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Fix-GPR curation for Purine metabolism #898

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@JHL-452b JHL-452b commented Nov 5, 2024

Main improvements in this PR:

As proposed in #852

  • Remove ENSG00000162836 from MAR00046;
  • Remove ENSG00000197217 from MAR03998;
  • Remove ENSG00000169418, ENSG00000132518, ENSG00000070019, ENSG00000101890, ENSG00000152402 from MAR04000;
  • Remove ENSG00000205309, ENSG00000141698, ENSG00000122643 from MAR04010;
  • Remove ENSG00000138735, ENSG00000160191, ENSG00000132915, ENSG00000133256 from MAR04014;
  • Remove ENSG00000164742, ENSG00000174233, ENSG00000162104, ENSG00000173175, ENSG00000129467 from MAR04022;
  • Remove ENSG00000143156 from MAR04044;
  • Remove ENSG00000105650, ENSG00000065989, ENSG00000205268, ENSG00000184588 from MAR04048;
  • Remove ENSG00000122643 from MAR04081;
  • Remove ENSG00000125458, ENSG00000205309, ENSG00000122643 from MAR04082;
  • Remove ENSG00000125877 from MAR04168;
  • Remove ENSG00000143156 from MAR04291;
  • Remove ENSG00000205309, ENSG00000141698, ENSG00000122643 from MAR04417;
  • Remove ENSG00000205309, ENSG00000146587 from MAR04449;
  • Remove ENSG00000125458 from MAR04450;
  • Remove ENSG00000151498, ENSG00000117054, ENSG00000087008, ENSG00000072778 from MAR04480;
  • Remove ENSG00000156510, ENSG00000160883 from MAR04495;
  • Remove ENSG00000160883 from MAR04496;
  • Remove ENSG00000205309 from MAR04602;
  • Remove ENSG00000122643, ENSG00000125458 from MAR04632;
  • Remove ENSG00000125458, ENSG00000205309 from MAR04705;
  • Remove ENSG00000100354 from MAR04812;
  • Remove ENSG00000117592 from MAR06603.

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

@JHL-452b JHL-452b changed the title fix-GPR_curation_for_Purine_metabolism Fix-GPR curation for Purine metabolism Nov 5, 2024
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github-actions bot commented Nov 5, 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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2 participants