d2 reloaded completed and tested

deconvolution/d2_graph.py

@@ -11,6 +11,17 @@ class D2Graph(object):
         super(D2Graph, self).__init__()
         self.graph = graph
         
+        # Number the edges from original graph
+        self.edge_idxs = {}
+        self.nb_uniq_edge = 0
+        for idx, edge in enumerate(self.graph.edges()):
+            if edge == (edge[1], edge[0]):
+                self.nb_uniq_edge += 1
+            if edge in self.edge_idxs:
+                print("Edge already present")
+            self.edge_idxs[edge] = idx
+            self.edge_idxs[(edge[1], edge[0])] = idx
+
 
     def construct_from_barcodes(self, index_size=3, verbose=True, debug=False):
         # Compute all the d-graphs
@@ -29,17 +40,6 @@ class D2Graph(object):
             d_graph.idx = idx
             self.node_by_idx[idx] = d_graph
         
-        # Number the edges from original graph
-        self.edge_idxs = {}
-        self.nb_uniq_edge = 0
-        for idx, edge in enumerate(self.graph.edges()):
-            if edge == (edge[1], edge[0]):
-                self.nb_uniq_edge += 1
-            if edge in self.edge_idxs:
-                print("Edge already present")
-            self.edge_idxs[edge] = idx
-            self.edge_idxs[(edge[1], edge[0])] = idx
-        
         # Index all the d-graphes
         if verbose:
             print("Compute the dmer index")
@@ -75,8 +75,31 @@ class D2Graph(object):
 
         # Extract d-graphs from nx graph
         self.all_d_graphs = []
-        for node in self.nx_graph.nodes():
-            self.all_d_graphs.append(Dgraph.load(node, self.graph))
+        self.node_by_idx = {}
+        for idx, node in enumerate(self.nx_graph.nodes()):
+            dg = Dgraph.load(node, self.graph)
+            self.all_d_graphs.append(dg)
+            if dg.idx == -1:
+                dg.idx = idx
+            self.node_by_idx[dg.idx] = dg
+
+        # Extract edges and re-compute distances
+        self.distances = {}
+        for edge in self.nx_graph.edges():
+            # Get the dg pair
+            idx1 = int(edge[0].split(' ')[0])
+            idx2 = int(edge[1].split(' ')[0])
+            dg1 = self.node_by_idx[idx1]
+            dg2 = self.node_by_idx[idx2]
+
+            # Compute and save the distance
+            dist = dg1.distance_to(dg2)
+            if not idx1 in self.distances:
+                self.distances[idx1] = {}
+            self.distances[idx1][idx2] = dist
+            if not idx2 in self.distances:
+                self.distances[idx2] = {}
+            self.distances[idx2][idx1] = dist
 
 
     def create_index_from_tuples(self, tuple_size=3):

deconvolution/d_graph.py

@@ -29,10 +29,15 @@ class Dgraph(object):
 
         # Head parsing
         head = head.split(' ')
-        dg = Dgraph(head[-3])
+        dg = Dgraph(int(head[-3]))
         if len(head) == 4:
             dg.idx = int(head[0])
 
+        # Reload halves
+        h1 = [int(x.split(' ')[-2]) for x in h1.split(',')]
+        h2 = [int(x.split(' ')[-2]) for x in h2.split(',')]
+        dg.put_halves(h1, h2, barcode_graph)
+
         return dg
         
 

tests/d2_graph_test.py

@@ -113,6 +113,15 @@ class TestD2Graph(unittest.TestCase):
             for dg in d2.all_d_graphs:
                 self.assertTrue(dg.idx in reloaded_idxs)
 
+            # Verify distances
+            self.assertEquals(len(d2.distances), len(d2_reloaded.distances))
+            for idx1 in d2.distances:
+                self.assertTrue(idx1 in d2_reloaded.distances)
+                self.assertEquals(len(d2.distances[idx1]), len(d2_reloaded.distances[idx1]))
+                for idx2 in d2.distances[idx1]:
+                    self.assertTrue(idx2 in d2_reloaded.distances[idx1])
+                    self.assertEquals(d2.distances[idx1][idx2], d2_reloaded.distances[idx1][idx2])
+
 
 if __name__ == "__main__":
     unittest.main()