path simple

deconvolution/main/d2_to_path_simple.py

@@ -5,6 +5,7 @@ import argparse
 import sys
 
 from deconvolution.d2graph import d2_graph as d2, path_optimization as po
+from deconvolution.d2graph.d2_path import Path
 
 
 def parse_arguments():
@@ -50,22 +51,17 @@ def main():
     spl2 = nx.shortest_path_length(largest_component,one_extremity)
     other_extremity = max(spl2.items(),key=lambda x:x[1])[0]
 
-    path = nx.shortest_path(largest_component,one_extremity, other_extremity)
+    node_path = nx.shortest_path(largest_component,one_extremity, other_extremity)
+    nodes = [largest_component.node_by_idx[int(x)] for x in node_path]
+    path = Path(d2g)
+    path.add_path(nodes)
 
-    solution = po.Solution(largest_component) 
-
-    nodes = [largest_component.node_by_idx[int(x)] for x in path]
-    solution.add_path(nodes)
-
-    print(f"covering score: {solution.covering_score()}")
+    print(f"covering score: {path.covering_score()}")
 
     # solution.save_path_in_graph(f"{args.out_prefix}_d2_path.gexf")
-    solution.save_path(f"{args.out_prefix}_path.gexf")
-    solution.save_barcode_path(f"{args.out_prefix}_barcode_count.gexf")
+    path.save_gexf(f"{args.out_prefix}_path.gexf")
     print("Solution saved")
 
-    # from d2_path import d2_path_to_barcode_path
-    # d2_path_to_barcode_path(solution)
 
 if __name__ == "__main__":
     main()