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: add "G_" prefix when exporting model to SBML #534

Closed
wants to merge 1 commit into from

Conversation

simas232
Copy link
Collaborator

Main improvements in this PR:

  • Fix:
    • exportModel now adds the "G_" prefix to gene IDs. It is needed for the genes which begin with numeral chars

I hereby confirm that I have:

  • Selected develop as a target branch

Copy link

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

 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
> Checking RAVEN release DEVELOPMENT
> Checking MATLAB release 2020b
> Checking system architecture glnxa64
> Set RAVEN in MATLAB path Pass
> Save MATLAB path Pass
> Make binaries executable Pass

> Add Java paths for Excel format Pass
> Checking libSBML version 5.19.0
> Checking model import and export
> Import Excel format Pass
> Export Excel format Pass
> Import SBML format Pass
> Export SBML format Pass

> Checking for LP solvers
> glpk Pass
> gurobi Pass
> scip Fail
> cobra Pass
> Set RAVEN solver gurobi

> Checking BLAST+ Pass
> Checking DIAMOND Pass
> Checking HMMER Pass

> Checking function uniqueness Pass

*** checkInstallation complete ***

Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
.
Done checkTasksTests

Running diamondTests
.
Done diamondTests

Running fillGapsLargeTests
..
Done fillGapsLargeTests

Running fillGapsSmallTests
...
Done fillGapsSmallTests

Running hmmerTests
.
Done hmmerTests

Running importExportTests
....
Done importExportTests

Running mafftTests
.
Done mafftTests

Running miriamTests
.
Done miriamTests

Running modelAbilitiesTests
........
Done modelAbilitiesTests

Running modelConversionTests
.
Done modelConversionTests

Running modelCurationTests
.......... ........
Done modelCurationTests

Running modelSortingTests
..
Done modelSortingTests

Running solverTests
..
Error occurred in solverTests/testSCIP and it did not run to completion.
---------
Error ID:
---------
''
--------------
Error Details:
--------------
Error using solverTests>testSCIP (line 80)
SCIP MEX binary not installed or not functional, test skipped
..
Done solverTests

Running tinitTests
..........
Done tinitTests

Failure Summary:

Name Failed Incomplete Reason(s)
=====================================================
solverTests/testSCIP X X Errored.

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

@simas232 simas232 closed this Apr 26, 2024
@simas232 simas232 deleted the fix/exportModel branch April 26, 2024 11:40
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.

1 participant