Updated go-workflow.

workflows/geneontology.py

@@ -42,6 +42,12 @@ class GeneOntology(networkx.XDiGraph):
             for link in node[linkattr]:
                 self.add_edge(self.by_id[link], node, linkattr)
 
+    def link_relationships(self):
+        for node in self.nodes():
+            for link in node['relationship']:
+                link_type, term = link.split(' ')
+                self.add_edge(self.by_id[term.strip()], node, link_type.strip())
+
     def get_bp(self):
         """Returns the root node of the biological_process tree"""
         return self.by_id['GO:0008150']
@@ -114,13 +120,13 @@ def read_gene_ontology(fd):
 #                print "[Term]"
             else:
                 term = None
-                print "ignoring: %s" %s
+                #print "ignoring: %s" %s
         else:
             if term:
                 _add_term_attribute(term, k, v, c)
 #                print "    %s: %s" % (k, v)
-            else:
-                print "no term: ignoring: %s" %line
+#            else:
+#                print "no term: ignoring: %s" %line
 #        print '.',
         line = fd.readline()
 
@@ -133,6 +139,7 @@ def read_default_go():
     f = open("/usr/share/gene-ontology/gene_ontology.obo")
     go = read_gene_ontology(f)
     go.link_ontology('is_a')
+    go.link_relationships()
     f.close()
     return go