Add new reactions annotated for genes related to Glycolysis pathway

[feiranl]

Main improvements in this PR:

• Add 87 new mets, 68 new reactions for genes related to Glycolysis pathway according to the Refine GPR annotation for Glycolysis pathway #507

• Fix one naming issuse identified in the process Duplicate IDs for same mets #519 :
  remove the metabolite MAM00077x, as it only relate to 2 rxns, while the duplicate MAM02766x is associated with 13 rxns from all compartments
  remove reaction MAR03489 and merge the GPR to its duplicate rxn MAR03387 as discussed
  remove reaction MAR03488 as discussed

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

[haowang-bioinfo]

The Yaml validation step verifies the consistency between Yaml model file and tsv files of reactions.tsv and metabolites.tsv. The failure of this step means that tsv files should be modified to match with the model, which, as demonstrated by the Yaml conversion step, appears to be fine.

[mihai-sysbio]

Looking into the logs of the validation check below, it seems many (all?) errors are caused: trailing spaces (trailing-spaces). This means that in Human-GEM.yml spaces have been added at the end of the line.

[mihai-sysbio]

After correcting the trailing spaces in commit 037e7b8, the error that @haowang-bioinfo indicated previously becomes obvious in the logs as well:

  File "/__w/Human-GEM/Human-GEM/code/test/sanityCheck.py", line 53, in checkMetAnnotation
    assert metList == mets, "Metabolite annotation mismatch!"
AssertionError: Metabolite annotation mismatch!
Error: Process completed with exit code 1.

[feiranl]

@mihai-sysbio could you tell me what should I do to fix this error? I thought it was that I reused the deprecated met IDs, but I intersected the mets in metabolites.tsv and deprecatedMetabolites.tsv and found none.

[mihai-sysbio]

@mihai-sysbio could you tell me what should I do to fix this error? I thought it was that I reused the deprecated met IDs, but I intersected the mets in metabolites.tsv and deprecatedMetabolites.tsv and found none.

My suspicion is that some of the new identifiers added in the YML file have not been added to the TSV. One can run the Python code locally as well (with a printout) to see the exact problem. Let me know if you can't find the root cause.

[feiranl]

Closing this PR since it was redo in #534 and #535. This error in yaml validation was caused by the inconsistent met order in model.mets and metAnnotation file.