feat: enable I/O of SBO terms from SBML file #235
Merged
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Main improvements in this PR:
The
exportModel
,importModel
, andravenCobraWrapper
functions were updated to enable writing and reading of gene, reaction, and metabolite SBO terms to and from an SBML file. This PR addresses Issue #196.exportModel
writes SBO terms from.xyzMiriams
model fields to SBML.sboTerm
fields.The default gene SBO term assigned in
exportModel
was changed fromSBO:0000252
("polypeptide chain") toSBO:0000243
("gene"), the latter of which is consistent with memote.importModel
reads SBO terms from the SBML.sboTerm
fields, and adds them to the corresponding.xyzMiriams
model fields.A check was implemented in
importModel
to prevent importing SBO terms if they are all identical for a given entity (e.g., if all metabolites have the same SBO term, it will not be imported into the model structure).ravenCobraWrapper
was updated to enable conversion of gene SBO terms between the.geneMiriams
and.geneSBOTerms
fields of RAVEN and COBRA model structures, respectively.I hereby confirm that I have:
devel
as a target branch