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

fix: remove non-associated genes #939

Merged
merged 2 commits into from
Dec 22, 2024
Merged

fix: remove non-associated genes #939

merged 2 commits into from
Dec 22, 2024

Conversation

edkerk
Copy link
Member

@edkerk edkerk commented Dec 22, 2024

Main improvements in this PR:

As proposed in #938

  • Remove ENSG00000116882, ENSG00000124302, ENSG00000133048, ENSG00000163684 and ENSG00000175229.

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected develop as a target branch
  • Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

@edkerk edkerk requested a review from JHL-452b December 22, 2024 00:47
Copy link

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
- Found 1514 dead-end metabolites.
- Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1977 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 447 reactions that were some type of duplicate:
- 0 were completely identical to at least one other reaction.
- 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
- 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.

@JHL-452b
Copy link
Collaborator

LGTM!

@edkerk edkerk merged commit 1a562ce into develop Dec 22, 2024
@edkerk edkerk deleted the fix/non-associated-genes branch December 22, 2024 12:23
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

Successfully merging this pull request may close these issues.

2 participants