Error in scsnvmisc cells -h
monoplasty opened this issue · 1 comments
monoplasty commented
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) [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
my env:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
anndata 0.9.1 pypi_0 pypi
autoconf 2.71 pl5321h2b4cb7a_1 conda-forge
binutils 2.39 hdd6e379_1 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_13 conda-forge
blosc2 2.0.0 pypi_0 pypi
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
c-compiler 1.5.2 h0b41bf4_0 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py38h4a40e3a_3 conda-forge
charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
click 8.1.3 unix_pyhd8ed1ab_2 conda-forge
cmake 3.25.2 h077f3f9_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
coloredlogs 15.0.1 pyhd8ed1ab_3 conda-forge
conda 23.5.0 py38h578d9bd_1 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.8.0 pyhd8ed1ab_0 conda-forge
contourpy 1.0.7 pypi_0 pypi
cryptography 38.0.4 py38h2b5fc30_0 conda-forge
cxx-compiler 1.5.2 hf52228f_0 conda-forge
cycler 0.11.0 pypi_0 pypi
cython 0.29.24 py38h709712a_1 conda-forge
cyvcf2 0.30.16 py38h79e5e23_1 bioconda
expat 2.5.0 hcb278e6_1 conda-forge
flammkuchen 1.0.2 pypi_0 pypi
fonttools 4.39.4 pypi_0 pypi
gcc 11.3.0 h02d0930_13 conda-forge
gcc_impl_linux-64 11.3.0 hab1b70f_19 conda-forge
gcc_linux-64 11.3.0 he6f903b_13 conda-forge
gxx 11.3.0 h02d0930_13 conda-forge
gxx_impl_linux-64 11.3.0 hab1b70f_19 conda-forge
gxx_linux-64 11.3.0 hc203a17_13 conda-forge
h5py 3.4.0 nompi_py38hfbb2109_102 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
htslib 1.15.1 h6bc39ce_1 bioconda
humanfriendly 10.0 py38h578d9bd_4 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-resources 5.12.0 pypi_0 pypi
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 pypi_0 pypi
krb5 1.20.1 hf9c8cef_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcurl 7.87.0 h6312ad2_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 11.3.0 h210ce93_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libsanitizer 11.3.0 h239ccf8_19 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 11.3.0 h210ce93_19 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libuv 1.44.2 h166bdaf_0 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
m4 1.4.18 h516909a_1001 conda-forge
matplotlib 3.7.1 pypi_0 pypi
msgpack 1.0.5 pypi_0 pypi
natsort 8.3.1 pypi_0 pypi
ncls 0.0.62 py38h4a8c8d9_0 bioconda
ncurses 6.3 h27087fc_1 conda-forge
numexpr 2.8.4 pypi_0 pypi
numpy 1.20.3 py38h8246c76_2 conda-forge
openssl 1.1.1u hd590300_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pandas 2.0.2 pypi_0 pypi
patsy 0.5.3 pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.5.0 pypi_0 pypi
pip 23.1.2 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
py-cpuinfo 9.0.0 pypi_0 pypi
pycosat 0.6.4 py38h0a891b7_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.0b2 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.12 ha38a3c6_3_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.8 3_cp38 conda-forge
pytz 2023.3 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rhash 1.4.3 h166bdaf_0 conda-forge
ruamel.yaml 0.17.31 py38h01eb140_0 conda-forge
ruamel.yaml.clib 0.2.7 py38h1de0b5d_1 conda-forge
scipy 1.7.1 py38h56a6a73_0 conda-forge
scsnvpy 1.0 pypi_0 pypi
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sqlite 3.42.0 h2c6b66d_0 conda-forge
statsmodels 0.14.0 pypi_0 pypi
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tables 3.8.0 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
tzdata 2023.3 pypi_0 pypi
urllib3 2.0.2 pyhd8ed1ab_0 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.15.0 pypi_0 pypi
zlib 1.2.13 h166bdaf_4 conda-forge
zstandard 0.19.0 py38h5945529_1 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge
GWW commented
Hi,
I apologize it's my fault. arparse
doesn't like %
characters in help messages. I have pushed a commit to resolve the issue.
Thanks for your patience.