fix: GPR curation for transport reactions (9)

[JHL-452b]

Main improvements in this PR:

As proposed in #908 #909 #910 :

• Remove ENSG00000103064 from MAR05723, MAR05725, MAR05731, MAR05733, MAR05735, MAR05738, MAR05740, MAR05745, MAR05746, MAR05747, MAR05748, MAR05750, MAR05751, MAR05753, MAR05754, MAR05756, MAR05758, MAR05760, MAR05761, MAR05763, MAR05765, MAR05769, MAR05770, MAR05771, MAR05774, MAR05775, MAR05777, MAR05778, MAR05779, MAR05780, MAR05783, MAR05789, MAR05790, MAR05792, MAR05793, MAR05794, MAR05795, MAR05797, MAR05798, MAR05800, MAR05803, MAR05804, MAR05805, MAR05806, MAR05808, MAR05809, MAR05813, MAR05816, MAR05822, MAR05824, MAR05876, MAR05886, MAR05989, MAR05996.

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.

[hhl-24]

LGTM!

[JHL-452b]

Reaction ID	issues
MAR05723, MAR05725, MAR05731, MAR05733, MAR05735, MAR05738, MAR05740, MAR05745, MAR05746, MAR05747, MAR05748, MAR05750, MAR05751, MAR05753, MAR05754, MAR05756, MAR05758, MAR05760, MAR05761, MAR05763, MAR05765, MAR05769, MAR05770, MAR05771, MAR05774, MAR05775, MAR05777, MAR05778, MAR05779, MAR05780, MAR05783, MAR05789, MAR05790, MAR05792, MAR05793, MAR05794, MAR05795, MAR05797, MAR05798	908
MAR05800, MAR05803, MAR05804, MAR05805, MAR05806, MAR05808, MAR05809, MAR05813, MAR05816, MAR05822, MAR05824, MAR05876, MAR05886	909
MAR05989, MAR05996	910

This PR focuses on the reactions that appears in 908, 909 and 910 .

[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.