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License: GNU General Public License v3.0
Python package to analyze DNA methylation data
License: GNU General Public License v3.0
(up_density, gene_density, down_density) = density_over_range(tmp2, cpg_ranges)
NameError: name 'density_over_range' is not defined
Please can I use this package on any of Pacbio or EM_seq-based methylation data?
Hi, I just realized that the prebuilt file doesn't include all 450K methylation sites. It would be very helpful if you can update it (or release a similar one for only for 450K sites). Thank you!
how can i make file like 'hg19.RefSeq.union.bed.gz', in my case, species is mmu/rno? thans
Is printlog() a custom function in your beta_PCA.py? If so, how have you defined it? Sorry if it is a stupid question and thanks for your response in advance!
I installed using pip3. I am trying to run the CpG_aggregation.py test. I downloaded the test files, and am now running CpG_aggregation.py -b hg19.RefSeq.union.1Kpromoter.bed.gz -i test_03_RRBS.bed -o out
. However, the output I get is just the help message. There are no errors or any other output. Any suggestions?
I am installing your tool but I get an error message. What is the best course of action for me?
pip install cpgtools
Collecting cpgtools
Using cached cpgtools-1.12.0-py3-none-any.whl (5.1 MB)
Requirement already satisfied: numpy in /Users/username/miniconda3/envs/gwaslab/lib/python3.8/site-packages (from cpgtools) (1.24.4)
Requirement already satisfied: scipy in /Users/username/miniconda3/envs/gwaslab/lib/python3.8/site-packages (from cpgtools) (1.10.1)
Collecting sklearn (from cpgtools)
Using cached sklearn-0.0.post9.tar.gz (3.6 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [18 lines of output]
The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
rather than 'sklearn' for pip commands.
Here is how to fix this error in the main use cases:
- use 'pip install scikit-learn' rather than 'pip install sklearn'
- replace 'sklearn' by 'scikit-learn' in your pip requirements files
(requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
- if the 'sklearn' package is used by one of your dependencies,
it would be great if you take some time to track which package uses
'sklearn' instead of 'scikit-learn' and report it to their issue tracker
- as a last resort, set the environment variable
SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
More information is available at
https://github.com/scikit-learn/sklearn-pypi-package
If the previous advice does not cover your use case, feel free to report it at
https://github.com/scikit-learn/sklearn-pypi-package/issues/new
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
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