An error occurred while using the getModelFromHomology function.

[Yuanmaosen]

Dear community,

I encountered an error while trying to build a model draft using the following command:
model = getModelFromHomology({modelMG1655, modelpcc7942, modelpcc6803}, blast, 'Rpal', ...
{'MG1655', 'pcc7942', 'pcc6803'}, 1, false, 10^-5, 100, 30);
Error Description:
When processing gene glcE removal, the function fails during logical expression evaluation:
geneToRemove: glcE
ruleGenes: {'glcF'}, {'glcD'}, {'glcE'}, {'slr0806'}
Evaluating expression:
true) && false && true)
Error in removeGenes>canRxnCarryFlux (line 135)
Invalid expression. Use parentheses for function calls or indexing, or check for mismatched delimiters.
Troubleshooting Attempts:

The error disappears if I exclude modelpcc6803 from the input.

Found that the problematic grRule was: ((glcD or slr0806) and glcE and glcF)

Simplified to (glcD or slr0806) and glcE and glcF but the error persists.

Interestingly, the same logic worked for glcD removal:

geneToRemove: glcD
Evaluating expression: ((false || true) && true && true)
Debugging Info:

Added diagnostic outputs showing the expression being evaluated.

The error occurs in canRxnCarryFlux when processing the modified gene rule.

Questions:

Why does the expression generation fail for glcE but work for glcD despite similar rules?

Could this be related to nested parentheses handling in strrep operations?

Are there known issues with gene removal when multiple models are combined?

[edkerk]

I won't be able to fully troubleshoot this at the moment, but the error is unlikely related to using multiple models, but indeed the parsing of nested parenthesis is a likely culprit. Have you tried to explicitly write out the gene association as ((glcD and glcE and glcF) or (slr0806 and glcE and glcF)?