prepare d2 graph to realoding by moving construction steps to annexe functions

deconvolution/d2_graph.py

@@ -7,10 +7,12 @@ from d_graph import compute_all_max_d_graphs, filter_dominated, list_domination_
 
 class D2Graph(object):
     """D2Graph (read it (d-graph)²)"""
-    def __init__(self, graph, index_size=3, verbose=True, debug=False):
+    def __init__(self, graph):
         super(D2Graph, self).__init__()
         self.graph = graph
 
+
+    def construct_from_barcodes(self, index_size=3, verbose=True, debug=False):
         # Compute all the d-graphs
         if verbose:
             print("Compute the unit d-graphs")
@@ -67,6 +69,10 @@ class D2Graph(object):
                     fp.write(f"{d_graph.idx} {neighbor_idx} {dist}\n")
 
 
+    def load_from_gexf(self, filename):
+        pass
+
+
     def create_index_from_tuples(self, tuple_size=3):
         index = {}
 

deconvolution/to_d2_graph.py

@@ -26,7 +26,8 @@ def main():
     
     G = nx.read_gexf(filename)
     # Index size must be changed for general purpose. 8 is good for d=5
-    d2g = d2.D2Graph(G, index_size=8)
+    d2g = d2.D2Graph(G)
+    d2g.construct_from_barcodes(index_size=8)
     d2g.save(f"{args.output_prefix}.tsv")
     
     G, names = d2g.to_nx_graph()