error in scsnvmisc cells

[ttt-404]

Hi,

I’m so sorry to bother you, I met some trouble when using scsnvmisc cells.

scsnvmisc cells -h

Traceback (most recent call last): File "/mnt/datadisk0/download/miniconda/envs/scsnv/bin/scsnvmisc", line 4, in import('pkg_resources').run_script('scsnvpy==1.0', 'scsnvmisc') File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/pkg_resources/init.py", line 672, in run_script self.require(requires)[0].run_script(script_name, ns) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/pkg_resources/init.py", line 1472, in run_script exec(code, namespace, namespace) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/scsnvpy-1.0-py3.9-linux-x86_64.egg/EGG-INFO/scripts/scsnvmisc", line 37, in cmds.COMMANDScmd File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/scsnvpy-1.0-py3.9-linux-x86_64.egg/scsnvpy/cells.py", line 200, in cells_cmd args = parser.parse_args(cargs[1:]) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 1825, in parse_args args, argv = self.parse_known_args(args, namespace) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 1858, in parse_known_args namespace, args = self._parse_known_args(args, namespace) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 2067, in _parse_known_args start_index = consume_optional(start_index) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 2007, in consume_optional take_action(action, args, option_string) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 1935, in take_action action(self, namespace, argument_values, option_string) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 1099, in call parser.print_help() File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 2555, in print_help self._print_message(self.format_help(), file) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 2539, in format_help return formatter.format_help() File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 283, in format_help help = self._root_section.format_help() File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 214, in format_help item_help = join([func(args) for func, args in self.items]) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 214, in item_help = join([func(args) for func, args in self.items]) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 214, in format_help item_help = join([func(args) for func, args in self.items]) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 214, in item_help = join([func(args) for func, args in self.items]) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 533, in _format_action help_text = self._expand_help(action) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/argparse.py", line 630, in _expand_help return self._get_help_string(action) % params ValueError: unsupported format character ')' (0x29) at index 10

(scsnv) root@VM-0-12-ubuntu:/mnt/datadisk0/SRR10439454# scsnvmisc cells --skip-mt -o /mnt/datadisk0/SRR10439454 /mnt/datadisk0/SRR10439454/summary.h5

Traceback (most recent call last): File "/mnt/datadisk0/download/miniconda/envs/scsnv/bin/scsnvmisc", line 4, in import('pkg_resources').run_script('scsnvpy==1.0', 'scsnvmisc') File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/pkg_resources/init.py", line 672, in run_script self.require(requires)[0].run_script(script_name, ns) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/pkg_resources/init.py", line 1472, in run_script exec(code, namespace, namespace) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/scsnvpy-1.0-py3.9-linux-x86_64.egg/EGG-INFO/scripts/scsnvmisc", line 37, in cmds.COMMANDScmd File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/scsnvpy-1.0-py3.9-linux-x86_64.egg/scsnvpy/cells.py", line 241, in cells_cmd ax.set_xscale('log', subsx=[2,3,4,5,6,7,8,9]) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 73, in wrapper return get_method(self)(*args, kwargs) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/matplotlib/axis.py", line 816, in _set_axes_scale ax._axis_map[name]._set_scale(value, kwargs) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/matplotlib/axis.py", line 773, in _set_scale self._scale = mscale.scale_factory(value, self, kwargs) File "/mnt/datadisk0/download/miniconda/envs/scsnv/lib/python3.9/site-packages/matplotlib/scale.py", line 714, in scale_factory return scale_cls(axis, kwargs) TypeError: init() got an unexpected keyword argument 'subsx'

Actually, I simply downloaded the external packages and added them into scsnv package, instead of using git. Although there are some warnings when installing scsnv, it does work with index/count/map/collapse, except for scsnvmisc. So I wonder if there's anything missing from the installation or other mistakes that caused the problem? Thank you for your help!

[GWW]

Hi,

I've pushed a fix that should fix the second error. You'll need to reclone the scsnv repository. I need to find time to try to figure out the second error but hopefully the cell command will work now. I will try to find a time to make a different cell command that can take your own list of barcodes instead of using my outdated barcode finding algorithm. For the pileups etc you can use your own barcode list instead of the one from scsnvmisc cells.

[ttt-404]

Thank you for your kindest help! It works now. Using user-defined barcode list is a very good idea, just take your time.

[GWW]

Just a note I looked at the pileup command. You can replace the passed_barcodes.txt.gz input file with one that has your own barcode list. It's an optionally gzipped text file with a header and one barcode per line:

barcode
GAACGGACATCCAACA
ACTGAACAGGAGTAGA
ACAGCCGAGTTACGGG
TTGAACGCAATAGCAA
TCGGTAATCAAGCCTA