From 5b3d4e29e1b8428ed7485bdcbfbf70a5efadab44 Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Thu, 16 Mar 2023 22:27:20 +0100
Subject: [PATCH] added debug option to algorithms
---
cami_src/algorithms/AlgorithmWrapper.py | 4 ++--
cami_src/algorithms/DiamondWrapper.py | 2 +-
cami_src/algorithms/DominoWrapper.py | 16 ++++++----------
cami_src/algorithms/RobustWrapper.py | 2 +-
4 files changed, 10 insertions(+), 14 deletions(-)
diff --git a/cami_src/algorithms/AlgorithmWrapper.py b/cami_src/algorithms/AlgorithmWrapper.py
index 6378fad..17de832 100644
--- a/cami_src/algorithms/AlgorithmWrapper.py
+++ b/cami_src/algorithms/AlgorithmWrapper.py
@@ -38,10 +38,10 @@ class AlgorithmWrapper(object):
def create_tmp_output_dir(self, tmp_dir):
out_dir = os.path.join(tmp_dir, self.name)
- print(tmp_dir)
+ #print(tmp_dir)
if not os.path.exists(out_dir):
os.mkdir(out_dir)
- print(f"created temporary directory for {self.name} named {out_dir}...")
+ if self.debug: print(f"created temporary directory for {self.name} named {out_dir}...")
self.output_dir = out_dir
def name_file(self, kind, ending='txt'):
diff --git a/cami_src/algorithms/DiamondWrapper.py b/cami_src/algorithms/DiamondWrapper.py
index 93ca932..ee61636 100644
--- a/cami_src/algorithms/DiamondWrapper.py
+++ b/cami_src/algorithms/DiamondWrapper.py
@@ -42,7 +42,7 @@ class DiamondWrapper(AlgorithmWrapper):
command = f'{diamond} "{ppi}" "{seeds}" {nof_predictions} {self.alpha} "{algo_output}"'
subprocess.call(command, shell=True, stdout=subprocess.PIPE)
assert os.path.exists(algo_output), f'DIAMOnD failed to save output to {algo_output}'
- print(f"DIAMOnD results saved in {algo_output}")
+ if self.debug: print(f"DIAMOnD results saved in {algo_output}")
return self.extract_output(algo_output)
def prepare_input(self):
diff --git a/cami_src/algorithms/DominoWrapper.py b/cami_src/algorithms/DominoWrapper.py
index d642ecf..34953a3 100644
--- a/cami_src/algorithms/DominoWrapper.py
+++ b/cami_src/algorithms/DominoWrapper.py
@@ -54,7 +54,7 @@ class DominoWrapper(AlgorithmWrapper):
command = f'mv "{algo_output}" "{os.path.join(self.output_dir, outputfilename)}"'
subprocess.call(command, shell=True, stdout=subprocess.PIPE)
algo_output = os.path.join(self.output_dir, outputfilename)
- print(f"{self.name} results saved in {algo_output}")
+ if self.debug: print(f"{self.name} results saved in {algo_output}")
return self.extract_output(algo_output)
@@ -64,8 +64,7 @@ class DominoWrapper(AlgorithmWrapper):
"""
inputparams = []
# prepare inputfiles
- if self.debug:
- print(f'creating {self.name} input files in {self.output_dir}')
+ if self.debug: print(f'creating {self.name} input files in {self.output_dir}')
ppi_filename = self.name_file('ppi', 'sif')
ppi_file = os.path.join(self.output_dir, ppi_filename)
@@ -81,26 +80,23 @@ class DominoWrapper(AlgorithmWrapper):
file.write(f"{str(edge.source()) + '_'}\tppi\t{str(edge.target()) + '_'}\n")
# the nodes need to be appended by '_' so that pandas recognizes the vertices as strings
inputparams.append(ppi_file)
- print(f'{self.name} ppi is saved in {ppi_file}')
+ if self.debug: print(f'{self.name} ppi is saved in {ppi_file}')
with open(seed_file, "w") as file:
file.write('#node\n')
for seed in self.seeds:
file.write(f"{seed}_\n")
inputparams.append(seed_file)
- if self.debug:
- print(f'{self.name} seeds are saved in {seed_file}')
+ if self.debug: print(f'{self.name} seeds are saved in {seed_file}')
slices_filename = self.name_file('slices')
slices_output = os.path.join(self.output_dir, slices_filename)
if not os.path.exists(slices_output):
- if self.debug:
- print('creating domino slices_file...')
+ if self.debug: print('creating domino slices_file...')
command = f'slicer --network_file "{ppi_file}" --output_file "{slices_output}"'
subprocess.call(command, shell=True, stdout=subprocess.PIPE)
- if self.debug:
- print(f'{self.name} slices are saved in {slices_output}')
+ if self.debug: print(f'{self.name} slices are saved in {slices_output}')
inputparams.append(slices_output)
return inputparams
diff --git a/cami_src/algorithms/RobustWrapper.py b/cami_src/algorithms/RobustWrapper.py
index 84d00ef..fb89b20 100755
--- a/cami_src/algorithms/RobustWrapper.py
+++ b/cami_src/algorithms/RobustWrapper.py
@@ -58,7 +58,7 @@ class RobustWrapper(AlgorithmWrapper):
{self.initialFraction} {self.reductionFactor} \
{self.numberSteinerTrees} {self.threshold}'
subprocess.call(command, shell=True, stdout=subprocess.PIPE)
- print(f"Robust results saved in {algo_output}")
+ if self.debug: print(f"Robust results saved in {algo_output}")
return self.extract_output(algo_output)
# inputparams = []
--
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