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fix-GPR curation for Xenobiotics metabolism #913

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merged 2 commits into from
Dec 4, 2024

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JHL-452b
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@JHL-452b JHL-452b commented Nov 6, 2024

Main improvements in this PR:

As proposed in #864

  • Remove ENSG00000147576, ENSG00000196616 from MAR07038;
  • Remove ENSG00000108242 from MAR07053;
  • Remove ENSG00000117594 from MAR07059;
  • Remove ENSG00000108242 from MAR07096;
  • Remove ENSG00000117592 from MAR06536;
  • Remove ENSG00000184254, ENSG00000006534 from MAR09569;
  • Remove ENSG00000130508 from MAR06535;
  • Remove ENSG00000108242 from MAR07019;
  • Remove ENSG00000108242 from MAR07021;
  • Remove ENSG00000186377, ENSG00000137869 from MAR04019;
  • Remove ENSG00000186160, ENSG00000186377 from MAR04041;
  • Remove ENSG00000108242 from MAR04051.

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 Nov 6, 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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JHL-452b commented Dec 2, 2024

Could you please help me to review this PR? @feiranl

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LGTM!

@feiranl feiranl merged commit 5e88b8a into develop Dec 4, 2024
@edkerk edkerk deleted the fix-Xenobiotics_metabolism branch December 17, 2024 14:58
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2 participants