@@ -101,11 +101,21 @@ def KGML2Graph(xmlfile, filter_by = ()): pathway.add_edge(e1, e2) pathway.relations[e1+'_'+e2] = rel + + # Add reactions to pathway object for reaction in tree.getiterator('reaction'): + id = reaction.get('name') - substrate = reaction.find('substrate').get('name') - product = reaction.find('product').get('name') - pathway.reactions[reaction] = reaction + substrates = [] + products = [] + + for sub in reaction.getiterator('substrate'): + substrates.append(sub.get('name')) + + for prod in reaction.getiterator('product'): + products.append(sub.get('name')) + + pathway.reactions[id] = {'reaction': reaction, 'substrates': substrates, 'products': products} return tree, pathway, nodes, genes parse_KGML.py 2c696d3f6d9587e99e7b46d1a7822a872167ac08 dalloliogm dalloliogm@gmail.com http://github.com/dalloliogm/kegg-kgml-parser--python-/commit/4ef95bedc5a5bbe582346c8c63cc86a9765b8265 4ef95bedc5a5bbe582346c8c63cc86a9765b8265 2009-10-20T03:50:46-07:00 2009-10-20T03:50:46-07:00 improved how reactions are stored in the pathway object 7a3bc6d3b1237b8d35fbf4bef2eb2f06d15a78b2 dalloliogm dalloliogm@gmail.com