fix: GPR curation for transport reactions (4)

[JHL-452b]

Main improvements in this PR:

As proposed in #918 and #919 :

• Remove ENSG00000165029 from MAR00235;
• Remove ENSG00000165029 from MAR00247;
• Remove ENSG00000165029 from MAR00307;
• Remove ENSG00000165029 from MAR00321;
• Remove ENSG00000165029 from MAR00339;
• Remove ENSG00000165029 from MAR00347;
• Remove ENSG00000165029 from MAR00359;
• Remove ENSG00000165029 from MAR00399;
• Remove ENSG00000021488 from MAR01898;
• Remove ENSG00000021488 from MAR01900;
• Remove ENSG00000091138 from MAR04946;
• Remove ENSG00000163581 from MAR04996;
• Remove ENSG00000139209 from MAR05071;
• Remove ENSG00000178537 from MAR05328;
• Remove ENSG00000103257 from MAR05468;
• Remove ENSG00000165029 from MAR05533;
• Remove ENSG00000103064 from MAR05593;
• Remove ENSG00000103064 from MAR05611;
• Remove ENSG00000103064 from MAR05612;
• Remove ENSG00000103064 from MAR05618;
• Remove ENSG00000103257 from MAR05630;
• Remove ENSG00000103064 from MAR05649;
• Remove ENSG00000103064 from MAR05651;
• Remove ENSG00000103064 from MAR05654;
• Remove ENSG00000103064 from MAR05665;
• Remove ENSG00000103064 from MAR05671;
• Remove ENSG00000103064 from MAR05673;
• Remove ENSG00000103064 from MAR05684;
• Remove ENSG00000103064 from MAR05698;
• Remove ENSG00000103064, ENSG00000105281 from MAR05708;
• Remove ENSG00000103064 from MAR05710;
• Remove ENSG00000103064 from MAR05729;
• Remove ENSG00000103064 from MAR05737;
• Remove ENSG00000103064 from MAR05743;
• Remove ENSG00000103064 from MAR05757;
• Remove ENSG00000103064 from MAR05759;
• Remove ENSG00000103064 from MAR05762;
• Remove ENSG00000103064 from MAR05772;
• Remove ENSG00000103064 from MAR05786;
• Remove ENSG00000103064 from MAR05802;
• Remove ENSG00000103064 from MAR05818;
• Remove ENSG00000103064 from MAR05821;
• Remove ENSG00000103064 from MAR05826;
• Remove ENSG00000103064 from MAR05891;
• Remove ENSG00000103064 from MAR05901;
• Remove ENSG00000108932 from MAR06007;
• Remove ENSG00000108932 from MAR06048;
• Remove ENSG00000100156 from MAR06054;
• Remove ENSG00000130304 from MAR08946;
• Remove ENSG00000196517 from MAR09597.

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 ENSG00000100156 from MAR06054;

I found that this gene has not been removed. Others look good to me.

[JHL-452b]

Indeed. Thanks haohao. I remove it now.

[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.

[hhl-24]

LGTM!

[JHL-452b]

Reaction ID	issues
MAR00235, MAR00247, MAR00307, MAR00321, MAR00339, MAR00347, MAR00359, MAR00399, MAR01898, MAR01900, MAR04946, MAR04996, MAR05071, MAR05328, MAR05468, MAR05533, MAR05593, MAR05611, MAR05612, MAR05618, MAR05630, MAR05649, MAR05651, MAR05654, MAR05665, MAR05671, MAR05673, MAR05684, MAR05698, MAR05708, MAR05710, MAR05729, MAR05737, MAR05743, MAR05757, MAR05759, MAR05762, MAR05772, MAR05786, MAR05802	918
MAR05818, MAR05821, MAR05826, MAR05891, MAR05901, MAR06007, MAR06048, MAR06054, MAR08946, MAR09597	919

This PR focuses on the reactions that appears in 918 and 919 .