def get_parameter_keys_dict(yaml_dir, parameter_key_dict={}, methods_list=[]):
""" get the list of yaml files in the yaml_dir, the list of methods in all those, and a dictionary of key types
Args:
yaml_dir: path the the yaml files
parameter_key_dict: (optional) dictionary to add key types
methods_list: (optional) list of methods to append
Returns:
yaml_files_list: the list of yaml files in the yaml_dir
methods_list: the list of methods in the yaml files
parameter_key_dict: key-name: key-type dictionary
"""
type_dict = {int: 'int', float: 'real', str: 'string', list: 'list'}
yaml_files_list = []
for f in os.listdir(yaml_dir):
ff = os.path.join(yaml_dir, f)
some_nombre, nombre_ext = os.path.splitext(f)
if os.path.isfile(ff) and nombre_ext == '.yml':
yaml_files_list.append(f)
for f_name in yaml_files_list:
run_parameters = kn.get_run_parameters(yaml_dir, f_name)
for k, v in run_parameters.items():
if k not in parameter_key_dict.keys():
parameter_key_dict[k] = type_dict[type(v)]
if k == 'method' and k not in methods_list:
methods_list.append(v)
methods_list = list(set(methods_list))
return parameter_key_dict, methods_list, yaml_files_list
def main():
import sys
from knpackage.toolbox import get_run_directory_and_file
from knpackage.toolbox import get_run_parameters
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
SELECT[run_parameters['method']](run_parameters)
def main():
import sys
from knpackage.toolbox import get_run_directory
from knpackage.toolbox import get_run_parameters
run_directory = get_run_directory(sys.argv)
run_parameters = get_run_parameters(run_directory)
SELECT[run_parameters["method"]](run_parameters)
def main():
import sys
from knpackage.toolbox import get_run_directory_and_file
from knpackage.toolbox import get_run_parameters
run_directory, run_file, num_of_process, num_of_boostraps = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
SELECT[run_parameters["method"]](run_parameters, num_of_process, num_of_boostraps)
def data_cleanup():
try:
logger.init()
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
run_pipelines(run_parameters, SELECT[run_parameters['pipeline_type']])
except Exception as err:
logger.logging.append("ERROR: {}".format(str(err)))
raise RuntimeError(str(err))
def main():
"""
This is the main function to perform general clustering
"""
import sys
from knpackage.toolbox import get_run_directory_and_file
from knpackage.toolbox import get_run_parameters
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
SELECT[run_parameters["method"]](run_parameters)
def checker():
try:
logger.init()
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
obj = Checker(run_parameters)
obj.condition_check()
except Exception as err:
logger.logging.append("ERROR: {}".format(str(err)))
raise RuntimeError(str(err))
def main():
"""
This is the main function to perform clustering evaluation.
"""
import sys
from knpackage.toolbox import get_run_directory_and_file
from knpackage.toolbox import get_run_parameters
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
clustering_evaluation(run_parameters)
def display_all_yaml_files(yaml_dir, yaml_files):
n_files = len(yaml_files)
count = 0
for f in yaml_files:
count += 1
print('\n\n%30s : %s' % (f, yaml_dir))
print('%30s : %s ' % (' "file[' + str(count - 1) + ']" :~) ' +
str(count), 'of ' + str(n_files)))
run_parameters = kn.get_run_parameters(yaml_dir, f)
for k, v in run_parameters.items():
print('%30s : %s' % (k, v))
def main():
"""
This is the main function to perform feature prioritization.
"""
import sys
from knpackage.toolbox import get_run_directory_and_file
from knpackage.toolbox import get_run_parameters
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
SELECT[run_parameters["method"]](run_parameters)
def main():
"""
This the main function to characterize gene
set from three methods: fisher, DRaWR, net path.
"""
import sys
from knpackage.toolbox import get_run_directory_and_file
from knpackage.toolbox import get_run_parameters
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
SELECT[run_parameters["method"]](run_parameters)
def network_prepper():
try:
logger.init()
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
run_pipelines(run_parameters, "network_prepper_pipeline")
except Exception as err:
logger.logging.append("ERROR: {}".format(str(err)))
# try to write the log
logger.generate_logging(
False, logger.logging, run_parameters["results_directory"] +
"/log_" + "network_prepper_pipeline" + ".yml")
raise RuntimeError(str(err))
def copy_yaml_with_path_edit(pipeline_directory_full_path, run_directory,
results_directory):
""" copy and convert the yaml file relative paths to work in users run_directory """
yaml_files_source_directory = os.path.join(pipeline_directory_full_path,
'data/run_files')
if not os.path.isdir(yaml_files_source_directory):
# do nothing if this pipeline has no yaml files
return
yaml_dir_list = os.listdir(yaml_files_source_directory)
if len(yaml_dir_list) < 1:
print('No files found in :\n\t', yaml_files_source_directory)
return
for maybe_yaml in yaml_dir_list:
if len(maybe_yaml) > 4 and maybe_yaml[-4:] == '.yml':
run_parameters = kn.get_run_parameters(yaml_files_source_directory,
maybe_yaml)
for k, v in run_parameters.items():
if k == 'results_directory':
run_parameters['results_directory'] = results_directory
elif k == 'tmp_directory':
run_parameters['tmp_directory'] = os.path.join(
results_directory, 'tmp')
elif k == 'run_directory':
run_parameters['run_directory'] = run_directory
elif isinstance(v, str) and len(v) > 1 and v[0:2] == './':
path_string = v[2:]
run_parameters[k] = os.path.join(
pipeline_directory_full_path, path_string)
elif isinstance(v, str) and len(v) > 1 and v[0:3] == '../':
path_string = v[3:]
run_parameters[k] = os.path.join(
pipeline_directory_full_path, path_string)
full_file_name = os.path.join(run_directory, maybe_yaml)
try:
with open(full_file_name, 'w') as fh:
yaml.dump(run_parameters, fh, default_flow_style=False)
except Exception:
print(full_file_name, '\n\t Exception Unknown')
pass
def get_yaml_df(yaml_dir, UNUSED_FILL='not used'):
""" read the yaml files in 'yaml_dir' and constuct a datafrme with rows of keys, columns of file names and
filled with the each yaml file values.
Args:
yaml_dir: path the the yaml files
UNUSED_FILL: string to use for fill where a yaml file has no entry for a key (row name)
"""
key_dict, methods_list, yaml_files_list = get_parameter_keys_dict(yaml_dir)
if 'run_file' in key_dict.keys():
key_dict.pop('run_file')
yaml_file_df = pd.DataFrame(data=None, index=key_dict.keys(), columns=None)
for f_name in yaml_files_list:
run_parameters = kn.get_run_parameters(yaml_dir, f_name)
if 'run_file' in run_parameters.keys():
run_parameters.pop('run_file')
yaml_file_df[f_name] = UNUSED_FILL
for k, v in run_parameters.items():
yaml_file_df[f_name].loc[k] = v
return yaml_file_df
def test_run_file(self):
self.createFile(self.config_dir, self.run_file, self.f_context)
run_parameters = knpkg.get_run_parameters(self.config_dir,
self.run_file)
self.assertDictEqual(run_parameters, self.golden_output)
def data_cleanup():
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
SELECT[run_parameters['pipeline_type']](run_parameters)
def main():
run_directory, run_file = get_run_directory_and_file(sys.argv)
run_parameters = get_run_parameters(run_directory, run_file)
pasted_gene_cleanup(run_parameters)