xml, format = "UP", get_short_name = false)
     doc = Nokogiri::XML(xml)
     pathways = {}
 
+    #{{{ Molecules
+    
     molecules = {}
     doc.xpath("//Molecule").each do |molecule|
       id = molecule.attribute('id').value
       type = molecule.attribute('molecule_type').value
       names = molecule.xpath("Name[@name_type='#{format}']").collect{|name| name.attribute("value").value}
       molecules[id] = {:xml => molecule, :proteins => names}
     end
 
 
+    #{{{ Interactions
+
     interactions = {}
     doc.xpath("//Interaction").each do |interaction|
       id = interaction.attribute('id').value
       type = interaction.attribute('interaction_type').value
       molecule_ids = interaction.xpath('InteractionComponentList/InteractionComponent').collect{|c| c.attribute('molecule_idref').value}.flatten.compact
       pathway_ids = interaction.xpath('Abstraction').collect{|c| c.attribute('pathway_idref').value}.flatten.compact
 
       interactions[id] = {:xml => interaction, :molecule_ids => molecule_ids, :pathway_ids => pathway_ids}
     end
 
+    #{{{ Pathways
+
     doc.xpath("//Pathway").each do |pathway|
       id = pathway.attribute('id').value
       subnet = pathway.attribute('subnet').value
       name = pathway.xpath('LongName').first.content
       short_name = pathway.xpath('ShortName').first.content if get_short_name
 
       interaction_ids = pathway.xpath("PathwayComponentList/PathwayComponent").collect{|component| component.attribute("interaction_idref").value}
-
       pathway_interactions = interaction_ids.collect{|i| interactions[i]}
+
       pathway_molecule_ids = pathway_interactions.collect{|info| info[:molecule_ids]}.compact.flatten
 
       pathway_uniprot_ids = pathway_molecule_ids.collect do |i| 
         next unless molecules.include? i
         molecules[i][:proteins]
@@ -45,23 +51,25 @@
       else
         pathways[id] = [[name], [pathway_uniprot_ids.flatten.compact.uniq]]
       end
     end
     
+    #{{{ Sub-pathways ???
+    
     doc.xpath("//Pathway").each do |pathway|
       id = pathway.attribute('id').value
       subnet = pathway.attribute('subnet').value
       name = pathway.xpath('LongName').first.content
 
       interaction_ids = pathway.xpath("PathwayComponentList/PathwayComponent").collect{|component| component.attribute("interaction_idref").value}
-
       pathway_interactions = interaction_ids.collect{|i| interactions[i]}
+
       pathway_subnet_ids = pathway_interactions.collect{|info| info[:pathway_ids]}.compact.flatten
 
       pathway_subnet_ids.collect do |nid| 
         next unless pathways.include? nid
-        new_genes = pathways[id].last
-        pathways[nid][1] = (pathways[nid][1] + new_genes).uniq
+        new_genes = pathways[nid].last
+        pathways[id][1] = (pathways[id][1] + new_genes).uniq
       end
     end
 
     pathways
   end