refactor mains and subgraph definition to be coherent with nx graph heritage

deconvolution/d2_graph.py

@@ -23,6 +23,14 @@ class D2Graph(nx.Graph):
             self.barcode_edge_idxs[(edge[1], edge[0])] = idx
 
 
+    """ Redefine subgraph to avoid errors type instantiation errors.
+    """
+    def subgraph(self, nodes):
+        G = nx.Graph()
+        G.add_edges_from(self.edges())
+        return G.subgraph(nodes)
+
+
     def construct_from_barcodes(self, index_size=3, verbose=True, debug=False):
         # Compute all the d-graphs
         if verbose:

deconvolution/d2_to_path.py

@@ -34,8 +34,8 @@ def main():
     d2g.load(d2_file)
 
     # Take the principal component
-    largest_component_nodes = max(nx.connected_components(d2g.nx_graph), key=len)
-    largest_component = d2g.nx_graph.subgraph(largest_component_nodes)
+    largest_component_nodes = max(nx.connected_components(d2g), key=len)
+    largest_component = d2g.subgraph(largest_component_nodes)
     unitigs = compute_unitigs(largest_component)
 
     # Write the simplificated graph

deconvolution/d2_transitive_reduction.py

@@ -37,7 +37,7 @@ def main():
     d2a.transitive_reduction(d2g)
 
     # Write the simplificated graph
-    nx.write_gexf(d2g.nx_graph, args.output_d2_name)
+    nx.write_gexf(d2g, args.output_d2_name)
 
 
 if __name__ == "__main__":

deconvolution/to_d2_graph.py

@@ -29,10 +29,9 @@ def main():
     # Index size must be changed for general purpose. 8 is good for d=5
     d2g = d2.D2Graph(G)
     d2g.construct_from_barcodes(index_size=8)
-    d2g.save(f"{args.output_prefix}.tsv")
     
-    G, names = d2g.to_nx_graph()
-    nx.write_gexf(G, f"{args.output_prefix}.gexf")
+    d2g.save(f"{args.output_prefix}.tsv")
+    nx.write_gexf(d2g, f"{args.output_prefix}.gexf")
 
 
 if __name__ == "__main__":