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License: GNU General Public License v3.0
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Update kitsune to v1.3.2 on PyPi
@natapol thanks for merging PR #9
The software is bumped to version 1.3.2 but a few extra steps are still required to finally deploy the new version.
You should now release a new version of the package on PyPi by simply triggering the Upload Python Package workflow.
I will be then able to update the sha256 in the conda recipe meta.yaml and finally create a PR in the bioconda recipes repository.
IndexError: list index out of range in datadict[dat[0]] = int(dat[1]) when using the command kitsune acf
The Files:
dengue-1.txt
NC_000852.5.txt
I ran kitsune acf --filenames dengue-1.fasta NC_000852.5.fasta -k $(seq 1 2 51) --canonical it ran normally from K1 to K15 but got this error from K17 onwards. The inputs are fasta and the ref file is relatively much larger than the query file. It can run normally on --fast option.
KITSUNE is not working
When I try to run kitsune cre it will never end. I know it takes long for large genomes, but after 24 hours, it is still at 0%.
When I run the provided example command with the example files, I get:
OSError: [Errno 24] Too many open files
Update kitsune to v.1.3.3 on PyPI
@natapol could you please update the kitsune version on pypi to v1.3.3?
Thanks a lot
ModuleNotFoundError: No module named 'kitsune.modules'; 'kitsune' is not a package
Hello I just installed kitsune on my mac from the GitHub source. When I use the help command: python3 kitsune.py --help it outputs the normal message:
usage: kitsune <command> [<args>]
Available commands:
acf Compute average number of common features between signatures
cre Compute cumulative relative entropy
dmatrix Compute distance matrix
kopt Compute recommended choice (optimal) of kmer within a given kmer interval for a set of genomes using the cre, acf and ofc
ofc Compute observed feature frequencies
Use --help in conjunction with one of the commands above for a list of available options (e.g. kitsune acf --help)
However when I do python3 kitsune.py kopt --help I get this message:
Traceback (most recent call last):
File "/Users/rimo/kitsune/kitsune/kitsune.py", line 75, in <module>
main()
File "/Users/rimo/kitsune/kitsune/kitsune.py", line 70, in main
module = importlib.import_module("kitsune.modules.{}".format(cmd))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/[email protected]/3.11.4_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1126, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1135, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'kitsune.modules'; 'kitsune' is not a package
This happens when I try to use the kopt command with parameters set and I don't understand what's wrong or how to fix it.
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