Error when running example data: "XLMHG error"

[msingerlab]

Error when running example data: "XLMHG error"

[Cnrdelaney]

Hello!

Thanks for reaching out, I think I have the solution. The 'mhg_cython' install is a codependency with the xlmhg package, which we use as our statistical test. I believe the xlmhg package is currently only supported by python 3.6 versions and it is very much necessary for the tool to run. If you use a python 3.6 virtual environment it should install correctly and work from there. Double-back here if you run into more issues!

[MeromitSinger]

Please see "Installing via a Virtual Environment" in our documentation:
https://hgmd.readthedocs.io/en/latest/quickstart.html
and let us know if that doesn't work for you.

[tilofrei]

Switching back to python3.6 did the trick indeed - thank you for your quick help @Cnrdelaney and @MeromitSinger!

(In case anybody else is using scanpy for scRNAseq data exploration, this is the export formatting I used:)

# markers.txt
markers = pd.DataFrame(data=adata.T.X, index=adata.var_names, columns=adata.obs_names)
markers.to_csv('markers.txt', sep='\t', index_label=False)

# vis.txt
vis = pd.DataFrame(data=adata.obsm['X_draw_graph_fa'], index=adata.obs_names)
vis.to_csv('vis.txt', header=False, sep='\t')

# cluster.txt
cluster = pd.DataFrame(data=adata.obs['cluster'], index=adata.obs_names)
cluster.to_csv('cluster.txt', header=False, sep='\t')

[MeromitSinger]

Thanks @tilofreiwald ! We indeed intend for COMET to be a simple expansion from scanpy, and your input is appreciated :-)

[EannaFennell]

Hello,
I'm getting the exact same error using Python 3.6.10.
I have a conda environment instead of virtualenv though, should this matter?

[kevinwang09]

Dear maintainer, I am wondering if anything can be done about supporting Python3.7 and beyond? Looking at this schedule, it looks like Python3.6 will no longer be supported at the end of this year. https://www.python.org/downloads/. Thank you.