Hi,
I’ve been using the UniProt.ws since a while now, never really had issues with it until now. When I now try to extract some data using select, it works fine and retrieve data correctly, but it is now so slow that it's impossible to use. It’s never been really fast, but it was more than fast enough for several hundred /thousand of keys. Currently, a quick test with microbenchmark shows that it takes select about 5/12/16s to extract 8 columns for 1/8/15 keys. I did the test with so little keys because for higher numbers it’s just hanging. I tried to update all packages and the rest, but I didn't see any changes. What am I missing? Thanks!
Here’s a quick version of the code I used to test:
library("microbenchmark")
libraryUniProt.ws)
UniprotDB <- UniProt.ws(10090)
For_uniprot_Mapping <- c("Q3TX55", "S4R267","A2A9P6", "D3YXA2", "Q80TM9", "Q6RT24", "Q5RJH6", "Q8JZM", "Q00519", "Q9D0B8","Q9WUM5","Q8R3E3", "R4GML0","E9PV80","Q8BJF9")
Uniprot_search1 <- c("PROTEIN-NAMES", "GENES","ENTRY-NAME", "UNIGENE", "ENSEMBL", "ENTREZ_GENE", "LENGTH", "SCORE")
microbenchmark (
select(UniprotDB, keys = For_uniprot_Mapping[1:2], columns = Uniprot_search1, keytype = "UNIPROTKB"),
select(UniprotDB, keys = For_uniprot_Mapping[1:8], columns = Uniprot_search1, keytype = "UNIPROTKB"),
select(UniprotDB, keys = For_uniprot_Mapping[1:15], columns = Uniprot_search1, keytype = "UNIPROTKB"),
times = 3)
The session info is as follow:
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BiocInstaller::biocValid() [1] TRUE |
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Alright then. In this case, I'll wait for UniProt to finish their transition to https and see whether after update(s) if that gets back to normal then. Would make total sense. Will see with them afterwards if the issue remains. Thanks a lot!
I’ve done some more tests and for what I can see: