Closed JosuaCarl closed 2 years ago
Hi @JosuaCarl
this sounds strange indeed! I need a bit more details to see what is going wrong. Do you mind providing your draft model plus temporary files (rxnWeights.RDS, rxnXgenes.RDS) and the actual command you used for gapseq fill
?
Hi @jotech So, I think I already got a little bit at what went wrong. I naively tried to use gapseq fill on my own model, which was drafted by CarveMe and used the naming convention from BiGG, while gapseq relies on Model SEED. I uses the rxnWeights and rxnXgenes, from gapseq find/find-transport/draft from the gene sequence of my organism. I suspect that the non matching sets of identifiers caused no ec-codes to be appended to the dataframe. The difference in naming convention unfortunatrly also makes it infeasible for me to compare both models, even when I use the completed draft by gapseq, but the method (gapseq fill) now works as it should. Thank you very much for your reply.
i see this makes sense and I agree the differences in namespace definitely caused the errors you encountered! For comparing bigg and seed namespaces, you might have a look at:
which at least could at assist you in matching reactions ids. In addition, comparing model quality by using memote (https://memote.io) or the predicted phenotype vs. literature/databases (e.g. https://bacdive.dsmz.de/) could maybe another alternative?
Hello, when I am executing gapseq fill with my model, in the end I get:
And when I print out mod@react_attr in the R file addReactAttr.R, I see, that it does not have a column named ec.
I would be very glad to find out the cause of the error.