Merge pull request #17 from Reed-CompBio/go-depth

added go_depth file and weights to nodes

main.py

@@ -21,6 +21,7 @@
     read_specific_columns,
     export_graph_to_pickle,
     read_pro_go_data,
+    read_go_depth_data
 )
 from tools.workflow import run_workflow
 
@@ -36,19 +37,21 @@ def main():
     if not os.path.exists("output/images"):
         os.makedirs("output/images")
 
-    fly_interactome_path = Path("./network/fly_propro.csv")
+    fly_interactome_path = Path("./network/fly_proPro.csv")
     fly_go_association_path = Path("./network/fly_proGo.csv")
-    zfish_interactome_path = Path("./network/zfish_propro.csv")
+    zfish_interactome_path = Path("./network/zfish_proPro.csv")
     zfish_go_association_path = Path("./network/zfish_proGo.csv")
-    bsub_interactome_path = Path("./network/bsub_propro.csv")
+    bsub_interactome_path = Path("./network/bsub_proPro.csv")
     bsub_go_association_path = Path("./network/bsub_proGo.csv")
+    go_depth_path = Path("./network/go_depth.csv")
+
 
     output_data_path = Path("./output/data/")
     output_image_path = Path("./output/images/")
     dataset_directory_path = Path("./output/dataset")
     graph_file_path = Path(dataset_directory_path, "graph.pickle")
-    sample_size = 10
-    repeats = 5
+    sample_size = 1000
+    repeats = 1
     new_random_lists = True
     print_graphs = True
 
@@ -76,10 +79,13 @@ def main():
         fly_go_association_path, go_inferred_columns, go_term_type, ","
     )
 
+    depth_columns = [0,1,2]
+    go_depth_dict = read_go_depth_data(go_depth_path, depth_columns, go_term_type, ',')
+
     protein_list = []
 
     # if there is no graph.pickle file in the output/dataset directory, uncomment the following lines
-    G, protein_list = create_ppi_network(interactome, go_protein_pairs)
+    G, protein_list = create_ppi_network(interactome, go_protein_pairs, go_depth_dict)
     export_graph_to_pickle(G, graph_file_path)
 
     # Define algorithm classes and their names