I installed scsnv successfully, but when I run scsnvmisc cells -h I get an error like this.
I don't know if it's my environment's problem or something else.
Hope to get your answer, look forward to your reply, thank you very much!
(scsnv) [root@scRNA scsnvpy]# scsnvmisc cells -h
Traceback (most recent call last):
File "/usr/local/miniconda3/envs/scsnv/bin/scsnvmisc", line 4, in <module>
__import__('pkg_resources').run_script('scsnvpy==1.0', 'scsnvmisc')
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/site-packages/pkg_resources/__init__.py", line 720, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1559, in run_script
exec(code, namespace, namespace)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/site-packages/scsnvpy-1.0-py3.8-linux-x86_64.egg/EGG-INFO/scripts/scsnvmisc", line 37, in <module>
cmds.COMMANDS[cmd](args)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/site-packages/scsnvpy-1.0-py3.8-linux-x86_64.egg/scsnvpy/cells.py", line 207, in cells_cmd
args = parser.parse_args(cargs[1:])
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 1768, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 1800, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 2006, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 1946, in consume_optional
take_action(action, args, option_string)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 1874, in take_action
action(self, namespace, argument_values, option_string)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 1044, in __call__
parser.print_help()
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 2494, in print_help
self._print_message(self.format_help(), file)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 2478, in format_help
return formatter.format_help()
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 282, in format_help
help = self._root_section.format_help()
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 213, in format_help
item_help = join([func(*args) for func, args in self.items])
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 213, in <listcomp>
item_help = join([func(*args) for func, args in self.items])
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 213, in format_help
item_help = join([func(*args) for func, args in self.items])
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 213, in <listcomp>
item_help = join([func(*args) for func, args in self.items])
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 529, in _format_action
help_text = self._expand_help(action)
File "/usr/local/miniconda3/envs/scsnv/lib/python3.8/argparse.py", line 621, in _expand_help
return self._get_help_string(action) % params
ValueError: unsupported format character ')' (0x29) at index 10
scsnv command success:
(scsnv) [root@scRNA src]# scsnv index -h
scsnv index -g genes.gtf -r genome.fa -l 100 out_prefix
-g, --gtf
GTF file (required)
-r, --ref
Genome fasta file (required)
--retained-introns
Keep retained introns, note alignments to these will be considered exonic
--nonsense-mediated
Keep nonsense mediated decay transcripts
--skip-build
Skip automatically building the BWA index (not recommended)
-l, --min-length
Minimum Transcript Length [100]
-h, --help
shows this help message
Hi. Thanks for creating this exciting tool.
I installed scsnv successfully, but when I run
scsnvmisc cells -h
I get an error like this. I don't know if it's my environment's problem or something else. Hope to get your answer, look forward to your reply, thank you very much!scsnv command success:
my env: