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_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 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 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)