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Fix: GPR curation for Glucocorticoid biosynthesis #947

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@JHL-452b JHL-452b commented Dec 24, 2024

Main improvements in this PR:

As proposed in #896 :

  • Remove ENSG00000197580 from MAR01985;
  • Remove ENSG00000197580 from MAR01987;
  • Remove ENSG00000197580 from MAR02000;
  • Remove ENSG00000197580 from MAR02001;
  • Remove ENSG00000213614 from MAR07587;
  • Remove ENSG00000120137, ENSG00000152782 from MAR04731.

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

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

Starting dead-end test...
- Found 1523 dead-end metabolites.
- Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1975 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.

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hhl-24 commented Dec 30, 2024

Remove ENSG00000213614 from MAR07587;
Remove ENSG00000213614 from MAR07587;

Is this a repetition or an input error?

@JHL-452b
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Just a repetition. I removed it.

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