diff --git a/cami/DominoWrapper.py b/cami/DominoWrapper.py
index ca94f59a9bed9305349808b52de4817d13ccfe35..2c8c6f70ffca323ae78cd23ddcf385805a40a284 100644
--- a/cami/DominoWrapper.py
+++ b/cami/DominoWrapper.py
@@ -17,6 +17,8 @@ class DominoWrapper(AlgorithmWrapper):
self.visualization_flag = config.get('domino', 'visualization_flag')
self.output_name = config.get('domino', 'output_name')
+ self.parallels = config.get('domino', 'para')
+ self.c = config.get('domino', 'c')
def run_algorithm(self, inputparams):
"""Run Domino algorithm
@@ -39,19 +41,18 @@ class DominoWrapper(AlgorithmWrapper):
#MC:
#CONFIG: visualization_flag = False
- command = f'domino -a {seeds} -n {ppi} -s {slices_file} \
- -o {self.output_dir} -v {self.visualization_flag}'
- subprocess.call(command, shell=True, stdout=subprocess.PIPE)
- outputname = (os.path.basename(seeds)).rsplit(".")[0]
+ command = f'domino -a "{seeds}" -n "{ppi}" -s "{slices_file}" \
+ -o "{self.output_dir}" -v {self.visualization_flag} -p {self.parallels} --use_cache {self.c}'
+ run = subprocess.run(command, shell=True, capture_output=True)
+ match = re.search("( final modules are reported at )(.*)(\n)", run.stdout.decode('utf-8'))
+ algo_output = match.group(2)
#MC:
#CONFIG output_name = 'modules.out'
- algo_output = os.path.join(self.output_dir, outputname, self.output_name)
+ assert os.path.exists(algo_output), f'Could not create output file {algo_output} for domino'
outputfilename = self.name_file('out', 'out')
- command = f'mv {algo_output} {os.path.join(self.output_dir, outputfilename)}'
+ 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)
-
- assert os.path.exists(algo_output), f'Could not find output file {algo_output} for domino'
print(f"{self.name} results saved in {algo_output}")
return self.extract_output(algo_output)
@@ -92,7 +93,7 @@ class DominoWrapper(AlgorithmWrapper):
if not os.path.exists(slices_output):
print('creating domino slices_file...')
- command = f'slicer --network_file {ppi_file} --output_file {slices_output}'
+ command = f'slicer --network_file "{ppi_file}" --output_file "{slices_output}"'
subprocess.call(command, shell=True, stdout=subprocess.PIPE)
print(f'{self.name} slices are saved in {slices_output}')
inputparams.append(slices_output)
diff --git a/cami/cami.py b/cami/cami.py
index ab789b5d7abc6bf582cb70988cbf4472e7c69839..98a12e66b392b0060a7bda8831ee1d84537cc79a 100755
--- a/cami/cami.py
+++ b/cami/cami.py
@@ -22,7 +22,7 @@ from configparser import ConfigParser
import ast
def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
- output_dir, identifier, save_temps, visualize, save_image, force, drugstone, ncbi, configuration, seed_variation):
+ output_dir, identifier, save_temps, nvenn, save_image, force, drugstone, ncbi, configuration, seed_variation, parallelization):
print('CAMI started')
config = ConfigParser()
config.read(configuration)
@@ -58,29 +58,28 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
# change directory to ~/cami/cami (home of cami.py)
cami_home = sys.argv[0].rsplit('/', 1)
os.chdir(cami_home[0])
- print(cami_home[0])
home_path = os.path.dirname(os.getcwd())
- print(home_path)
+ print(f"Home directory of cami: {home_path}")
if identifier==None:
identifier = str(uuid.uuid4())
if output_dir==None:
- output_dir = f'{home_path}/data/output/{identifier}'
+ output_dir = os.path.join(home_path, f'data/output/{identifier}')
+ output_dir = os.path.abspath(output_dir)
+ print(f"Output directory of cami: {output_dir}")
if not os.path.exists(output_dir):
os.makedirs(output_dir)
- while output_dir[-1] == '/':
- output_dir = output_dir[:-1]
-
if not os.path.exists(output_dir):
os.makedirs(output_dir)
#create temporary directory
- tmp_dir = f'{home_path}/data/tmp/{identifier}'
+ tmp_dir = os.path.join(home_path, f'data/tmp/{identifier}')
print(f'Creating unique temporary directory for CAMI: {tmp_dir}')
if not os.path.exists(tmp_dir):
os.makedirs(tmp_dir)
+
elif not force:
print(f'TemporaryDirectory {tmp_dir} already exists.')
choice = input('overwrite? [y/n]')
@@ -103,10 +102,8 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
for idx, tool in enumerate(tool_wrappers):
tool.set_weight(float(tool_weights[idx]))
- original_ppi = ppi_graph.copy()
- cami = cami_suite.cami(ppi_graph, seed_lst, tool_wrappers, output_dir, identifier, tmp_dir, home_path, configuration, seed_score)
+ cami = cami_suite.cami(ppi_graph, seed_lst, tool_wrappers, output_dir, identifier, tmp_dir, home_path, configuration, seed_score, parallelization)
-
if ncbi:
cami.ncbi = True
@@ -119,9 +116,10 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
result_sets = cami.make_predictions()
cami.create_consensus(result_sets)
- if visualize or save_image:
- url = cami.visualize()
- if visualize:
+ if nvenn or save_image:
+ print('Sending results to nVenn')
+ url = cami.use_nvenn()
+ if nvenn:
webbrowser.open(url)
if save_image:
cami.download_diagram(url)
@@ -145,8 +143,8 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
def make_consensus(vis=False):
result_sets = cami.make_predictions()
cami.create_consensus(result_sets)
- if visualize and vis:
- url = cami.visualize()
+ if nvenn and vis:
+ url = cami.nvenn()
cami.download_diagram(url)
with open('/Users/Mia/cami_local/cami/data/output/explorativeness.tsv', 'a') as f:
make_consensus(vis=True)
@@ -159,7 +157,6 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
for vertex in cami.ppi_graph.vertices():
node_degrees.write(f'{cami.ppi_vertex2gene[vertex]}\t{vertex.out_degree()}\t{vertex.in_degree()}\n')
-
# initialize cami and seed_var
base_seeds = cami.origin_seed_lst
original_seeds = [cami.ppi_vertex2gene[seed] for seed in base_seeds]
@@ -397,7 +394,7 @@ if __name__ == "__main__":
parser.add_argument('-o', '--output_dir', action='store', help="path to output directory")
parser.add_argument('-id', '--identifier', action='store', help="ID for the current excecution of cami. Defaults to a randomly generated ID")
parser.add_argument('-tmp', '--save_temps', action='store_true', help="keep all temporary files")
- parser.add_argument('-v', '--visualize', action='store_true', help="Visualize results using Degradome, an external webtool. Please note that degradome can only be used for visualization with up to 5 tools.")
+ parser.add_argument('-v', '--nvenn', action='store_true', help="Visualize results using nVenn by Degradome, an external webtool. Please note that degradome can only be used for visualization with up to 5 tools.")
parser.add_argument('-img', '--save_image', action='store_true', help="Save the venn diagram from the visualization as png. (Only possible for up to 5 tools)")
parser.add_argument('-f', '--force', action='store_true', help="Ignore warnings and overwrite everything when excecuting CAMI.")
parser.add_argument('-d', '--drugstone', nargs='*', action='store', default=None,
@@ -406,6 +403,8 @@ if __name__ == "__main__":
help="Save the NCBI URLs and Summaries of the genes in the CAMI output.")
parser.add_argument('-conf', '--configuration', nargs='*', action='store', default='camiconf',
help="Choose a configuration for the static variables.")
+ parser.add_argument('-p', '--parallelization', action='store_true',
+ help="run the tools for prediction parallelized")
#TODO List with additional arguments if needed by certain tools
args = vars(parser.parse_args())
diff --git a/cami/cami_suite.py b/cami/cami_suite.py
index be36532e7127387889e563f78c3484ed707dc4b8..753fea1f1f41ac877f886331ef1a7544d1c7f042 100644
--- a/cami/cami_suite.py
+++ b/cami/cami_suite.py
@@ -1,4 +1,4 @@
-import degradome, drugstone, ncbi, random
+import degradome, drugstone, ncbi, time, threading
def list_combinations(lst, k):
"""creates all possible combinations of length k with two objects in a list
@@ -31,7 +31,7 @@ class cami():
""" A module that is used for Active Module identifaction based on a
consensus approach
"""
- def __init__(self, ppi_graph, seed_lst, tool_wrappers, output_dir, uid, tmp_dir, home_path, config, seed_score):
+ def __init__(self, ppi_graph, seed_lst, tool_wrappers, output_dir, uid, tmp_dir, home_path, config, seed_score, parallelization):
"""Instance variables of CAMI
:param ppi_graph: The PPI-Graph on which all predictions in CAMI are based of
@@ -48,7 +48,7 @@ class cami():
:type tmp_dir: str
:param home_path: Path to the cami home directory (gitlab repository)
:type home_path: str
- """
+ """
self.ppi_graph = ppi_graph
self.origin_ppi_graph = ppi_graph.copy()
self.ppi_vertex2gene = self.ppi_graph.vertex_properties["name"]
@@ -69,6 +69,7 @@ class cami():
self.ncbi = False
self.config = config
self.seed_score = seed_score
+ self.threaded = parallelization
# set weights for seed genes in ppi_graph
for seed in self.seed_lst:
self.ppi_graph.vertex_properties["cami_score"][seed] = self.seed_score
@@ -113,6 +114,16 @@ class cami():
def make_evaluation(self):
print('Evaluation not implemented yet.')
+
+ def run_threaded_tool(self, tool, pred_sets):
+ """run a tool in one thread and save the results into a dictionary pred_sets
+
+ Args:
+ tool (AlgorithmWrapper): Wrapper class for a tool
+ pred_sets (dict): a dictionary that maps a tool to its result set
+ """
+ preds = self.run_tool(tool)
+ pred_sets[tool] = preds #- seed_set
def make_predictions(self):
"""create all predictions using the tools specified in tool_wrappers
@@ -122,11 +133,21 @@ class cami():
:rtype: dict(AlgorithmWrapper():set(Graph.vertex()))
"""
print(f'Creating result sets of all {self.nof_tools} tools...')
- pred_sets = {}
- for tool in self.tool_wrappers:
- preds = self.run_tool(tool)
- pred_sets[tool] = preds #- seed_set
+ pred_sets = {tool:None for tool in self.tool_wrappers}
+
+ if self.threaded:
+ threads = [threading.Thread(target=self.run_threaded_tool, args=(tool, pred_sets,))
+ for tool in self.tool_wrappers]
+ for thread in threads:
+ thread.start()
+
+ for thread in threads:
+ thread.join()
+ else:
+ for tool in self.tool_wrappers:
+ pred_sets[tool] = self.run_tool(tool)
+ assert(list(pred_sets.values()).count(None) < 1)
result_sets = {tool:set([self.ppi_graph.vertex(idx) for idx in pred_sets[tool]])
for tool in pred_sets}
return result_sets
@@ -272,7 +293,7 @@ class cami():
# for drugstone
self.cami_vertices = cami_vlist
- def visualize(self):
+ def use_nvenn(self):
"""Create Venn Diagrams via a external tool named degradome.
Sends a request via requests to the degradome server.
Returns the URL of the result.
@@ -282,7 +303,7 @@ class cami():
print('Visualizing results using Degradome...')
degradome_sets = {tool:self.result_gene_sets[tool]
for tool in self.result_gene_sets
- if len(self.result_gene_sets[tool])>0}
+ if len(self.result_gene_sets[tool])>0}
url = degradome.send_request(degradome_sets)
with open(f'{self.output_dir}/venn_link_{self.uid}.txt', 'w') as f:
f.write(url)
@@ -320,6 +341,7 @@ class cami():
print('The link was also saved in the outputfolder for later.')
with open(f'{self.output_dir}/drugstone_link_{self.uid}.txt', 'w') as f:
f.write(url)
+ return url
def remove_seeds(self, idx_lst):
"""remove seeds at indices idx
diff --git a/cami/camiconf b/cami/camiconf
index ddbef63ec9b5a935b7febdb77323f60a12a6519e..b91c2bd53d83f36bab59ee0092545bfe337bb4e7 100644
--- a/cami/camiconf
+++ b/cami/camiconf
@@ -10,6 +10,8 @@
[domino]
visualization_flag = False
output_name = 'modules.out'
+para = 1
+c = 'false'
[diamond]
alpha : 1
diff --git a/cami/example_run.py b/cami/example_run.py
index af0657ecaa0d162a6bfa97db777f03398490a62b..372f7a6623c272414c74d32e9a02a454ad877b59 100755
--- a/cami/example_run.py
+++ b/cami/example_run.py
@@ -9,5 +9,5 @@ chdir((sys.argv[0].rsplit('/', 1))[0])
networkfile = "../data/input/networks/example_network.tsv"
seedfile = "../data/input/seeds/example_seeds.txt"
identifier = "example_run"
-command = f'./cami.py -n {networkfile} -s {seedfile} -id {identifier} -ncbi -img -d --f;'
+command = f'./cami.py -n {networkfile} -s {seedfile} -id {identifier} -d -img -p --f;'
subprocess.call(command, shell=True)
\ No newline at end of file