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fix: avoid duplicity in gene name storage #217

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2 tasks done
BenjaSanchez opened this issue Apr 23, 2020 · 0 comments
Open
2 tasks done

fix: avoid duplicity in gene name storage #217

BenjaSanchez opened this issue Apr 23, 2020 · 0 comments
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format fix things associated to format of any of the model/data/script files standby work somewhere else is needed before advancing
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@BenjaSanchez
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Description of the issue:

In PR #216 we are forcing the model to save the proteins COBRA field with the same information as geneNames, in order to allow both cobratoolbox and cobrapy to load gene names from the xml file. There is now opencobra/cobrapy#950 to address the problem in one of the two solvers. Once it is solve, we can revert the model to avoid this duplicity.

Current feature/value/output:

<fbc:geneProduct metaid="G_YPL078C" fbc:id="G_YPL078C" fbc:name="ATP4" fbc:label="ATP4"/>

Expected feature/value/output:

The gene name should be uniquely either in fbc:name or fbc:label, depending on which package adapts to the other.

I hereby confirm that I have:

  • Tested my code with all requirements for running the model
  • Checked that a similar issue does not exist already
@BenjaSanchez BenjaSanchez added format fix things associated to format of any of the model/data/script files standby work somewhere else is needed before advancing labels Apr 23, 2020
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Labels
format fix things associated to format of any of the model/data/script files standby work somewhere else is needed before advancing
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