Fix: GPR curation for Arg_Pro_Tyr_metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #850

• Remove ENSG00000117592 from MAR03391;
• Remove ENSG00000117305 from MAR03935;
• Remove ENSG00000142920 from MAR04191;
• Remove ENSG00000184254 from MAR04683;
• Remove ENSG00000184254 from MAR04685;
• Remove ENSG00000184254 from MAR04686;
• Remove ENSG00000184254 from MAR04687;
• Remove ENSG00000118514, ENSG00000064763 from MAR06953;
• Remove ENSG00000064763 from MAR06954;
• Remove ENSG00000064763 from MAR06973;
• Remove ENSG00000198099, ENSG00000196616 from MAR08530;
• Remove ENSG00000077498 from MAR08630;
• Remove ENSG00000131873, ENSG00000123989, ENSG00000169826, ENSG00000198108, ENSG00000147408 from MAR12002;
• Remove ENSG00000131873, ENSG00000123989, ENSG00000169826, ENSG00000198108, ENSG00000147408 from MAR12003;
• Remove ENSG00000142920 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 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.

[github-actions]

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

     cellLine     TP     TN     FP     FN     accuracy    sensitivity    specificity       F1         MCC   
    __________    __    ____    ___    ___    ________    ___________    ___________    ________    ________

    {'DLD1'  }    50    2147     85    272    0.86022       0.15528        0.96192       0.21882     0.17386
    {'GBM'   }    57    2138     78    280    0.85977       0.16914         0.9648       0.24153     0.20259
    {'HCT116'}    71    2179     70    289     0.8624       0.19722        0.96888       0.28343     0.25335
    {'HELA'  }    35    2219    106    251    0.86327       0.12238        0.95441       0.16393      0.1061
    {'RPE1'  }    21    2163    114    255    0.85546      0.076087        0.94993       0.10219    0.036105
    {'all'   }     8    2357    133    113    0.90578      0.066116        0.94659      0.061069    0.011814

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