From ab48d2c3990193a91ccba0b525380340d5359fe1 Mon Sep 17 00:00:00 2001
From: Mia_Le <64813807+mlmial@users.noreply.github.com>
Date: Sun, 6 Feb 2022 01:13:33 +0100
Subject: [PATCH] =?UTF-8?q?output=20messages=20hinzugef=C3=BCgt?=
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---
cami/cami.py | 15 +++++++++------
cami/cami_suite.py | 3 ++-
2 files changed, 11 insertions(+), 7 deletions(-)
diff --git a/cami/cami.py b/cami/cami.py
index 8a1389e..2335f01 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 ef92149..d198a21 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
--
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