Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Hierarchy error in full tissue network #7

Open
davidfstein opened this issue Jan 20, 2023 · 0 comments
Open

Hierarchy error in full tissue network #7

davidfstein opened this issue Jan 20, 2023 · 0 comments

Comments

@davidfstein
Copy link

I am attempting to run ohmnet on the full tissue ppi network from http://snap.stanford.edu/ohmnet/. There appears to be an error with the provided hierarchy file. The following error is produced.

Traceback (most recent call last):
  File "main.py", line 66, in <module>
    main(args)
  File "main.py", line 62, in main
    on.embed_multilayer()
  File "/local/david/ohmnet/ohmnet/ohmnet.py", line 212, in embed_multilayer
    all_nodes, leaf_vectors, internal_vectors)
  File "/local/david/ohmnet/ohmnet/ohmnet.py", line 91, in update_internal_vectors
    assert len(parents) == 1, 'Problem'
AssertionError: Problem

I am running ohmnet as follows python2.7 main.py --input data/tissues.list --outdir . --hierarchy bio-tissue-hierarchy/tissue.hierarchy

When run on the example brain network provided the code executes properly. I can see that the brain hierarchy seems to follow a different format than the provided tissue hierarchy. Do you have a working tissue hierarchy file or can you guide me on how to construct one?

Thanks!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant