From d1b84282718392fa95d189249c63a6ec6edda2c7 Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Mon, 13 Mar 2023 23:37:20 +0100
Subject: [PATCH] seed variation implementation with iterative find_bridges
function
---
cami_src/algorithms/AlgorithmWrapper.py | 4 +-
cami_src/algorithms/DiamondWrapper.py | 2 +-
cami_src/algorithms/DominoWrapper.py | 16 ++---
cami_src/algorithms/RobustWrapper.py | 2 +-
cami_src/cami.py | 71 ++++++++++---------
cami_src/cami_suite.py | 91 ++++++++++++-------------
cami_src/seed_variation_2.py | 2 +-
cami_src/utils/degradome.py | 5 +-
cami_src/utils/networks.py | 72 +++++++++++++++++--
9 files changed, 161 insertions(+), 104 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 = []
diff --git a/cami_src/cami.py b/cami_src/cami.py
index 7747d8d..12cf3ef 100755
--- a/cami_src/cami.py
+++ b/cami_src/cami.py
@@ -21,7 +21,7 @@ from configparser import ConfigParser
def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
output_dir, identifier, save_temps, nvenn, save_image, force, drugstone, ncbi, configuration,
- seed_variation, parallelization, external_results):
+ seed_variation, parallelization, external_results, debug):
print('CAMI started')
config = ConfigParser()
config.read(configuration)
@@ -55,7 +55,8 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
# rename seeds with their corresponding indices in the ppi_graph
name2index = preprocess.name2index_dict(ppi_graph)
checked_seed_lst = [name2index[v] for v in seed_lst if v in name2index]
- print('Created the PPI-network Graph and seed list.')
+ if debug:
+ print('Created the PPI-network Graph and seed list.')
n = len(checked_seed_lst)
m = len(seed_lst)
if n != m and not force:
@@ -69,20 +70,22 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
exit(1)
seed_lst = checked_seed_lst.copy()
- print(f'Continuing with vertices at indices {[int(seed) for seed in seed_lst]} as input seeds')
+ if debug: print(f'Continuing with vertices at indices {[int(seed) for seed in seed_lst]} as input seeds')
# change directory to ~/cami/cami (home of cami.py)
cami_home = sys.argv[0].rsplit('/', 1)
os.chdir(cami_home[0])
home_path = os.path.dirname(os.getcwd())
- print(f"Home directory of cami: {home_path}")
+ if debug:
+ print(f"Home directory of cami: {home_path}")
if identifier==None:
identifier = str(uuid.uuid4())
if output_dir==None:
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 debug:
+ print(f"Output directory of cami: {output_dir}")
if not os.path.exists(output_dir):
os.makedirs(output_dir)
@@ -91,7 +94,8 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
#create temporary directory
tmp_dir = os.path.join(home_path, f'data/tmp/{identifier}')
- print(f'Creating unique temporary directory for CAMI: {tmp_dir}')
+ if debug:
+ print(f'Creating unique temporary directory for CAMI: {tmp_dir}')
if not os.path.exists(tmp_dir):
os.makedirs(tmp_dir)
@@ -114,6 +118,9 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
if ncbi:
cami.ncbi = True
+
+ if debug:
+ cami.debug = True
for tool in tool_wrappers:
cami.initialize_tool(tool)
@@ -126,7 +133,7 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
cami.set_initial_seed_lst(initial_seedlst)
- if consensus or (not consensus and not evaluate and not seed_variation):
+ if (consensus or (not consensus and not evaluate and not seed_variation)) and not seed_variation:
result_sets = cami.make_predictions()
if len(external_results) > 0:
assert(len(ext_wrappers) == len(external_results))
@@ -169,7 +176,7 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
result_sets = cami.make_predictions()
cami.create_consensus(result_sets)
if nvenn and vis:
- url = cami.nvenn()
+ url = cami.use_nvenn()
cami.download_diagram(url)
with open(f'{output_dir}/00_node_degrees.tsv', 'w') as node_degrees:
@@ -281,25 +288,20 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
tools = [tool for tool in rediscovery_rates_results[0].keys()]
tool_labels = tools.copy()
redisc_rates = [[res[tool] for res in rediscovery_rates_results] for tool in tools]
- for idx,tool in enumerate(tool_labels):
+ for idx,tool in enumerate(tools):
if '_' in tool:
# find the index of the second occurrence of the character
second_occurrence_index = tool.find('_', tool.find('_') + 1)
if second_occurrence_index > -1:
# replace the character at that index with the replacement character
tool_name = tool[:second_occurrence_index] + '\n' + tool[second_occurrence_index + 1:]
-
- tool_labels[idx] = tool_name
-
+ tool_labels[idx] = tool_name
#PLOT
-
# Create a figure instance
- fig, axs = plt.subplots(2, 1, figsize=(20,15))
- plt.subplots_adjust(left=0.2)
-
- ax1 = axs[0]
- ax5 = axs[1]
+ #print(sys.getrecursionlimit())
+ fig, (ax1, ax5, ax4) = plt.subplots(3, 1, figsize=(20,20))
+ fig.subplots_adjust(left=0.2)
# Extract Figure and Axes instance
# Create a plot
@@ -307,6 +309,7 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
for violinpart in list(violins1.keys())[2:]:
violins1[violinpart].set_color('k')
+
for violin in violins1['bodies']:
violin.set_facecolor('red')
# Add title
@@ -319,19 +322,19 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
ax1.set_ylabel('Rediscovery rate (<rediscovered seeds>/<removed seeds>)', wrap=True, fontsize=14)
- # ax4 = plt.subplot(1,3,2, label='ax4')
- # violins2 = ax4.violinplot([tp_rate_dict[tool] for tool in tools], showmeans=True, showextrema=True)
- # for violinpart in list(violins2.keys())[2:]:
- # violins2[violinpart].set_color('k')
- # for violin in violins2['bodies']:
- # violin.set_facecolor('orange')
- # # Add title
- # ax4.set_title(f'True positive rates after randomly removing {nof_removals} seeds\n{nof_iterations} times from {identifier} seeds.', wrap=True)
+ violins2 = ax4.violinplot([tp_rate_dict[tool] for tool in tools], showmeans=True, showextrema=True)
+ for violinpart in list(violins2.keys())[2:]:
+ violins2[violinpart].set_color('k')
+ for violin in violins2['bodies']:
+ violin.set_facecolor('orange')
+ # Add title
+ ax4.set_title(f'True positive rates after randomly removing {nof_removals} seeds {nof_iterations} times from {identifier} seeds.', wrap=True, fontsize=14)
- # ax4.set_xticks(list(range(1,len(tools)+1)))
- # ax4.set_xticklabels(tools)
+ ax4.set_xticks(list(range(1,len(tools)+1)))
+ ax4.set_xticklabels(tool_labels)
+ ax4.tick_params(axis='x', labelsize=11)
- # ax4.set_ylabel('Sensitivity (TP/TP + FN)', wrap=True)
+ ax4.set_ylabel('Sensitivity (TP/TP + FN)', wrap=True, fontsize=14)
violins3 = ax5.violinplot([module_size_dict[tool] for tool in tools], showmeans=True, showextrema=True)
# Add title
@@ -345,11 +348,11 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
ax5.set_xticks(list(range(1,len(tools)+1)))
ax5.set_xticklabels(tool_labels)
- ax5.set_ylabel('(<rediscovered seeds>/<module size>)', fontsize=14)
+ ax5.set_ylabel('precision (<rediscovered seeds>/<module size>)', fontsize=14)
ax5.tick_params(axis='x', labelsize=11)
- plt.tight_layout()
+ fig.tight_layout()
fig.savefig(f'{output_dir}/00_{identifier}_seed_variation_result.png', bbox_inches="tight")
-
+ plt.close(fig)
print(f'Violin plot saved under: 00_{identifier}_seed_variation_result.png')
if save_temps:
@@ -401,6 +404,8 @@ if __name__ == "__main__":
help="Choose a configuration for the static variables.")
parser.add_argument('-p', '--parallelization', action='store_true',
help="run the tools for prediction parallelized")
+ parser.add_argument('-db', '--debug', action='store_true',
+ help="run CAMI with verbose outputs")
#TODO List with additional arguments if needed by certain tools
args = vars(parser.parse_args())
@@ -412,7 +417,7 @@ if __name__ == "__main__":
# add name for implemented tools here:
implemented_tools = [
- "domino",
+ "domino",
"diamond",
"robust",
"hotnet"
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index 235b624..b8ac144 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -180,9 +180,9 @@ class cami():
:rtype: set()
"""
tool.create_tmp_output_dir(self.tmp_dir) # creates the temporary input directory
- print(f"preparing {tool.name} input...")
+ if self.debug: print(f"preparing {tool.name} input...")
inputparams = tool.prepare_input()
- print(f'running {tool.name}...')
+ if self.debug: print(f'running {tool.name}...')
preds = set(tool.run_algorithm(inputparams))
if self.debug:
print(f'{tool.name} predicted {len(preds)} active vertices (seeds not excluded):')
@@ -224,7 +224,8 @@ class cami():
to the corresponding tool
:rtype: dict(AlgorithmWrapper():set(Graph.vertex()))
"""
- print(f'Creating result sets of all {self.nof_tools} tools...')
+ if self.debug:
+ print(f'Creating result sets of all {self.nof_tools} tools...')
pred_sets = {tool:None for tool in self.tool_wrappers}
if self.threaded:
@@ -337,18 +338,21 @@ class cami():
}},
}
- # create integer codes for cami_versions (needed for predicted_by vertex property)
-
+ # 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]])
+
for cami_method_name, cami_params in camis.items():
- print("Running " + cami_method_name)
+ if self.debug:
+ print("Running " + cami_method_name)
+ # create integer codes for cami_versions (needed for predicted_by vertex property)
tool_code = max(list(tool_name_map.keys())) + 1
tool_name_map[tool_code] = cami_method_name
cami_vertices, putative_vertices, codes2tools = cami_params['function'](result_sets, ppi_graph, seed_list,
- predicted_by, cami_scores,
- tool_name_map, tool_code,
- cami_params['params'])
-
+ predicted_by, cami_scores,
+ tool_name_map, tool_code,
+ cami_params['params'])
# sort the resulting vertices according to their cami_score
cami_vlist = sorted(cami_vertices, key=lambda v: cami_scores[v], reverse=True)
@@ -362,29 +366,23 @@ class cami():
for vertex in cami_vlist:
print(f'{gene_name_map[vertex]}\t{cami_scores[vertex]}\t{codes2tools[vertex]}')
else:
- print(f'With the {len(seed_genes)} seed genes CAMI ({cami_method_name}) proposes {len(cami_vlist)} to add to the Active Module')
-
+ print(f'With the {len(seed_genes)} seed genes CAMI ({cami_method_name}) proposes {len(cami_vlist)} genes to add to the Active Module')
+
# for visualization with nvenn
- self.result_gene_sets[cami_method_name] = 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 tool in result_sets:
- self.result_module_sets[tool.name] = set([gene_name_map[vertex] for vertex in result_sets[tool]]).union(self.seed_lst)
+ self.result_gene_sets[cami_method_name] = set(cami_genes)
- assert(self.code2toolname == tool_name_map)
+ # 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]))
# 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
- print('Saving the results...')
+ if self.debug:
+ print('Saving the results...')
with open(f'{self.output_dir}/all_predictions_{self.uid}.tsv', 'w') as outputfile:
outputfile.write(f'CAMI predictions with {len(self.seed_lst)} of initially {len(self.initial_seed_lst)} seeds: {seed_genes},\n'+
f'initially: {self.initial_seed_lst}\n')
@@ -394,11 +392,15 @@ class cami():
outputfile.write(f'{gene_name_map[vertex]}\t{codes2tools[vertex]}\t{cami_scores[vertex]}\t{str(vertex)}\t{vertex.out_degree()}\n')
print(f'saved all predictions by the used tools in: {self.output_dir}/all_predictions_{self.uid}.tsv')
+
+ def generate_output(self, cami_method, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
+ gene_name_map, codes2tools, cami_scores):
+
# save the predictions made by cami
ncbi_url = ('\tncbi_url' if self.ncbi else '')
ncbi_summary = ('\tncbi_summary' if self.ncbi else '')
- with open(f'{self.output_dir}/CAMI_output_{self.uid}.tsv', 'w') as outputfile:
+ with open(f'{self.output_dir}/{cami_method}_output_{self.uid}.tsv', 'w') as outputfile:
outputfile.write(f'gene\tindex_in_graph\tcami_score\tdegree_in_graph{ncbi_url}{ncbi_summary}\n')
for vertex in cami_vlist:
if self.ncbi:
@@ -412,32 +414,28 @@ class cami():
url, summary = '',''
outputfile.write(f'{gene_name_map[vertex]}\t{str(vertex)}\t{cami_scores[vertex]}\t{vertex.out_degree()}{url}{summary}\n')
- # save the whole module
- whole_module = []
- with open(f'{self.output_dir}/CAMI_module_{cami_method}_{self.uid}.txt', 'w') as modfile:
- for vertex in seed_genes:
- modfile.write(f'{vertex}\n')
- whole_module.append(vertex)
- for vertex in cami_genes:
- modfile.write(f'{vertex}\n')
- whole_module.append(vertex)
-
- print(f'saved cami output in: {self.output_dir}/CAMI_output_{self.uid}.tsv')
- print(f'saved the Consensus Active Module by CAMI in: {self.output_dir}/CAMI_nodes_{cami_method}_{self.uid}.txt')
+ # # save the whole module
+ # whole_module = []
+ # with open(f'{self.output_dir}/{cami_method}_module_{self.uid}.txt', 'w') as modfile:
+ # for vertex in seed_genes:
+ # modfile.write(f'{vertex}\n')
+ # whole_module.append(vertex)
+ # for vertex in cami_genes:
+ # modfile.write(f'{vertex}\n')
+ # whole_module.append(vertex)
+
+ # print(f'saved {cami_method} output in: {cami_method}_output_{self.uid}.tsv')
+ # print(f'saved the Consensus Active Module by CAMI in: {self.output_dir}/{cami_method}_module_{self.uid}.txt')
- # save predictions by the other tools
- for tool in self.result_gene_sets:
+ # save predicted modules by all other tools
+ for tool in self.result_module_sets:
with open(f'{self.output_dir}/{tool}_output_{self.uid}.tsv', 'w') as outputfile:
outputfile.write('gene\n')
for gene in self.result_gene_sets[tool]:
outputfile.write(f'{gene}\n')
- print(f'saved {tool} output in: {self.output_dir}/{tool}_output_{self.uid}.tsv')
-
- # return values
- consensus = {}
- consensus['module'] = whole_module
- consensus['seeds'] = self.seed_lst
+ if self.debug:
+ print(f'saved {tool} output in: {self.output_dir}/{tool}_output_{self.uid}.tsv')
def use_nvenn(self):
@@ -486,7 +484,6 @@ class cami():
#print(list(set(cami_symbol_edges)))
url = drugstone.send_request(cami_symbols, cami_symbol_edges)
print(f'You can find a network visualization of the CAMI module via: {url}')
- 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
diff --git a/cami_src/seed_variation_2.py b/cami_src/seed_variation_2.py
index 12bd963..278ed7d 100755
--- a/cami_src/seed_variation_2.py
+++ b/cami_src/seed_variation_2.py
@@ -9,5 +9,5 @@ seedfiles = sys.argv[2:]
config = 'seed_variationconf'
for seeds in seedfiles:
identifier = basename(seeds).rsplit('.')[0] + '_seedvar_different_consensus_approaches'
- command = f'./cami.py -n {network} -s {seeds} -id {identifier} -conf {config} -var 100 -f;'
+ command = f'./cami.py -n {network} -s {seeds} -id {identifier} -conf {config} -var 10 -f;'
subprocess.call(command, shell=True)
\ No newline at end of file
diff --git a/cami_src/utils/degradome.py b/cami_src/utils/degradome.py
index b295427..1b13755 100644
--- a/cami_src/utils/degradome.py
+++ b/cami_src/utils/degradome.py
@@ -1,14 +1,13 @@
import requests, re
-def send_request(sets=dict(), seeds=list()):
+def send_request(sets=dict()):
url = 'http://degradome.uniovi.es/cgi-bin/nVenn/nvenn.cgi'
groups = '['
for tool in sets:
groups += '{' + f'"name":"{tool}","els":['
for node in sets[tool]:
- if node not in seeds:
- groups += f'"{node}",'
+ groups += f'"{node}",'
groups = groups[:-1]
groups += ']},'
groups = groups[:-1]
diff --git a/cami_src/utils/networks.py b/cami_src/utils/networks.py
index f045996..244388e 100644
--- a/cami_src/utils/networks.py
+++ b/cami_src/utils/networks.py
@@ -121,14 +121,45 @@ def steiner_tree(g, seeds, seed_map, weights, non_zero_hub_penalty):
except:
pass
g2.remove_vertex(node)
-
return g2
+def find_bridges_it(g):
+ r"""Finds all bridges in a graph."""
+ global __time
+ __time = 0
+ visited = g.new_vertex_property("boolean", False)
+ disc = g.new_vertex_property("float", float("inf"))
+ low = g.new_vertex_property("float", float("inf"))
+ is_bridge = g.new_edge_property("boolean", False)
+ stack = [(None, g.get_vertices()[0])]
+ while stack:
+ parent_node, node = stack.pop()
+ if not visited[node]:
+ visited[node] = True
+ disc[node] = __time
+ low[node] = __time
+ __time += 1
+ for neighbor in g.get_all_neighbors(node):
+ if not visited[neighbor]:
+ stack.append((node, neighbor))
+ elif neighbor != parent_node:
+ low[node] = min(low[node], disc[neighbor])
+ if low[node] == disc[node] and parent_node is not None:
+ try:
+ is_bridge[g.edge(node, parent_node)] = True
+ except Exception as err:
+ print(f'{err}')
+ pass
+ elif parent_node is not None:
+ low[parent_node] = min(low[parent_node], disc[node])
+ return is_bridge
+
+
def find_bridges(g):
r"""Finds all bridges in a graph."""
global __time
__time = 0
- sys.setrecursionlimit(g.num_vertices() + 1)
+ #sys.setrecursionlimit(g.num_vertices() + 1)
visited = g.new_vertex_property("boolean", False)
disc = g.new_vertex_property("float", float("inf"))
low = g.new_vertex_property("float", float("inf"))
@@ -139,13 +170,43 @@ def find_bridges(g):
__dfs_find_bridges(g, node, visited, disc, low, parent, is_bridge)
return is_bridge
-def __dfs_find_bridges(g, node, visited, disc, low, parent, is_bridge):
+def __dfs_find_bridges_it(g, node, visited, disc, low, parent, is_bridge):
visited[node] = True
global __time
disc[node] = __time
low[node] = __time
__time += 1
-
+ stack = []
+ for nb in g.get_all_neighbors(node):
+ if not visited[nb]:
+ parent[nb] = node
+ stack.append(nb)
+ low[node] = min(low[node], low[nb])
+ if low[nb] > disc[node]:
+ try:
+ is_bridge[g.edge(node, nb)] = True
+ except:
+ pass
+ elif int(nb) != parent[node]: #TODO can in theory be removed
+ low[node] = min(low[node], disc[nb])
+
+ while (stack):
+ next_node = stack.pop()
+ if not visited[next_node]:
+ visited[next_node] = True
+ for nb in g.get_all_neighbors(next_node):
+ parent[nb] = next_node
+ stack.append(nb)
+ low[next_node] = min(low[next_node], low[nb])
+ if low[nb] > disc[next_node]:
+ try:
+ is_bridge[g.edge(next_node, nb)] = True
+ except:
+ pass
+ elif int(nb) != parent[node]: #TODO can in theory be removed
+ low[next_node] = min(low[next_node], disc[nb])
+
+def __dfs_find_bridges(g, node, visited, disc, low, parent, is_bridge):
for nb in g.get_all_neighbors(node):
if not visited[nb]:
parent[nb] = node
@@ -159,7 +220,6 @@ def __dfs_find_bridges(g, node, visited, disc, low, parent, is_bridge):
elif int(nb) != parent[node]: #TODO can in theory be removed
low[node] = min(low[node], disc[nb])
-
def must(g, seed_ids, num_trees, hub_penalty, weights=None, tolerance=10):
if gt.openmp_enabled():
gt.openmp_set_num_threads(6)
@@ -186,7 +246,7 @@ def must(g, seed_ids, num_trees, hub_penalty, weights=None, tolerance=10):
for vertex in tree_nodes:
scores[vertex] +=1
if num_trees > 1:
- is_bridge = find_bridges(g)
+ is_bridge = find_bridges_it(g)
edge_filter = g.new_edge_property("boolean", True)
while len(tree_edges) > 0:
tree_edge = tree_edges.pop()
--
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