attachment:kegg_relation_mapper_for_bioruby_console.rb of Presentations/08_Web_Services

Attachment 'kegg_relation_mapper_for_bioruby_console.rb'

   1 include_class 'cytoscape.Cytoscape'
   2 include_class 'cytoscape.CyNode'
   3 include_class 'cytoscape.CyEdge'
   4 include_class 'cytoscape.CyNetwork'
   5 include_class 'cytoscape.layout.CyLayouts'
   6 
   7 if pathway_id == nil  
   8   puts 'Warning: Specify target pathway!'
   9   return
  10 end
  11 
  12 puts '\n\n Target Pathway: ' + pathway_id
  13 
  14 species = pathway_id[5..7]
  15 
  16 elm = keggapi.get_elements_by_pathway(pathway_id)
  17 rel = keggapi.get_element_relations_by_pathway(pathway_id)
  18 
  19 kegg_id_map = Hash.new
  20 
  21 # Extract name and ID
  22 elm.each do |e|
  23     kegg_id_map[e.element_id] = e.names  
  24 end
  25 
  26 # Create pathway
  27 pathway = Cytoscape.createNetwork("KEGG Pathway #{pathway_id}")
  28 rel.each do |r|
  29   node_id1 = "#{pathway_id}:#{r.element_id1}"
  30   node_id2 = "#{pathway_id}:#{r.element_id2}"
  31   node1 = Cytoscape.getCyNode( node_id1, true)
  32   node2 = Cytoscape.getCyNode( node_id2, true)
  33   edge = Cytoscape.getCyEdge(node1, node2, "interaction", r['type'], true)
  34   pathway.addEdge(edge)
  35   kegg_id1 = kegg_id_map[r.element_id1][0]
  36   kegg_id2 = kegg_id_map[r.element_id2][0]
  37   Cytoscape.getNodeAttributes.setAttribute(node_id1, 'KEGG ID', kegg_id1)
  38   Cytoscape.getNodeAttributes.setAttribute(node_id2, 'KEGG ID', kegg_id2)
  39   
  40   if kegg_id1.index(species) != nil
  41     Cytoscape.getNodeAttributes.setAttribute(node_id1, 'Entrez Gene ID', kegg_id1.sub(/#{species}\:/, ""))
  42   end
  43     
  44   if kegg_id2.index(species) != nil
  45     Cytoscape.getNodeAttributes.setAttribute(node_id2, 'Entrez Gene ID', kegg_id2.sub(/#{species}\:/, ""))
  46   end
  47 end
  48 
  49 # Layout nodes
  50 CyLayouts.getLayout("force-directed").doLayout();
  51 Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
  52 

Attached Files

• [get | view] (2011-10-20 20:44:40, 16.4 KB) [[attachment:agilent1.png]]
• [get | view] (2011-10-20 20:44:40, 89.4 KB) [[attachment:agilent2.png]]
• [get | view] (2011-10-20 20:44:40, 7.0 KB) [[attachment:agilent3.png]]
• [get | view] (2011-10-20 20:44:40, 15.1 KB) [[attachment:entrez_ruby1.png]]
• [get | view] (2011-10-20 20:44:40, 106.8 KB) [[attachment:entrez_ruby2.png]]
• [get | view] (2011-10-20 20:44:40, 85.5 KB) [[attachment:gpml1.png]]
• [get | view] (2011-10-20 20:44:40, 127.9 KB) [[attachment:gpml2.png]]
• [get | view] (2011-10-20 20:44:40, 21.5 KB) [[attachment:intact1.png]]
• [get | view] (2011-10-20 20:44:40, 101.4 KB) [[attachment:intact2.png]]
• [get | view] (2011-10-20 20:44:40, 311.3 KB) [[attachment:intact3.png]]
• [get | view] (2011-10-20 20:44:40, 43.7 KB) [[attachment:kegg1.png]]
• [get | view] (2011-10-20 20:44:40, 67.8 KB) [[attachment:kegg2.png]]
• [get | view] (2011-10-20 20:44:40, 17.6 KB) [[attachment:kegg3.png]]
• [get | view] (2011-10-20 20:44:40, 1.6 KB) [[attachment:kegg_relation_mapper_for_bioruby_console.rb]]
• [get | view] (2011-10-20 20:44:40, 710.8 KB) [[attachment:merge_final.png]]
• [get | view] (2011-10-20 20:44:40, 507.6 KB) [[attachment:ncbi1.png]]
• [get | view] (2011-10-20 20:44:40, 3.8 KB) [[attachment:ncbi2.png]]
• [get | view] (2011-10-20 20:44:40, 26.3 KB) [[attachment:ncbi3.png]]
• [get | view] (2011-10-20 20:44:40, 46.3 KB) [[attachment:ncbi35.png]]
• [get | view] (2011-10-20 20:44:40, 112.1 KB) [[attachment:ncbi4.png]]
• [get | view] (2011-10-20 20:44:40, 132.0 KB) [[attachment:ncbi_gene_list1.png]]
• [get | view] (2011-10-20 20:44:40, 92.4 KB) [[attachment:ncbi_gene_list2.png]]
• [get | view] (2011-10-20 20:44:40, 2.8 KB) [[attachment:ncbi_gene_list3.png]]
• [get | view] (2011-10-20 20:44:40, 178.4 KB) [[attachment:ncbi_gene_list4-1.png]]
• [get | view] (2011-10-20 20:44:40, 8.3 KB) [[attachment:ncbi_gene_list4.png]]
• [get | view] (2011-10-20 20:44:40, 16.0 KB) [[attachment:ncbi_gene_list5.png]]
• [get | view] (2011-10-20 20:44:40, 190.0 KB) [[attachment:ncbi_gene_list6.png]]
• [get | view] (2011-10-20 20:44:40, 3731.2 KB) [[attachment:sampleSession1.cys]]

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