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feat: add rxnMAIDfield to JSON file #175

Merged
merged 3 commits into from
Jun 2, 2020
Merged

feat: add rxnMAIDfield to JSON file #175

merged 3 commits into from
Jun 2, 2020

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haowang-bioinfo
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Main improvements in this PR:

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected devel as a target branch

@haowang-bioinfo
fix: adjust the recognition patter of last element in array
56706c2 
- Since the addition of `spontaneous` field, there could be non-string elements in array. This adjustment allows the recognition of last element regardless of its type.
@haowang-bioinfo
chore: update the content by appending rxnMAID field
cf1521a 
The change of this commit is made through following command:
`rxnAssoc.rxnMAID = regexprep(rxnAssoc.rxns,'^HMR_','MA_');`
@JonathanRob
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Two comments/suggestions:

  1. Maybe leave the rxnMAID field blank for reactions that do not have an ID of the form MA_####, instead of just using their original ID? I realize it's temporary and probably doesn't matter, but this would at least keep all of the IDs in the rxnMAID field consistent.

  2. Consider adding an extra digit, since we're already surpassing 10,000 reactions; e.g., MA_3905 would be MA_03905.

@haowang-bioinfo
chore: reformat rxnMAID elements
f0152bb 
1. Remove ids that do not start with `MA_` prefix;
2. Pad in zero to digital part to ensure the elements with identical length.
@haowang-bioinfo
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@JonathanRob the elements are reformatted as suggested.

@haowang-bioinfo haowang-bioinfo merged commit e8d4799 into devel Jun 2, 2020
@haowang-bioinfo haowang-bioinfo deleted the feat/rxnMAID branch June 2, 2020 17:58
@haowang-bioinfo haowang-bioinfo mentioned this pull request Jun 11, 2020
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@JonathanRob JonathanRob JonathanRob approved these changes

@mihai-sysbio mihai-sysbio Awaiting requested review from mihai-sysbio

@pecholleyc pecholleyc Awaiting requested review from pecholleyc

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@haowang-bioinfo @JonathanRob