INNER CODE UNIT · Python
starting_iteration
nickjcroucher/gubbins · python/gubbins/common.py:146
starting_iteration = int(search_itr.group(1)) + 1
if starting_iteration > input_args.iterations:
sys.stderr.write('Run has already reached the number of specified iterations\n')
exit(1)
else:
sys.stderr.write('Resuming Gubbins analysis at iteration ' + str(starting_iteration) + '\n')
input_args.starting_tree = input_args.resume
current_tree_name = input_args.starting_tree
os.symlink(os.path.join(current_directory,snp_alignment_filename),os.path.join(temp_working_dir,snp_alignment_filename))
# Check if intermediate files from a previous run exist
intermediate_files = [basename + ".iteration_"]
if not input_args.no_cleanup and input_args.resume is None:
utils.delete_files(".", intermediate_files, "", input_args.verbose)
if utils.do_files_exist(".", intermediate_files, "", input_args.verbose) and input_args.resume is None:
sys.exit("Intermediate files from a previous run exist. Please rerun without the --no-cleanup option "
"to automatically delete them or with the --use-time-stamp to add a unique prefix.")