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In some cases it would be helpful to parse comments from BNGL files #2

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jonrkarr opened this issue Jun 8, 2021 · 1 comment
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enhancement New feature or request

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@jonrkarr
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jonrkarr commented Jun 8, 2021

bionetgen.bngmodel nicely parses models. In some cases, it may be helpful to parse the comments out of files.

For example, the comment of Vec is currently parsed to None

begin parameters
 Vec   1000*Vcell # Volume of extracellular space around each cell (1/cell density)
end parameters
model = bionetgen.bngmodel(...)
model.parameters['Vec'].comment
@jonrkarr jonrkarr changed the title Parse comments from BNGL files In some cases it would be helpful to parse comments from BNGL files Jun 8, 2021
@ASinanSaglam
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The comments are not parsed at all right now due to how parsing works currently (conversion to an XML file and reading off of that). XML conversion rips out all comments so it's not possible to parse the comments with this method. We are working on a new parsing method right now and once that's done, all comments will be parsed and will be added to .comment attribute. I'll update the issue as I make progress on this.

@ASinanSaglam ASinanSaglam added the enhancement New feature or request label Jun 14, 2021
ASinanSaglam pushed a commit that referenced this issue Aug 23, 2021
Rearranged & updated info subcommand process, also added more documen…
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