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Fix: GPR curation for Sulfur metabolism #937

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merged 2 commits into from
Dec 16, 2024
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JHL-452b
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@JHL-452b JHL-452b commented Dec 7, 2024

Main improvements in this PR:

As proposed in #892

  • Remove ENSG00000104331 from MAR04187;
  • Remove ENSG00000108602 from MAR04842;
  • Remove ENSG00000204386 from MAR07530;
  • Remove ENSG00000204386 from MAR07542;
  • Remove ENSG00000204386 from MAR07560;
  • Remove ENSG00000204386 from MAR07526;
  • Remove ENSG00000204386 from MAR07547;
  • Remove ENSG00000135702 from MAR07369;
  • Remove ENSG00000106304 from MAR07503.

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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github-actions bot commented Dec 7, 2024

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.

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hhl-24 commented Dec 11, 2024

LGTM!

@feiranl feiranl merged commit 0e0d55a into develop Dec 16, 2024
@feiranl feiranl deleted the Fix-Sulfur_metabolism branch December 16, 2024 11:38
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3 participants