Fix: GPR curation for transport reactions (3)

[JHL-452b]

Main improvements in this PR:

As proposed in #916 #917 #919 #922 #925 #920 :

• Remove ENSG00000170522, ENSG00000026652, ENSG00000125505, ENSG00000197977, ENSG00000123684, ENSG00000186792, ENSG00000100344, ENSG00000143797, ENSG00000176454, ENSG00000146648, ENSG00000141446, ENSG00000160216, ENSG00000012660, ENSG00000111684, ENSG00000102125 from MAR00158;
• Remove ENSG00000135917 from MAR00095;
• Remove ENSG00000113396 from MAR00164;
• Remove ENSG00000165029 from MAR00198;
• Remove ENSG00000103569 from MAR01485;
• Remove ENSG00000130821, ENSG00000130822 from MAR03011;
• Remove ENSG00000130821 from MAR03013;
• Remove ENSG00000108932 from MAR04930;
• Remove ENSG00000123643 from MAR05048;
• Remove ENSG00000123643 from MAR05051;
• Remove ENSG00000123643 from MAR05062;
• Remove ENSG00000107819 from MAR07759;
• Remove ENSG00000125454 from MAR07835;
• Remove ENSG00000125454 from MAR07837;
• Remove ENSG00000125454 from MAR07838;
• Remove ENSG00000125454 from MAR07839;
• Remove ENSG00000125454 from MAR07840;
• Remove ENSG00000125454 from MAR07841;
• Remove ENSG00000125454 from MAR07842;
• Remove ENSG00000125454 from MAR07843;
• Remove ENSG00000125454 from MAR07845;
• Remove ENSG00000125454 from MAR07846;
• Remove ENSG00000125454 from MAR07847;
• Remove ENSG00000125454 from MAR07849;
• Remove ENSG00000125454 from MAR07850;
• Remove ENSG00000125454 from MAR07851;
• Remove ENSG00000125454 from MAR07852;
• Remove ENSG00000125454 from MAR07853;
• Remove ENSG00000125454 from MAR07854;
• Remove ENSG00000152779, ENSG00000165449 from MAR08496;
• Remove ENSG00000115902 from MAR08972;
• Remove ENSG00000149150, ENSG00000167703 from MAR09274;
• Remove ENSG00000005471, ENSG00000121270 from MAR09882;
• Remove ENSG00000085563 from MAR11768;
• Remove ENSG00000015520 from MAR11815;
• Remove ENSG00000073734 from MAR12184;
• Remove ENSG00000184343, ENSG00000130821 from MAR03014;
• Remove ENSG00000117620, ENSG00000205060 from MAR08857;
• Remove ENSG00000174669, ENSG00000112759 from MAR11801;
• Remove ENSG00000130821, ENSG00000184343, ENSG00000130822 from MAR03008;
• Remove ENSG00000130821, ENSG00000184343 from MAR03017;
• Remove ENSG00000186198, ENSG00000163959 from MAR12185;
• Remove ENSG00000130958, ENSG00000117620 from MAR00918;
• Remove ENSG00000102125 and ENSG00000117620 from the model as they are 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.

[hhl-24]

Remove ENSG00000170522, ENSG00000026652, ENSG00000125505, ENSG00000197977, ENSG00000123684, ENSG00000186792, ENSG00000100344, ENSG00000143797, ENSG00000176454, ENSG00000146648, ENSG00000141446, ENSG00000160216, ENSG00000012660, ENSG00000111684, ENSG00000102125 from MAR00158;

ENSG00000146648 has already been removed in the develop branch.