dyneofdata
commented
1 year ago Hello,
Thanks for bringing this to my attention. As you noted, the version of python you’re using (3.9) is not compatible with one of the dependencies (pyBigWig) + by default uses a version of matplotlib with a bug (https://github.com/matplotlib/matplotlib/issues/22576).
To get around this, please create a conda environment by specifying the versions of each dependency (this command might take a while).
conda create --name grinch_env python=3.7.12 numpy=1.20.3 pandas=1.3.5 matplotlib=3.3.3 seaborn=0.12.1 pyBigWig=0.3.18 -c conda-forge -c bioconda
Then activate the environment and run all scripts within that environment.
conda activate grinch_env
python diamond.py diamond.ini
python pyramid.py pyramid.ini
conda deactivate #to go back to your base pythonI updated the github documentation with the version information.
Erika
Hello,
Thanks for the useful tool!
While I've been learning your tool with the following commands with your shared 'tarball' data ( https://drive.google.com/file/d/1-iopSH7uI_Fra9wE6k6uGXeRXrwYQDoJ/view?usp=sharing), I've got some error messages in our system. It would be great if you help us to fix those issues.
Drawing heatmap 1... Drawing heatmap 2...
Traceback (most recent call last): File "~/grinch-master/visualization/diamond.py", line 88, in
main(sys.argv[1])
File "~/grinch-master/visualization/diamond.py", line 84, in main
gs.tight_layout(fig)
File "~/.local/lib/python3.9/site-packages/matplotlib/gridspec.py", line 465, in tight_layout
subplotspec_list = tight_layout.get_subplotspec_list(
File "~/.local/lib/python3.9/site-packages/matplotlib/tight_layout.py", line 234, in get_subplotspec_list
subplotspec = axes_or_locator.get_subplotspec()
File "~/.local/lib/python3.9/site-packages/matplotlib/colorbar.py", line 283, in get_subplotspec
ss = self._orig_locator.get_subplotspec()
AttributeError: 'AnchoredSizeLocator' object has no attribute 'get_subplotspec'
Our environments are as follows:
Thanks for your help!