fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #847

• Remove ENSG00000166840 from MAR03750;
• Remove ENSG00000138796 from MAR03757;
• Remove ENSG00000166840, ENSG00000156689 from MAR03772;
• Remove ENSG00000161653 from MAR03794;
• Remove ENSG00000111237 from MAR03843;
• Remove ENSG00000137106 from MAR03856;
• Remove ENSG00000158578 from MAR03939;
• Remove ENSG00000188676 from MAR06924;
• Remove ENSG00000121039, ENSG00000240857, ENSG00000160439, ENSG00000176387, ENSG00000139988, ENSG00000087076, ENSG00000198610 and ENSG00000099377 from MAR06925;
• Remove ENSG00000116882 from MAR07703;
• Remove ENSG00000166800 from MAR11476;
• Remove ENSG00000111237 from model as it's not connected to any reactions after this curation.

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

[github-actions]

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.

A more detailed output from this test run is also committed to data/macawResults/macaw_results.csv.

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