Closed jiangshan529 closed 1 year ago
Try installing numpy before installing coolpuppy? You might also have to do the same for cython. It's actually for cooltools, which is a dependency.
pip install coolpuppy
Hi, I have succeeded in installing it. However, when I try to run "plotpup.py --enrichment", there's no argument "--enrichment".
Where did you find this argument? Indeed it doesn't exist, perhaps we had it in an old version, I don't even remember anymore though.
Where did you find this argument? Indeed it doesn't exist, perhaps we had it in an old version, I don't even remember anymore though.
from some other github issues or papers(one example is https://github.com/open2c/coolpuppy/issues/9). By the way, when I try to plot the figure by using other's published data, I got a result like this:
here's the code that I used: coolpup.py DN3EV.cool CTCF.bed --outname test.txt --pad 250 --local --coverage_norm --clr_weight_name "" plotpup.py --input_pups test.txt --rownames WT --colnames CTCF --output Figure4C.pdf
Please check the docs, there have been very big updates recently. E.g. in this case the problem is from the --pad argument - now it should be specified in bp, while it used to be in kb. So try changing it to 250000.
That's because of the ignore-diags argument. In some datasets the first two diagonals are very noisy and weird things happen in pileups, but feel free to set the argument to 0 and check how it is with your data.
Hi, I created a conda environment with python=3.8 and install coolpuppy using "pip install coolpuppy".
However, there's an error:
Collecting coolpuppy Using cached coolpuppy-1.0.0-py3-none-any.whl (44 kB) Collecting numpy>=1.16.5 Using cached numpy-1.23.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB) Collecting cooler Using cached cooler-0.8.11-py2.py3-none-any.whl (100 kB) Collecting pyyaml Using cached PyYAML-6.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (701 kB) Collecting scipy Using cached scipy-1.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (33.8 MB) Requirement already satisfied: Cython in /home/jib79/miniconda2/envs/coolpuppy/lib/python3.8/site-packages (from coolpuppy) (0.29.32) Collecting cooltools>=0.5.2 Using cached cooltools-0.5.2.tar.gz (8.1 MB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [6 lines of output] Traceback (most recent call last): File "", line 2, in
File "", line 34, in
File "/tmp/pip-install-47zixv6p/cooltools_24b1e652c68c40b79a3e70d99c3f8f79/setup.py", line 10, in
import numpy as np
ModuleNotFoundError: No module named 'numpy'
[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.