Small updates.

workflows/geneontology.py

@@ -61,7 +61,29 @@ class GeneOntology(networkx.XDiGraph):
         """Returns the root node of the molecular_function tree"""
         return self.by_id['GO:0003674']
 
+    def _subsumer(self, t1, t2, heap):
+        while heap != []:
+            t = heap[0]
+            heap = heap[1:]
+
+            p1 = networkx.shortest_path(self, t, t1)
+            p2 = networkx.shortest_path(self, t, t2)
+            if p1 and p2:
+                return t
+
+            heap += self.in_neighbors(t)
+        return None
+
     def subsumer(self, t1, t2):
+        if t1 == t2:
+            return t1
+        if networkx.shortest_path(self, t1, t2):
+            return t1
+        elif networkx.shortest_path(self, t2, t1):
+            return t2
+        return self._subsumer(t1, t2, self.in_neighbors(t1))
+
+    def old_subsumer(self, t1, t2):
         if t1 == t2:
             return t1
 
@@ -83,6 +105,8 @@ class GeneOntology(networkx.XDiGraph):
                 return t
 
         print "GeneOntology.subsumer: should not reach this point"
+        print "path is now: %s" % path
+        print "ids are: %s " % [x['id'] for x in path]
 
 def _split_obo_line(line):
     """Splits a line from an obo file in its three constituent parts.