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SBML File Import error #164

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SpencerUyematsu opened this issue Feb 9, 2023 · 0 comments
Open

SBML File Import error #164

SpencerUyematsu opened this issue Feb 9, 2023 · 0 comments
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@SpencerUyematsu
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Hi,

I received the following error when trying to import an sbml file of level 2, version 4.


TypeError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_29976/3388929290.py in
1 from bioscrape.types import Model
----> 2 M = Model(sbml_filename = "pone_0161260_s012.xml")

bioscrape\types.pyx in bioscrape.types.Model.init()

~\anaconda3\envs\e164\lib\site-packages\bioscrape\sbmlutil.py in import_sbml(sbml_file, bioscrape_model, input_printout, **kwargs)
50 allparams = import_sbml_parameters(model)
51 allreactions, allspecies = import_sbml_reactions(model, allspecies, allparams, input_printout)
---> 52 allrules, allreactions = import_sbml_rules(model, allspecies, allparams, allreactions, input_printout)
53 # Check and warn if there are any unrecognized components (function definitions, packages, etc.)
54 if len(model.getListOfCompartments()) > 0 or len(model.getListOfUnitDefinitions()) > 0 or len(model.getListOfEvents()) > 0:

~\anaconda3\envs\e164\lib\site-packages\bioscrape\sbmlutil.py in import_sbml_rules(sbml_model, allspecies, allparams, allreactions, input_printout)
337 rule_string = rulevariable + '=' + rule_formula
338 elif rulevariable in allparams:
--> 339 rule_string = rulevariable + '=' + rule_formula
340 else:
341 warnings.warn('SBML: Attempting to assign something that is not a parameter or species %s'

TypeError: can only concatenate str (not "NoneType") to str

Thanks!

@ayush9pandey ayush9pandey self-assigned this Feb 16, 2023
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