diff --git a/cami/cami.py b/cami/cami.py index 8a1389e82910f29e26d02a466c90ac21c0760f5b..2335f01a93ada237294278e608d90cb41637fcee 100755 --- a/cami/cami.py +++ b/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) @@ -38,7 +36,9 @@ 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: diff --git a/cami/cami_suite.py b/cami/cami_suite.py index ef92149b95be03cc494b663b77e8895e84b5703d..d198a2196ae23ab4c6b6be18a9f992acab02376c 100644 --- a/cami/cami_suite.py +++ b/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