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.

Sign up for GitHub

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

feat: store summary macaw results #882

Merged
merged 4 commits into from
Nov 5, 2024
Merged

feat: store summary macaw results #882

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
cd98819
fix: style of macaw summary output
edkerk Oct 18, 2024
7911e20
chore: add macaw test result
edkerk Oct 18, 2024
546d855
Merge branch 'develop' into feat/macaw_output
edkerk Oct 28, 2024
25dbea8
chore: add macaw test result
edkerk Oct 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions .github/workflows/commentMacaw.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,16 @@
<<<<<<<< HEAD:.github/workflows/commentMacaw.md
This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the [MACAW](https://github.com/Devlin-Moyer/macaw) test:
========
This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the gene essentiality test:
>>>>>>>> develop:.github/workflows/commentsFromTests.md

<pre>
{TEST_RESULTS}
</pre>

<<<<<<<< HEAD:.github/workflows/commentMacaw.md
This and a more detailed output from MACAW are also committed to `data/macawResults/`.

========
>>>>>>>> develop:.github/workflows/commentsFromTests.md
> _Note: In the case of multiple test runs, this post will be edited._
7 changes: 0 additions & 7 deletions .github/workflows/commentsFromTests.md
View file
Open in desktop

This file was deleted.

2 changes: 1 addition & 1 deletion data/testResults/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.

The test results shown here were obtained by the GitHub Actions run in **PR #675** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
The test results shown here were obtained by the GitHub Actions run in **PR #882** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.

### MACAW: `dead_end_test`
Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.
Expand Down