def __make_membership(self):
"""returns the seeded membership on demand"""
if 'random_seed' in self['debug']:
util.r_set_seed(10)
new_membs = memb.create_membership(self.ratios,
self.row_seeder, self.column_seeder,
self.config_params)
return new_membs
def __make_membership(self):
"""returns the seeded membership on demand"""
if 'random_seed' in self['debug']:
util.r_set_seed(10)
new_membs = memb.create_membership(self.ratios, self.row_seeder,
self.column_seeder,
self.config_params)
return new_membs
def setup_default(args, config_parser):
"""default configuration method"""
# no organism provided -> dummy organism
if args.organism is None:
logging.warn("no organism provided - assuming that you want to score ratios only or don't use automatic download")
if not args.rsat_dir:
args.nomotifs = True
if not args.string and not args.operons:
args.nonetworks = True
# user overrides in config files
if args.config is not None:
config_parser.read(args.config)
# Initial configuration from default + user config
params = set_config(config_parser)
ratios = read_ratios(params, args)
args.clusters_per_row = params['memb.clusters_per_row']
# debug options
debug_options = set(args.debug.split(',')) if args.debug is not None else set()
if 'dump_results' in debug_options:
debug_options.add('keep_memeout')
if debug_options == {'all'}:
debug_options = ALL_DEBUG_OPTIONS
"""The overrides dictionary holds all the values that will overwrite or add
to the settings defined in the default and user-defined ini files
"""
overrides = {'organism_code': args.organism,
'ratios_file': args.ratios,
'string_file': args.string,
'logfile': args.logfile,
'rsat_organism': args.rsat_organism,
'num_clusters': __num_clusters(config_parser, args, ratios),
'memb.clusters_per_row': args.clusters_per_row,
'remap_network_nodes': args.remap_network_nodes,
'ncbi_code': args.ncbi_code,
'operon_file': args.operons,
'rsat_dir': args.rsat_dir,
'rsat_base_url': args.rsat_base_url,
'rsat_features': args.rsat_features,
'rsat_organism': args.rsat_organism,
'rsat_dir': args.rsat_dir,
'use_operons': True,
'use_string': True,
'debug': debug_options,
'nomotifs': False,
'minimize_io': args.minimize_io,
'nonetworks': args.nonetworks,
'checkratios': args.checkratios,
'random_seed': args.random_seed,
'pipeline_file': args.pipeline,
'synonym_file': args.synonym_file,
'fasta_file': args.fasta_file,
'interactive': args.interactive,
'resume': args.resume,
'case_sensitive': args.case_sensitive,
'command_line': args.command_line,
'use_BSCM': args.use_BSCM,
'use_chi2': args.use_chi2,
'db_url': args.dburl}
if overrides['random_seed'] is None:
del overrides['random_seed']
if overrides['case_sensitive'] is None:
del overrides['case_sensitive']
if overrides['pipeline_file'] is None:
del overrides['pipeline_file']
if overrides['rsat_base_url'] is None:
del overrides['rsat_base_url']
if overrides['db_url'] is None:
del overrides['db_url']
# membership update default parameters
# these come first, since a lot depends on clustering numbers
num_clusters = overrides['num_clusters']
if ratios.num_columns >= 60:
overrides['memb.clusters_per_col'] = int(round(num_clusters / 2.0))
else:
overrides['memb.clusters_per_col'] = int(round(num_clusters * 2.0 / 3.0))
params['MEME']['version'] = meme.check_meme_version()
overrides['nomotifs'] = args.nomotifs or not params['MEME']['version']
overrides['use_string'] = not args.nostring
overrides['use_operons'] = not args.nooperons
if args.num_cores is not None:
overrides['num_cores'] = args.num_cores
if args.out:
overrides['output_dir'] = args.out
if args.cachedir:
overrides['cache_dir'] = args.cachedir
if args.num_iterations is not None:
overrides['num_iterations'] = args.num_iterations
for key, value in overrides.items():
params[key] = value
if params['random_seed'] is not None:
random.seed(params['random_seed'])
util.r_set_seed(params['random_seed'])
params['out_database'] = os.path.join(params['output_dir'], params['dbfile_name'])
params['new_data_file'] = False #It should only be possible to change data files in a resume
# we return the args here, too, in case we have some parameters not
# processed
return args, params, ratios
set_config(cmonkey_run, config)
cmonkey_run['output_dir'] = args.out
cmonkey_run['cache_dir'] = args.cachedir
cmonkey_run['debug'] = args.debug
cmonkey_run['keep_memeout'] = args.keep_memeout or args.debug
cmonkey_run['donetworks'] = not args.nonetworks
cmonkey_run['domotifs'] = not args.nomotifs and cmonkey_run['meme_version']
cmonkey_run['use_string'] = not args.nostring
cmonkey_run['use_operons'] = not args.nooperons
if args.random_seed:
cmonkey_run['random_seed'] = args.random_seed
if cmonkey_run['random_seed']:
random.seed(cmonkey_run['random_seed'])
util.r_set_seed(cmonkey_run['random_seed'])
proceed = True
checkratios = args.checkratios
if args.checkratios:
thesaurus = cmonkey_run.organism().thesaurus()
logging.info("Checking the quality of the input matrix names...")
found = [name for name in matrix.row_names if name in thesaurus]
num_found = len(found)
total = len(matrix.row_names)
percent = (float(num_found) / float(total)) * 100.0
proceed = percent > 50.0
# Set update frequency to every iteration, so the full results are written
if cmonkey_run['debug']:
def arg_ext(argparser):
"""additional parameters added for ensembles"""
argparser.add_argument('--ensemble_run_id', type=int, default=None)
BGORDER = [None, 0, 1, 2, 3, 4, 5]
if __name__ == '__main__':
"""process configuration"""
args, params, ratios = conf.setup(arg_ext)
if args.ensemble_run_id is not None:
# setup for ensemble run
params['random_seed'] = args.ensemble_run_id
random.seed(params['random_seed'])
util.r_set_seed(params['random_seed'])
# these currently are experimental and very eco-centric
params['num_clusters'] = random.randint(150, 550)
# row, net scaling
params['Rows']['scaling'] = ('scaling_const', random.uniform(0.0, 3.0))
params['Networks']['scaling'] = ('scaling_const',
random.uniform(0.0, 1.0))
# MEME parameters
maxw = random.randint(12, 30) # meme parameter
mmotifs = random.randint(1, 3)
motif_upstream_scan = (random.randint(-50,
0), random.randint(150, 250))
motif_upstream_search = (random.randint(-20,
0), random.randint(100, 200))
set_config(cmonkey_run, config)
cmonkey_run['output_dir'] = args.out
cmonkey_run['cache_dir'] = args.cachedir
cmonkey_run['debug'] = args.debug
cmonkey_run['keep_memeout'] = args.keep_memeout or args.debug
cmonkey_run['donetworks'] = not args.nonetworks
cmonkey_run['domotifs'] = not args.nomotifs and cmonkey_run['meme_version']
cmonkey_run['use_string'] = not args.nostring
cmonkey_run['use_operons'] = not args.nooperons
if args.random_seed:
cmonkey_run['random_seed'] = args.random_seed
if cmonkey_run['random_seed']:
random.seed(cmonkey_run['random_seed'])
util.r_set_seed(cmonkey_run['random_seed'])
proceed = True
checkratios = args.checkratios
if args.checkratios:
thesaurus = cmonkey_run.organism().thesaurus()
logging.info("Checking the quality of the input matrix names...")
found = [name for name in matrix.row_names if name in thesaurus]
num_found = len(found)
total = len(matrix.row_names)
percent = (float(num_found) / float(total)) * 100.0
proceed = percent > 50.0
# Set update frequency to every iteration, so the full results are written
if cmonkey_run['debug']:
def setup_default(args, config_parser):
"""default configuration method"""
# no organism provided -> dummy organism
if args.organism is None:
logging.warn(
"no organism provided - assuming that you want to score ratios only or don't use automatic download"
)
if not args.rsat_dir:
args.nomotifs = True
if not args.string and not args.operons:
args.nonetworks = True
# user overrides in config files
if args.config is not None:
config_parser.read(args.config)
# Initial configuration from default + user config
params = set_config(config_parser)
ratios = read_ratios(params, args)
args.clusters_per_row = params["memb.clusters_per_row"]
# debug options
debug_options = set(args.debug.split(",")) if args.debug is not None else set()
if "dump_results" in debug_options:
debug_options.add("keep_memeout")
if debug_options == {"all"}:
debug_options = ALL_DEBUG_OPTIONS
"""The overrides dictionary holds all the values that will overwrite or add
to the settings defined in the default and user-defined ini files
"""
overrides = {
"organism_code": args.organism,
"ratios_file": args.ratios,
"string_file": args.string,
"logfile": args.logfile,
"rsat_organism": args.rsat_organism,
"num_clusters": __num_clusters(config_parser, args, ratios),
"memb.clusters_per_row": args.clusters_per_row,
"remap_network_nodes": args.remap_network_nodes,
"ncbi_code": args.ncbi_code,
"operon_file": args.operons,
"rsat_dir": args.rsat_dir,
"rsat_base_url": args.rsat_base_url,
"rsat_features": args.rsat_features,
"rsat_organism": args.rsat_organism,
"rsat_dir": args.rsat_dir,
"use_operons": True,
"use_string": True,
"debug": debug_options,
"nomotifs": False,
"minimize_io": args.minimize_io,
"nonetworks": args.nonetworks,
"checkratios": args.checkratios,
"random_seed": args.random_seed,
"pipeline_file": args.pipeline,
"synonym_file": args.synonym_file,
"fasta_file": args.fasta_file,
"interactive": args.interactive,
"resume": args.resume,
"case_sensitive": args.case_sensitive,
"command_line": args.command_line,
"use_BSCM": args.use_BSCM,
"use_chi2": args.use_chi2,
}
if overrides["random_seed"] is None:
del overrides["random_seed"]
if overrides["case_sensitive"] is None:
del overrides["case_sensitive"]
if overrides["pipeline_file"] is None:
del overrides["pipeline_file"]
if overrides["rsat_base_url"] is None:
del overrides["rsat_base_url"]
# membership update default parameters
# these come first, since a lot depends on clustering numbers
num_clusters = overrides["num_clusters"]
if ratios.num_columns >= 60:
overrides["memb.clusters_per_col"] = int(round(num_clusters / 2.0))
else:
overrides["memb.clusters_per_col"] = int(round(num_clusters * 2.0 / 3.0))
params["MEME"]["version"] = meme.check_meme_version()
overrides["nomotifs"] = args.nomotifs or not params["MEME"]["version"]
overrides["use_string"] = not args.nostring
overrides["use_operons"] = not args.nooperons
if args.num_cores is not None:
overrides["num_cores"] = args.num_cores
if args.out:
overrides["output_dir"] = args.out
if args.cachedir:
overrides["cache_dir"] = args.cachedir
if args.num_iterations is not None:
overrides["num_iterations"] = args.num_iterations
for key, value in overrides.items():
params[key] = value
if params["random_seed"] is not None:
random.seed(params["random_seed"])
util.r_set_seed(params["random_seed"])
params["out_database"] = os.path.join(params["output_dir"], params["dbfile_name"])
params["new_data_file"] = False # It should only be possible to change data files in a resume
# we return the args here, too, in case we have some parameters not
# processed
return args, params, ratios