From f1466dac28558b17688949067bdd64d7b331ca00 Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Thu, 16 Mar 2023 22:51:24 +0100
Subject: [PATCH] redundant lines while saving the output in create_consensus
---
cami_src/cami_suite.py | 17 ++++++-----------
1 file changed, 6 insertions(+), 11 deletions(-)
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index a7df6f7..4825d62 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -342,7 +342,7 @@ class cami():
# 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]])
-
+
# create integer codes for cami_versions (needed for predicted_by vertex property)
recursion_limit = sys.getrecursionlimit()
for cami_method_name, cami_params in camis.items():
@@ -374,20 +374,15 @@ 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]])
-
- # 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)
+
+ # 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')
def generate_output(self, cami_method, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
gene_name_map, codes2tools, cami_scores):
--
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