non-matching identifiers when running getModelFromHomology

[glou123]

sedUnix('CDT1.faa'); modelaceto = importModel('RehMBEL1391_sbml_L3V1.xml'); modelaceto.mets = regexprep(modelaceto.mets, '[[a-z]+]$', ''); WARNING: The following metabolites are never used in a reaction: fol_c

WARNING: The following genes are not associated to a reaction: H16_B2371 H16_A0184 H16_B1757 H16_A3290 H16_A2106

modelaceto.id = 'aceto'; blast = getBlast('aceto1', ['CN.faa'], {'aceto'}, ... { 'CDT1.faa'}); BLASTing "aceto" against "aceto1".. BLASTing "aceto1" against "aceto".. {'aceto'}, 1, false, 10^-30, 150, 35); {'aceto'}, 1, false, 10^-30, 150, 35); ↑ Invalid expression. When calling a function or indexing a variable, use parentheses. Otherwise, check for mismatched delimiters.

model = getModelFromHomology({modelaceto}, blast, 'aceto1', ... {'aceto'}, 1, false, 10^-30, 150, 35); Error using getModelFromHomology (line 145) Less than 5% of the genes in the template model with model.id "aceto" can be found in the blastStructure. Ensure that the protein FASTA used in getBlast and the template model used in getModelFromHomology use the same style of gene identifiers

[edkerk]

From the warning message that is thrown when you load the model, we can see that a typical gene is formatted like “H16_B2371”. The CN.faa file that you use as input to getBlast uses some other style identifiers. This is why getModelFromHomology complains of non-matching of identifiers beteen the FASTA file and the template model.