There some unescaped '%' characters in amplicon_sorter.py in the argument parsing section that cause this error
Traceback (most recent call last):
File "/amplicon_sorter/amplicon_sorter.py", line 1821, in <module>
args = get_arguments()
File "/amplicon_sorter/amplicon_sorter.py", line 167, in get_arguments
args = parser.parse_args()
File "/usr/lib/python3.8/argparse.py", line 1780, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python3.8/argparse.py", line 1812, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python3.8/argparse.py", line 2018, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python3.8/argparse.py", line 1958, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python3.8/argparse.py", line 1886, in take_action
action(self, namespace, argument_values, option_string)
File "/usr/lib/python3.8/argparse.py", line 1056, in __call__
parser.print_help()
File "/usr/lib/python3.8/argparse.py", line 2506, in print_help
self._print_message(self.format_help(), file)
File "/usr/lib/python3.8/argparse.py", line 2490, in format_help
return formatter.format_help()
File "/usr/lib/python3.8/argparse.py", line 294, in format_help
help = self._root_section.format_help()
File "/usr/lib/python3.8/argparse.py", line 225, in format_help
item_help = join([func(*args) for func, args in self.items])
File "/usr/lib/python3.8/argparse.py", line 225, in <listcomp>
item_help = join([func(*args) for func, args in self.items])
File "/usr/lib/python3.8/argparse.py", line 225, in format_help
item_help = join([func(*args) for func, args in self.items])
File "/usr/lib/python3.8/argparse.py", line 225, in <listcomp>
item_help = join([func(*args) for func, args in self.items])
File "/usr/lib/python3.8/argparse.py", line 541, in _format_action
help_text = self._expand_help(action)
File "/usr/lib/python3.8/argparse.py", line 633, in _expand_help
return self._get_help_string(action) % params
ValueError: unsupported format character ')' (0x29) at index 23
It's this section here where the troublesome characters reside:
parser.add_argument('-ldc', '--length_diff_consensus', type = range_limited_float_0_200,
required=False, default=8.0 ,
help='Length difference (in %) allowed between consensuses to\
COMBINE groups based on the consensus sequence\
(value between 0 and 200). Default=8.0 %')
As they're just help docs I suggest changing them to the word 'percent' .
There some unescaped '%' characters in amplicon_sorter.py in the argument parsing section that cause this error
It's this section here where the troublesome characters reside:
As they're just help docs I suggest changing them to the word 'percent' .