path_output_sub = path_output_main + "/output" HelperUtils.mkdirs(path_output_sub) path_stdout = path_output_main + "/stdout" HelperUtils.mkdirs(path_stdout) ###################################### ARGUMENTS ###################################### args = ParseArguments() ###################################### LOGGER ###################################### ## Setup-logger #logger = Logger(__name__, path_stdout).get() # gives __name__ == main logger = Logger(current_script_name, path_stdout).get() #loglevel = getattr(logging, args.logger_lvl.upper(), logging.INFO) # returns some numeric value loglevel = getattr(logging, args.logger_lvl.upper()) # returns some numeric value logger.setLevel(loglevel) #logger.setLevel(logging.INFO) #logger.setLevel(logging.WARNING) ###################################### RUN FUNCTIONS ###################################### # NOW RUN FUNCTIONS LogArguments() processes = submit() start_time_check_jobs = time.time() check_jobs(processes, logger) # TODO: parse multiprocess argument? elapsed_time = time.time() - start_time_check_jobs logger.info( "Total Runtime for check_jobs: %s s (%s min)" % (elapsed_time, elapsed_time/60) ) logger.critical( "%s: finished" % current_script_name)
#path_snplist = "/home/projects/tp/childrens/snpsnap/data/gwas/gwascatalog_140201_listsBIGbim" #path_snplist = "/home/projects/tp/childrens/snpsnap/data/gwas/gwascatalog_140201_lists" #path_output_main = "/home/projects/tp/childrens/snpsnap/data/query/gwascatalog" path_output_main = "/cvar/jhlab/snpsnap/data/query/gwascatalog" path_output_sub = path_output_main + "/subprocess_output" HelperUtils.mkdirs(path_output_sub) path_stdout = path_output_main + "/subprocess_stdout" HelperUtils.mkdirs(path_stdout) ## Setup-logger #logger = Logger(__name__, path_stdout).get() # gives __name__ == main logger = Logger(current_script_name, path_stdout).get() #logger.setLevel(logging.WARNING) logger.setLevel(logging.INFO) ## NEXT: run 10000.5.20.20 ## arguments N_sample_sets=10000 freq=5 dist=20 gene_count=20 processes = submit() # run_Pipe() method calls for p in processes: p.get_pid()
