known issue: module 45, 200 should be skipped in yash dataset, improved...

known issue: module 45, 200 should be skipped in yash dataset, improved efficiency, now outputs time used

bayespairing/src/display_modules.py

@@ -203,7 +203,7 @@ def plot_module(graphs,name,latex=False):
             #print(elabels)
             nx.draw_networkx_edge_labels(g0, pos, elabels, font_size=10)
             nx.draw_networkx_edges(g0, pos, edgelist=NC_edges, edge_color='purple', width=4, arrows=False)
-            nx.draw_networkx_edges(g0, pos, edgelist=C_edges, edge_color='green', width=4, arrows=False)
+            nx.draw_networkx_edges(g0, pos, edgelist=C_edges, edge_color='lightseagreen', width=4, arrows=False)
             nx.draw_networkx_edges(g0, pos, edgelist=backbone, edge_color='black', width=3, arrowsize=18)
             nx.draw_networkx_edges(g0, pos, edgelist=stacking, edge_color='orange', width=1, arrows=False)
             plt.title("Module " + str(m), fontsize=24)
@@ -216,7 +216,7 @@ def plot_module(graphs,name,latex=False):
             # plt.legend(handles=[NCP,CP,BP,SP],prop={'size': 16})
             #plt.show()
             plt.savefig("../Graphs/" + name + "graph" + str(m) + ".png", format="png")
-
+            plt.clf()
 
 
 def logo_module(aln,name):
@@ -292,4 +292,4 @@ if __name__ == "__main__":
     #   print(len(list(i.nodes)))
     logo_module(aln,model_name)
     plot_module(aln,model_name,latex=latex)
-    print('done')
\ No newline at end of file
+    print('done')

bayespairing/src/parse_sequences.py

@@ -102,7 +102,7 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
     if "t" in arguments:
         t = float(arguments["t"])
     else:
-        t = 25
+        t = 20
     if "w" in arguments:
         w = int(arguments["w"])
     else:
@@ -357,6 +357,8 @@ def present_output(all_maxes, threshold, offset=0):
 
 if __name__ == "__main__":
     # Manages arguments
+    START_TIME = timer.time()
+
     arguments = {}
     parser = argparse.ArgumentParser()
     parser.add_argument("--verbose", help="increase output verbosity", action="store_true")
@@ -437,6 +439,8 @@ if __name__ == "__main__":
     #timer.sleep(5)
     # executes BayesPairing on the sequence
     print(run_fasta(seq, modules_to_check, dataset, ss, arguments)[0])
+    END_TIME = timer.time()
+    print("TOTAL TIME USED:",round(END_TIME-START_TIME,3))
 
 #if __name__ != "__main__":
 #    parse_sequences("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")