refactor name to idx

deconvolution/d2_algorithms.py

@@ -21,8 +21,8 @@ def transitive_reduction(d2g):
         dg1_name, dg2_name, data = edges.pop(0)
 
         # Extract dgs
-        dg1 = d2g.node_by_name[dg1_name]
-        dg2 = d2g.node_by_name[dg2_name]
+        dg1 = d2g.node_by_idx[int(dg1_name)]
+        dg2 = d2g.node_by_idx[int(dg2_name)]
 
         # Extract common neighbors
         nei1 = frozenset(d2g.neighbors(dg1_name))
@@ -32,7 +32,7 @@ def transitive_reduction(d2g):
         # Look for all the common neighbors, if edge must be remove or not
         current_dist = d2g[dg1_name][dg2_name]["distance"]
         for node in common:
-            com_dg = d2g.node_by_name[node]
+            com_dg = d2g.node_by_idx[int(node)]
             extern_dist = d2g[dg1_name][node]["distance"] + d2g[node][dg2_name]["distance"]
 
             # If better path, remove the edge