问题描述
我正在尝试编写一个带有很多参数的 Python 脚本，我想使用 argparse 模块将这些参数分解成清晰的组，如下所示:
I'm trying to write a Python script with a lot of arguments that I'd like to break up into clear groups using the argparse module as follows:
import argparse
parser = argparse.ArgumentParser(description='Placeholder text', add_help=False)
req = parser.add_argument_group('required arguments')
req.add_argument('-m','--mode', action='store', dest='mode', help='Operation mode', choices=['single', 'multi'], required=True, metavar='')
req.add_argument('-s','--snps', action='store', dest='snps', help='SNP BED file', required=True, metavar='')
req.add_argument('-r','--reads', action='store', dest='reads', help='Mapped reads file [sam or bam]', required=True, metavar='')
uni = parser.add_argument_group('universal optional arguments')
uni.add_argument('-p','--prefix', action='store', dest='prefix', help='Prefix for temp files and output [Default: TEST]', default='TEST', metavar='')
uni.add_argument('-b','--bam', action='store_true', dest='bam', help='Mapped read file type is bam (auto-detected if *.bam)')
uni.add_argument('-t','--single', action='store_true', dest='single', help='Mapped reads are single-end [Default: False]')
uni.add_argument('-n','--noclean', action='store_true', dest='noclean', help='Do not delete intermediate files (for debuging)')
uni.add_argument('-h', '--help', action='help', help='show this help message and exit')
mult = parser.add_argument_group('multi(plex) mode arguments')
mult.add_argument('-j','--jobs', action='store', dest='jobs', type=int, help='Divide into # of jobs [Default: 100]', default=100, metavar='')
mult.add_argument('-w','--walltime', action='store', dest='walltime', help='Walltime for each job [Default: 3:00:00]', default='3:00:00', metavar='')
mult.add_argument('-k','--mem', action='store', dest='memory', help='Memory for each job [Default: 5000MB]', default='5000MB', metavar='')
single = parser.add_argument_group('single mode arguments')
single.add_argument('-f','--suffix', action='store', dest='suff', help='Suffix for multiplexed files [set automatically]', default='', metavar='')
args = parser.parse_args()
但是，当我使用-h"选项运行此脚本时，它没有打印帮助文本，而是吐出以下错误:
However, when I run this script, with the '-h' option, instead of printing the help text, it spits out the following error:
Traceback (most recent call last):
File "CountSNPLevelASE.py", line 61, in <module>
args = parser.parse_args()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 1688, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 1720, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 1926, in _parse_known_args
start_index = consume_optional(start_index)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 1866, in consume_optional
take_action(action, args, option_string)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 1794, in take_action
action(self, namespace, argument_values, option_string)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 994, in __call__
parser.print_help()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 2327, in print_help
self._print_message(self.format_help(), file)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 2301, in format_help
return formatter.format_help()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 279, in format_help
help = self._root_section.format_help()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 209, in format_help
func(*args)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.py", line 330, in _format_usage
assert ' '.join(opt_parts) == opt_usage
AssertionError
奇怪的是，如果我注释掉任何非必需参数，我会得到正确的帮助文本输出，如下所示:
The odd thing is that if I comment out ANY of the non-required arguments, I get the proper help text output, like this:
usage: CountSNPLevelASE.py -m -s -r [-b] [-t] [-n] [-h] [-j] [-w] [-k] [-f]
Placeholder text
required arguments:
-m , --mode Operation mode
-s , --snps SNP BED file
-r , --reads Mapped reads file [sam or bam]
universal optional arguments:
-b, --bam Mapped read file type is bam (auto-detected if *.bam)
-t, --single Mapped reads are single-end [Default: False]
-n, --noclean Do not delete intermediate files (for debuging)
-h, --help show this help message and exit
multi(plex) mode arguments:
-j , --jobs Divide into # of jobs [Default: 100]
-w , --walltime Walltime for each job [Default: 3:00:00]
-k , --mem Memory for each job [Default: 5000MB]
single mode arguments:
-f , --suffix Suffix for multiplexed files [set automatically]
我找不到明确的解释为什么会发生这种情况.我试过删除所有空格无济于事.有任何想法吗?(如果有帮助的话，我在 Mac OS X 10.10.2 上使用 Python 2.7.6).
I can't find a clear explanation for why this is happening. I've tried removing all whitespace to no avail. Any ideas? (I'm using Python 2.7.6 on Mac OS X 10.10.2 if that's helpful).
推荐答案
问题在于包装用法.当 usage 适合一行时显示正常，但将其分成 2 行时显示失败.
The problem lies in wrapping the usage. It displays fine when usage fits on one line, but fails when it splits it into 2.
存在与此 assertion 相关的已知错误问题.使用格式代码很脆弱，当使用中包含常用"字符(包括空格和额外空格)时，可能会引发此 assertion 错误.
There's a known bug issue involving this assertion. The usage formatting code is fragile, and can raise this assertion error when there are 'usual' characters in the usage, including and extra spaces.
是 3 个必需参数中的 metavar='' 导致了问题.可选的选项可以有一个 '' 元变量.
It's the metavar='' of the 3 required arguments that's giving the problem. The optional optionals can have a '' metavar.
注意到短用法行中这些参数之间的双空格了吗?
Notice the double spaces between these arguments in the short usage line?
...py -m -s -r [-b]...
断言错误是那些空格没有完整地通过包装代码的结果.
The assertion error is the result of those spaces not making it through the wrapping code intact.
如果您无法为这 3 个参数找到合适的替代元变量，那么我们将不得不弄清楚如何修改您的 argparse 代码.可能性包括注释掉断言语句，或从一行用法中删除那些额外的空白.最大的修复是更强大的使用格式化程序.
If you can't find suitable alternative metavars for those 3 arguments, then we'll have to figure out how to modify your argparse code. Possibilities include commenting out the assertion statement, or trimming out those extra blanks from the one line usage. The big fix is a more robust usage formatter.
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