Fix gpr curation for histidine metabolism, propanoate metabolism and nucleotide metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #843 #844 #846

• Remove ENSG00000173418, ENSG00000139977, ENSG00000156269 from MAR04426;

• Remove ENSG00000132437 from MAR04428;

• Remove ENSG00000138744, ENSG00000078124, ENSG00000172264, ENSG00000068903 from MAR05336;

• Remove ENSG00000117682, ENSG00000183665 from MAR05337;

• Remove ENSG00000012660, ENSG00000170522, ENSG00000118402 from MAR05338;

• Remove ENSG00000078124, ENSG00000156795 from MAR05339;

• Remove ENSG00000138744, ENSG00000078124, ENSG00000133315, ENSG00000172264, ENSG00000142082 from MAR05340;

• Remove ENSG00000116133 from MAR04497;

• Remove ENSG00000121039, ENSG00000176387, ENSG00000170786, ENSG00000187134, ENSG00000087076, ENSG00000160439, ENSG00000099377 from MAR09804;

• Remove ENSG00000125877 from MAR03966;

• Remove ENSG00000168393 from MAR03968;

• Remove ENSG00000196839 from MAR04633;

• Remove ENSG00000168393 from MAR04640;

• Remove ENSG00000125458, ENSG00000205309, ENSG00000122643 from MAR07713;

• Remove ENSG00000125458 from MAR07716;

• Remove ENSG00000125458, ENSG00000205309 from MAR07721;

• Remove ENSG00000122643, ENSG00000076685, ENSG00000141698 from MAR07725;

• Remove ENSG00000205309 from MAR07728;

• Remove ENSG00000143156 from MAR07883;

• Remove ENSG00000143156 from MAR07890;

• Remove ENSG00000143156 from MAR07895;

• Remove ENSG00000073417, ENSG00000065989, ENSG00000205268, ENSG00000113231 from MAR08083;

• Remove ENSG00000065989, ENSG00000205268, ENSG00000184588, ENSG00000113231, ENSG00000171408 from MAR08085;

• Remove ENSG00000095464, ENSG00000132915, ENSG00000160191, ENSG00000133256, ENSG00000138735 from MAR08087;

• Remove ENSG00000170502 from MAR08443;

• Remove ENSG00000170502 from MAR08444;

• Remove ENSG00000162368 from MAR08450;

• Remove ENSG00000171302 from MAR08474;

• Remove ENSG00000156269, ENSG00000139977 and ENSG00000183665 from 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 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.

[feiranl]

LGTM! Please fix those conflicts and merge this PR

[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'  }    36    2179    61    278    0.86727       0.11465        0.97277       0.17518     0.15018
    {'GBM'   }    34    2159    63    297    0.85899       0.10272        0.97165       0.15888     0.13067
    {'HCT116'}    45    2200    56    309    0.86015       0.12712        0.97518        0.1978      0.1816
    {'HELA'  }    30    2258    71    252    0.87629       0.10638        0.96951       0.15666     0.12216
    {'RPE1'  }    15    2198    82    258    0.86682      0.054945        0.96404      0.081081    0.030679
    {'all'   }     7    2401    94    109    0.92225      0.060345        0.96232      0.064516    0.024222

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