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Commit f1466dac authored by Le, Mia's avatar Le, Mia
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redundant lines while saving the output in create_consensus

parent 5b3d4e29
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......@@ -374,21 +374,16 @@ class cami():
# for visualization with nvenn
self.result_gene_sets[cami_method_name] = set(cami_genes)
# transform all vertex indices to their corresponding gene names in a result set
for tool in result_sets:
self.result_gene_sets[tool.name] = set([gene_name_map[vertex] for vertex in result_sets[tool]])
sys.setrecursionlimit(recursion_limit)
# save the results in outputfiles
self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
gene_name_map, codes2tools, cami_scores)
# add seeds to result sets for drugstone and digest
for toolname in self.result_gene_sets:
self.result_module_sets[toolname] = self.result_gene_sets[toolname].union(set([gene_name_map[svertex] for svertex in self.seed_lst]))
print(f'With the {len(seed_genes)} seed genes the module predicted by {toolname} contains {len(self.result_module_sets[toolname])} genes')
sys.setrecursionlimit(recursion_limit)
# save the results in outputfiles
self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
gene_name_map, codes2tools, cami_scores)
def generate_output(self, cami_method, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
gene_name_map, codes2tools, cami_scores):
# save all predictions by all tools
......
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