Several functions no longer working

[PhilPlantMan]

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!

[missuse]

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

[missuse]

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

[PhilPlantMan]

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