def set_config_scoring_functions(config, params):
"""processing scoring function specific stuff"""
def set_scaling(section):
try:
params[section]['scaling'] = ('scaling_const',
config.getfloat(section, 'scaling_const'))
return
except:
pass
try:
params[section]['scaling'] = ('scaling_rvec', config.get(section, 'scaling_rvec'))
except:
raise Exception("no scaling found for section '%s'" % section)
ids = [section for section in config.sections()
if section not in {'General', 'Scoring', 'Membership'}]
for id in ids:
params[id] = {}
for option, value in config.items(id):
if option == 'schedule':
params[id]['schedule'] = make_schedule(value)
elif option.startswith('scaling_'):
set_scaling(id)
else:
params[id][option] = value
def set_config_scoring_functions(config, params):
"""processing scoring function specific stuff"""
def set_scaling(section):
try:
params[section]["scaling"] = ("scaling_const", config.getfloat(section, "scaling_const"))
return
except:
pass
try:
params[section]["scaling"] = ("scaling_rvec", config.get(section, "scaling_rvec"))
except:
raise Exception("no scaling found for section '%s'" % section)
ids = [section for section in config.sections() if section not in {"General", "Scoring", "Membership"}]
for id in ids:
params[id] = {}
for option, value in config.items(id):
if option == "schedule":
params[id]["schedule"] = make_schedule(value)
elif option.startswith("scaling_"):
set_scaling(id)
else:
params[id][option] = value
def set_config(cmonkey_run, config):
def set_scaling(section, prefix):
try:
cmonkey_run[prefix + 'scaling_const'] = config.getfloat(section, 'scaling_const')
return
except:
pass
try:
cmonkey_run[prefix + 'scaling_rvec'] = config.get(section, 'scaling_rvec')
except:
raise Exception("no scaling found for section '%s'" % section)
# override directories
tmp_dir = config.get('General', 'tmp_dir')
if tmp_dir:
tempfile.tempdir = tmp_dir
cmonkey_run['output_dir'] = config.get('General', 'output_dir')
cmonkey_run['cache_dir'] = config.get('General', 'cache_dir')
cmonkey_run['num_iterations'] = config.getint("General", "num_iterations")
cmonkey_run['start_iteration'] = config.getint("General", "start_iteration")
cmonkey_run['out_database'] = os.path.join(cmonkey_run['output_dir'],
config.get("General", "dbfile_name"))
cmonkey_run['multiprocessing'] = config.getboolean('General', 'use_multiprocessing')
cmonkey_run['postadjust'] = config.getboolean('General', 'postadjust')
cmonkey_run['log_subresults'] = config.getboolean('General', 'log_subresults')
cmonkey_run['add_fuzz'] = config.get('General', 'add_fuzz')
cmonkey_run['checkpoint_interval'] = config.getint('General', 'checkpoint_interval')
try:
cmonkey_run['random_seed'] = config.getint('General', 'random_seed')
except:
cmonkey_run['random_seed'] = None
# Quantile normalization is false by default in cMonkey-R
cmonkey_run['quantile_normalize'] = config.getboolean('Scoring', 'quantile_normalize')
# membership default parameters
cmonkey_run['memb.min_cluster_rows_allowed'] = config.getint('Membership', 'min_cluster_rows_allowed')
cmonkey_run['memb.max_cluster_rows_allowed'] = config.getint('Membership', 'max_cluster_rows_allowed')
cmonkey_run['memb.prob_row_change'] = config.getfloat('Membership', 'probability_row_change')
cmonkey_run['memb.prob_col_change'] = config.getfloat('Membership', 'probability_column_change')
cmonkey_run['memb.max_changes_per_row'] = config.getint('Membership', 'max_changes_per_row')
cmonkey_run['memb.max_changes_per_col'] = config.getint('Membership', 'max_changes_per_column')
cmonkey_run['sequence_types'] = config.get('Motifs', 'sequence_types').split(',')
cmonkey_run['search_distances'] = {}
cmonkey_run['scan_distances'] = {}
for seqtype in cmonkey_run['sequence_types']:
cat = "SequenceType-%s" % seqtype
cmonkey_run['search_distances'][seqtype] = tuple(
map(int, config.get(cat, 'search_distance').split(',')))
cmonkey_run['scan_distances'][seqtype] = tuple(
map(int, config.get(cat, 'scan_distance').split(',')))
cmonkey_run['row_schedule'] = make_schedule(config.get("Rows", "schedule"))
cmonkey_run['column_schedule'] = make_schedule(config.get("Columns", "schedule"))
cmonkey_run['meme_schedule'] = make_schedule(config.get("MEME", "schedule"))
cmonkey_run['motif_schedule'] = make_schedule(config.get("Motifs", "schedule"))
cmonkey_run['network_schedule'] = make_schedule(config.get("Networks", "schedule"))
cmonkey_run['stats_freq'] = config.getint('General', 'stats_frequency')
cmonkey_run['result_freq'] = config.getint('General', 'result_frequency')
# parse the scalings
set_scaling('Motifs', 'motif_')
set_scaling('Rows', 'row_')
set_scaling('Networks', 'network_')
try:
cmonkey_run['nmotifs_rvec'] = config.get('MEME', 'nmotifs_rvec')
except:
raise Exception("no setting found to retrieve the MEME nmotifs function")
def set_config(cmonkey_run, config):
def set_scaling(section, prefix):
try:
cmonkey_run[prefix + 'scaling_const'] = config.getfloat(
section, 'scaling_const')
return
except:
pass
try:
cmonkey_run[prefix + 'scaling_rvec'] = config.get(
section, 'scaling_rvec')
except:
raise Exception("no scaling found for section '%s'" % section)
# override directories
tmp_dir = config.get('General', 'tmp_dir')
if tmp_dir:
tempfile.tempdir = tmp_dir
cmonkey_run['output_dir'] = config.get('General', 'output_dir')
cmonkey_run['cache_dir'] = config.get('General', 'cache_dir')
cmonkey_run['num_iterations'] = config.getint("General", "num_iterations")
cmonkey_run['start_iteration'] = config.getint("General",
"start_iteration")
cmonkey_run['out_database'] = os.path.join(
cmonkey_run['output_dir'], config.get("General", "dbfile_name"))
cmonkey_run['multiprocessing'] = config.getboolean('General',
'use_multiprocessing')
cmonkey_run['postadjust'] = config.getboolean('General', 'postadjust')
cmonkey_run['log_subresults'] = config.getboolean('General',
'log_subresults')
cmonkey_run['add_fuzz'] = config.get('General', 'add_fuzz')
cmonkey_run['checkpoint_interval'] = config.getint('General',
'checkpoint_interval')
try:
cmonkey_run['random_seed'] = config.getint('General', 'random_seed')
except:
cmonkey_run['random_seed'] = None
# Quantile normalization is false by default in cMonkey-R
cmonkey_run['quantile_normalize'] = config.getboolean(
'Scoring', 'quantile_normalize')
# membership default parameters
cmonkey_run['memb.min_cluster_rows_allowed'] = config.getint(
'Membership', 'min_cluster_rows_allowed')
cmonkey_run['memb.max_cluster_rows_allowed'] = config.getint(
'Membership', 'max_cluster_rows_allowed')
cmonkey_run['memb.prob_row_change'] = config.getfloat(
'Membership', 'probability_row_change')
cmonkey_run['memb.prob_col_change'] = config.getfloat(
'Membership', 'probability_column_change')
cmonkey_run['memb.max_changes_per_row'] = config.getint(
'Membership', 'max_changes_per_row')
cmonkey_run['memb.max_changes_per_col'] = config.getint(
'Membership', 'max_changes_per_column')
cmonkey_run['sequence_types'] = config.get('Motifs',
'sequence_types').split(',')
cmonkey_run['search_distances'] = {}
cmonkey_run['scan_distances'] = {}
for seqtype in cmonkey_run['sequence_types']:
cat = "SequenceType-%s" % seqtype
cmonkey_run['search_distances'][seqtype] = tuple(
map(int,
config.get(cat, 'search_distance').split(',')))
cmonkey_run['scan_distances'][seqtype] = tuple(
map(int,
config.get(cat, 'scan_distance').split(',')))
cmonkey_run['row_schedule'] = make_schedule(config.get("Rows", "schedule"))
cmonkey_run['column_schedule'] = make_schedule(
config.get("Columns", "schedule"))
cmonkey_run['meme_schedule'] = make_schedule(config.get(
"MEME", "schedule"))
cmonkey_run['motif_schedule'] = make_schedule(
config.get("Motifs", "schedule"))
cmonkey_run['network_schedule'] = make_schedule(
config.get("Networks", "schedule"))
cmonkey_run['stats_freq'] = config.getint('General', 'stats_frequency')
cmonkey_run['result_freq'] = config.getint('General', 'result_frequency')
# parse the scalings
set_scaling('Motifs', 'motif_')
set_scaling('Rows', 'row_')
set_scaling('Networks', 'network_')
try:
cmonkey_run['nmotifs_rvec'] = config.get('MEME', 'nmotifs_rvec')
except:
raise Exception(
"no setting found to retrieve the MEME nmotifs function")