Closed PhilPlantMan closed 3 years ago
Hello
Thanks for the report. I was starting to get worried no one uses my package.
I was able to reproduce the problem and will try to get to the bottom of it asap.
All the best,
Milan
EDIT. I was able to find and fix the problem for get_phobius
. The server address changed from http...
to https..
. Will update when I see what I can do with get_big_pi
This should be resolved after reinstalling ragp
devtools::install_github("missuse/ragp")
library(ragp)
ids <- c("Q9FLL2",
"Q9LS14",
"Q9S7I8",
"Q9M2Z2",
"Q9FIN5")
seqs <- unlist(protr::getUniProt(ids))
p1 <- get_big_pi(sequence = seqs,
id = ids)
p1
id is.gpi Quality omega_site PValue
1 Q9FLL2 FALSE None 481 0.5643914
2 Q9LS14 FALSE None 233 0.4607197
3 Q9S7I8 FALSE None 409 0.4728589
4 Q9M2Z2 FALSE None 283 0.6891588
5 Q9FIN5 FALSE None 162 0.1168932
p2 <- get_phobius(sequence = seqs,
id = ids)
p2
Name tm sp prediction cut_site is.phobius
1 Q9FLL2 1 Y n11-22c27/28o282-305i 28 TRUE
2 Q9LS14 2 0 i161-180o192-213i <NA> FALSE
3 Q9S7I8 0 0 i <NA> FALSE
4 Q9M2Z2 0 0 i <NA> FALSE
5 Q9FIN5 0 Y n9-19c30/31o 31 TRUE
If you confront any additional problems, or have ideas on how to enhance ragp please let me know. Especially in terms of interesting web servers that could be scraped.
Thanks for the report.
Kind regards,
Milan
Its a great package! Many thanks for sorting this so quickly and I can confirm this is now working for me. Looking to publish relatively soon so will definitely cite your work!
All the best Phil
Hello, Thank you for providing these tools, they are very useful. All these tools were working several months ago (apart from get_netGPI but I see you've fixed this now...thanks!!) but unfortunately I can no longer get get_big_pi or get_phobius to work anymore. Any ideas what the problem might be?
For get_phobius I get this error: Error in (grep("SEQENCE", res) + 1):(grep("_uacct", res) - 1) :
And for get_big_pi I get this error: Error in strsplit(resulti, "Query sequence")[[1]] : subscript out of bounds
I don't think it is me because it works for other 'get' functions and I'm following the vignette closely. Cheers in advance!