forked from yana-safonova/ig_repertoire_constructor
/
dense_subgraph_finder.py
executable file
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/
dense_subgraph_finder.py
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#!/usr/bin/env python2
import sys
import os
import init
import logging
import shutil
import ntpath
home_directory = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) + '/'
spades_src = os.path.join(home_directory, "src/python_pipeline/")
config_dir = os.path.join(home_directory, "configs/dense_sgraph_finder/")
ig_binary = os.path.join(home_directory, "build/release/bin/ig_repertoire_constructor")
sys.path.append(spades_src)
import process_cfg
import support
def CheckParamsCorrectness(params, log, parser):
if not "output" in params or params.output == "":
log.info("ERROR: Output directory (-o) was not specified")
parser.print_help()
sys.exit(-1)
if not "graph" in params or params.graph == "":
log.info("ERROR: Graph (-g/--graph) was not specified")
parser.print_help()
sys.exit(-1)
if not os.path.exists(params.graph):
log.info("ERROR: File with graph " + params.graph + " was not found")
parser.print_help()
sys.exit(-1)
if not os.path.isabs(params.graph):
params.graph = os.path.abspath(params.graph)
def PrintParams(params, log):
log.info("DSF parameters:")
log.info(" Input graph:\t\t\t\t\t" + params.graph)
log.info(" Output directory:\t\t\t\t" + params.output)
log.info(" Number of threads:\t\t\t\t" + str(params.num_threads))
log.info(" Minimum size of processed graphs:\t\t" + str(params.min_graph_size))
log.info(" Minimum edge fill-in of dense subgraph:\t" + str(params.min_fillin))
if params.create_trivial_decomposition:
log.info(" Trivial decomposition will be created")
log.info(" Output auxiliary files:\t\t\t" + str(params.save_aux_files))
log.info("\n")
def supportInfo(log):
log.info("\nIn case you have troubles running DSF, you can write to igtools_support@googlegroups.com.")
log.info("Please provide us with dense_sungraph_finder.log file from the output directory.")
def SetOutputParams(params, output_dir):
params.output = os.path.abspath(output_dir)
params.config_dir = os.path.join(params.output, params.config_dir)
params.config_file = os.path.join(params.config_dir, params.config_file)
def PrepareOutputDir(params, log):
if os.path.exists(params.output):
shutil.rmtree(params.output)
if not os.path.isdir(params.output):
os.makedirs(params.output)
def CopyConfigs(params, log):
if os.path.exists(params.config_dir):
shutil.rmtree(params.config_dir)
shutil.copytree(config_dir, params.config_dir)
def CreateParamDict(params):
param_dict = dict()
param_dict['output_dir'] = params.output
param_dict['graph_filename'] = params.graph
param_dict['threads_count'] = params.num_threads
param_dict['min_fillin_threshold'] = params.min_fillin
param_dict['min_graph_size'] = params.min_graph_size
param_dict['create_trivial_decomposition'] = process_cfg.bool_to_str(params.create_trivial_decomposition)
param_dict['path_to_metis'] = os.path.join(home_directory, "build/release/bin/")
param_dict['min_supernode_size'] = params.min_snode_size
return param_dict
def PrepareConfigs(params, log):
CopyConfigs(params, log)
param_dict = CreateParamDict(params)
if not os.path.exists(params.config_file):
log.info("ERROR: config file was not found")
sys.exit(1)
process_cfg.substitute_params(params.config_file, param_dict, log)
def Cleanup(params, log):
params.sgraph_dir = os.path.join(params.output, "connected_components")
params.decomposition_dir = os.path.join(params.output, "dense_subgraphs")
params.metis_output = os.path.join(params.output, "metis.output")
if os.path.exists(params.metis_output):
os.remove(params.metis_output)
if not "save_aux_files" in params or not params.save_aux_files:
if os.path.exists(params.sgraph_dir):
shutil.rmtree(params.sgraph_dir)
if os.path.exists(params.decomposition_dir):
shutil.rmtree(params.decomposition_dir)
def main(argv, external_logger = ""):
from src.python_add.argparse_ext import ArgumentHiddenParser
parser = ArgumentHiddenParser(description="== DSF: an algorithm for corrupted cliques search ==",
epilog="""
In case you have troubles running DSF, you can write to igtools_support@googlegroups.com.
Please provide us with dense_subgraph_finder.log file from the output directory.
""",
add_help=False)
req_args = parser.add_argument_group("Input")
input_args = req_args.add_mutually_exclusive_group(required=True)
input_args.add_argument("-g", "--graph",
type=str,
default="",
dest="graph",
help="Input graph in GRAPH format")
input_args.add_argument("--test",
action="store_const",
const=os.path.join(home_directory, "test_dataset/dsf/test.graph"),
dest="graph",
help="Running test dataset")
out_args = parser.add_argument_group("Output")
out_args.add_argument("-o", "--output",
type=str,
default=os.path.join(home_directory, "dsf_test"),
help="Output directory")
optional_args = parser.add_argument_group("Optional arguments")
optional_args.add_argument("-t", "--threads",
type=int,
default=16,
dest="num_threads",
help="Threads number [default: %(default)d]")
optional_args.add_argument("-f", '--min-fillin',
type=float,
default=0.6,
dest="min_fillin",
help='Minimum fill-in of dense subgraphs [default: %(default)f]')
optional_args.add_argument("-n", "--min-snode-size",
type=int,
default=5,
dest="min_snode_size",
help="Minimum vertex weight that prevents its gluing with other heavy vertex "
"[default: %(default)d]")
optional_args.add_argument("-s", "--min-size",
type=int,
default=5,
dest="min_graph_size",
help="Minimum size of graph where dense subgraphs will be computed "
"[default: %(default)d]")
optional_args.add_argument("--create-triv-dec",
action="store_const",
const=True,
dest="create_trivial_decomposition",
help='Creating decomposition according to connected components [default: False]')
optional_args.add_argument("--save-aux-files",
action="store_const",
const=True,
dest="save_aux_files",
help="Saving auxiliary files: subgraphs in GRAPH format and their decompositions "
"[default: False]")
optional_args.add_argument("-h", "--help",
action="help",
help="Help message and exit")
parser.set_defaults(config_dir="configs",
config_file="config.info")
# prepare log
log = logging.getLogger('dense_subgraph_finder')
log.setLevel(logging.DEBUG)
console = logging.StreamHandler(sys.stdout)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.DEBUG)
log.addHandler(console)
if external_logger != "":
external_log_handler = logging.FileHandler(external_logger, mode = "a")
log.addHandler(external_log_handler)
args = [arg for arg in argv if ntpath.basename(arg) != 'dense_subgraph_finder.py']
params = parser.parse_args(args)
CheckParamsCorrectness(params, log, parser)
SetOutputParams(params, params.output)
PrepareOutputDir(params, log)
# log file
params.log_filename = os.path.join(params.output, "dense_subgraph_finder.log")
if os.path.exists(params.log_filename):
os.remove(params.log_filename)
log_handler = logging.FileHandler(params.log_filename, mode='a')
log.addHandler(log_handler)
# print command line
command_line = "Command_line: "
if argv[0] != "dense_subgraph_finder.py":
command_line += "dense_subgraph_finder.py "
command_line += " ".join(argv)
log.info(command_line + "\n")
PrintParams(params, log)
log.info("Log will be written to " + params.log_filename + "\n")
PrepareConfigs(params, log)
# run dense subgraph finder
try:
dsf_command_line = init.PathToBins.run_dense_sgraph_finder + " " + params.config_file
support.sys_call(dsf_command_line, log)
Cleanup(params, log)
log.info("\nThank you for using Dense Subgraph Finder!\n")
except (KeyboardInterrupt):
log.info("\nDense subgraph finder was interrupted!")
except Exception:
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
log.exception(exc_value)
log.info("\nERROR: Exception caught.")
supportInfo(log)
except BaseException:
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
log.exception(exc_value)
log.info("\nERROR: Exception caught.")
supportInfo(log)
log.info("Log was written to " + params.log_filename)
if __name__ == '__main__':
main(sys.argv)