transformXML2Map not working.

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Hari Sundar

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Feb 3, 2023, 12:39:13 AMFeb 3
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Hi. I am trying to map of of Streptomyces hygroscopicus to overlay my flux (FBAsol.v) values for different inputs.

I tried using transformXML2Map but it gave the following error.
Error in transformXML2Map (line 55)
for mol =
1:length(xmlStruct.sbml.model.annotation.celldesigner_colon_extension.celldesigner_colon_listOfSpeciesAliases.celldesigner_colon_speciesAlias)
Reference to non-existent field 'annotation'.

Then I tried using the model iML1515 downloaded form BIGG. It gave the same error. Is there an other tool I can use for maps and overlaying my flux values.

Thanks in advance.

Hari Sundar

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Feb 3, 2023, 12:42:21 AMFeb 3
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These are the files I have used.



AscoFS35.xml

Hari Sundar

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Feb 3, 2023, 1:34:05 AMFeb 3
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https://file.io/Sp7x0LO4ZgbJ -iML1515 file link.

bs2019

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May 12, 2023, 3:11:19 AMMay 12
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Hi!
I am also receiving the same error with the .xml file of my model. Has anyone able to resolve this error? Looks like the transformXML2Map.m was written specifically for the ecoli core model. That's my opinion.

Ronan M.T. Fleming

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May 12, 2023, 3:23:35 AMMay 12
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What specifically is the error?

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bs2019

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May 12, 2023, 4:21:01 AMMay 12
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Hi Ronan,
Here is the code and the error:

>> [xmlStruct, map] = transformXML2Map('/test/models/xml/suppinfo_ivs1191.xml');
Unrecognized field name "annotation".


Error in transformXML2Map (line 55)
for mol = 1:length(xmlStruct.sbml.model.annotation.celldesigner_colon_extension.celldesigner_colon_listOfSpeciesAliases.celldesigner_colon_speciesAlias)

Thanks!

dtusso

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May 16, 2023, 4:40:21 PMMay 16
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Hello everyone

I get the same error
>> [xmlStruct, map] = transformXML2Map('/Users/diana/cobratoolbox/iMM904.xml')
Reference to non-existent field 'annotation'.


Error in transformXML2Map (line 55)
for mol =
1:length(xmlStruct.sbml.model.annotation.celldesigner_colon_extension.celldesigner_colon_listOfSpeciesAliases.celldesigner_colon_speciesAlias)

Does anyone know how to solve it?

Thank you.
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