Fix-GPR curation for Purine metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #852

• Remove ENSG00000162836 from MAR00046;
• Remove ENSG00000197217 from MAR03998;
• Remove ENSG00000169418, ENSG00000132518, ENSG00000070019, ENSG00000101890, ENSG00000152402 from MAR04000;
• Remove ENSG00000205309, ENSG00000141698, ENSG00000122643 from MAR04010;
• Remove ENSG00000138735, ENSG00000160191, ENSG00000132915, ENSG00000133256 from MAR04014;
• Remove ENSG00000164742, ENSG00000174233, ENSG00000162104, ENSG00000173175, ENSG00000129467 from MAR04022;
• Remove ENSG00000143156 from MAR04044;
• Remove ENSG00000105650, ENSG00000065989, ENSG00000205268, ENSG00000184588 from MAR04048;
• Remove ENSG00000122643 from MAR04081;
• Remove ENSG00000125458, ENSG00000205309, ENSG00000122643 from MAR04082;
• Remove ENSG00000125877 from MAR04168;
• Remove ENSG00000143156 from MAR04291;
• Remove ENSG00000205309, ENSG00000141698, ENSG00000122643 from MAR04417;
• Remove ENSG00000205309, ENSG00000146587 from MAR04449;
• Remove ENSG00000125458 from MAR04450;
• Remove ENSG00000151498, ENSG00000117054, ENSG00000087008, ENSG00000072778 from MAR04480;
• Remove ENSG00000156510, ENSG00000160883 from MAR04495;
• Remove ENSG00000160883 from MAR04496;
• Remove ENSG00000205309 from MAR04602;
• Remove ENSG00000122643, ENSG00000125458 from MAR04632;
• Remove ENSG00000125458, ENSG00000205309 from MAR04705;
• Remove ENSG00000100354 from MAR04812;
• Remove ENSG00000117592 from MAR06603.

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.

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.

[feiranl]

LGTM! Please fix the conflict 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'  }    37    2175    62    277    0.86711       0.11783        0.97228       0.17918      0.1533
    {'GBM'   }    34    2156    65    295    0.85882       0.10334        0.97073       0.15888     0.12855
    {'HCT116'}    46    2198    57    306    0.86076       0.13068        0.97472        0.2022     0.18491
    {'HELA'  }    31    2254    72    251    0.87615       0.10993        0.96905       0.16104     0.12592
    {'RPE1'  }    15    2194    84    257    0.86627      0.055147        0.96313      0.080863    0.029199
    {'all'   }     7    2396    96    109     0.9214      0.060345        0.96148      0.063927    0.023098

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