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GWW / scsnv

scSNV Mapping tool for 10X Single Cell Data
MIT License
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Error in scsnvmisc cells -h #28

Closed monoplasty closed 1 year ago

monoplasty commented 1 year ago

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 1 year ago

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.