output messages hinzugefügt

cami/cami.py

@@ -27,9 +27,7 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
             seed_lst = [name2index[v] for v in seed_lst]
             # set weights for seed genes in ppi_graph
             for seed in seed_lst:
-                ppi_graph.vertex_properties["weight"][seed] = 10.0
-            for seed in seed_lst:
-                print(ppi_graph.vertex_properties["weight"][seed])
+                ppi_graph.vertex_properties["cami_score"][seed] = 10.0
         else:
             print('Abort. Please try again.')
             exit(1)
@@ -38,6 +36,8 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
 
     if output_dir==None:
         output_dir = f'{home_path}/data/output'
+        if not os.path.exists(output_dir):
+            os.mkdir(output_dir)
             
     while output_dir[-1] == '/':
         output_dir = output_dir[:-1]
@@ -80,17 +80,20 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
 
 
     cami = cami_suite.cami(ppi_graph, seed_lst, tool_wrappers, output_dir, identifier, tmp_dir)
-    if visualize:
-        cami.visualize = True
 
     if consensus:
         cami.create_consensus()
 
+        if visualize:
+            cami.visualize()
+
     if evaluate:
         cami.make_evaluation()
 
     if not consensus and not evaluate:
         cami.create_consensus()
+        if visualize:
+            cami.visualize()
         cami.make_evaluation()
 
     if save_temps:

cami/cami_suite.py

@@ -122,12 +122,13 @@ class cami():
             all_vertices = cami_vertices.union(putative_vertices)
             for vertex in all_vertices:
                 outputfile.write(f'{name[vertex]}\t{[self.code2toolname[idx] for idx,code in enumerate(predicted_by[vertex]) if code == 1]}\t{cami_scores[vertex]}\t{str(vertex)}\n')
+        print(f'saved all predictions by the used tools in: {self.output_dir}/all_predictions_{self.uid}.tsv')
 
         with open(f'{self.output_dir}/CAMI_{self.uid}_output.tsv', 'w') as outputfile:
             outputfile.write('gene\tindex_in_graph\tcami_score\n')
             for vertex in cami_vlist:
                 outputfile.write(f'{name[vertex]}\t{str(vertex)}\t{cami_scores[vertex]}\n')
-
+        print(f'saved cami output in: {self.output_dir}/CAMI_{self.uid}_output.tsv')
         # for visualization
         # transform the vertex indices to their corresponding gene names
         self.result_gene_sets['CAMI'] = cami_genes