cannot open the connection to NetGPI

missuse commented 2 years ago

EDIT: 11.07.2024. Discussion is about issue reported by MohamedBelal999 in the next comment.

Original issue: Given a sliding window (which can be changed) find regions with biased amino acid composition. What is a biased composition should be defined by an argument.

Need to think about an efficient implementation. Perhaps this is already implemented.

MohamedBelal999 commented 1 month ago

I have this error: cannot open the connection to 'https://services.healthtech.dtu.dk/services/NetGPI-1.1/tmp/668DA0120027B9E1CEC1EF97/output_protein_type.txt'

missuse commented 1 month ago

Hi MohamedBelal999, could you post the code you used and the error?

EDIT: when I check

library(ragp)
netGPI_pred <- get_netGPI(data = at_nsp[1:10,],
                          sequence,
                          Transcript.id)
netGPI_pred
#output:
            id length is.gpi omega_site likelihood
1  ATCG00660.1    117  FALSE         NA      0.996
2  AT2G43600.1    273  FALSE         NA      0.992
3  AT2G28410.1    115   TRUE         95      0.321
4  AT2G22960.1    184  FALSE         NA      0.993
5  AT2G19580.1    270  FALSE         NA      0.988
6  AT2G19690.2    148  FALSE         NA      0.992
7  AT2G19690.1    147  FALSE         NA      0.994
8  AT2G33130.1    103  FALSE         NA      0.987
9  AT2G05520.1    145  FALSE         NA      0.993
10 AT2G05520.2    138  FALSE         NA      0.993

it works and returns the predictions. Could it be that in the above link its simple an outdated prediction file which was removed from the server?

MohamedBelal999 commented 1 month ago

Hi Milan I used this code and I have this error

p1 <- plot_prot(sequence = seqs,

id = ids) Error in file(file, "rt") : cannot open the connection to 'https://services.healthtech.dtu.dk/services/NetGPI-1.1/tmp/668DA46F0027C21F71324025/output_protein_type.txt' In addition: Warning message: In file(file, "rt") : cannot open URL 'https://services.healthtech.dtu.dk/services/NetGPI-1.1/tmp/668DA46F0027C21F71324025/output_protein_type.txt': HTTP status was '404 Not Found'

missuse commented 1 month ago

And this happens reproducibly every time you run the code you get the same error? I've checked plot_prot and it seems I am having a problem with get_phobius. Will investigate

EDIT: httr::set_config(httr::config(ssl_verifypeer = 0L))

and

library(ragp)
library(ggplot2)
ind <- c(23, 5, 80, 81, 345)
tm <- get_phobius(data = at_nsp[ind,],
                  id = Transcript.id,
                  sequence = sequence)

seems to work. I think phobius has a problem with SSL certificate.

MohamedBelal999 commented 1 month ago

Yes I have the same error every time I use, I get the same error when I try (get_netGPI) as well. Thank you

missuse commented 1 month ago

You could try to call plot_plot more manually:


library(ragp)
library(ggplot2)
ind <- c(23, 5, 80, 81, 345)
httr::set_config(httr::config(ssl_verifypeer = 0L)) #due to phobius SSL problem

pred <- plot_prot(sequence = at_nsp$sequence[ind],
                  id = at_nsp$Transcript.id[ind])

nsp <- get_signalp(data = at_nsp[ind,],
                   id = Transcript.id,
                   sequence = sequence)

hmm <- get_hmm(data = at_nsp[ind,], #default is to use get_cdd()
               id = Transcript.id,
               sequence = sequence) 

gpi <- get_netGPI(data = at_nsp[ind,],
                  id = Transcript.id,
                  sequence = sequence)                                    

tm <- get_phobius(data = at_nsp[ind,],
                  id = Transcript.id,
                  sequence = sequence)                                                        

disorder <- get_espritz(data = at_nsp[ind,],    
                        id = Transcript.id, 
                        sequence = sequence)

pred2 <- plot_prot(sequence = at_nsp$sequence[ind],
                   id = at_nsp$Transcript.id[ind],
                   tm = tm,
                   nsp = nsp,
                   gpi = gpi,
                   domain = hmm,
                   disorder = disorder)

I will investigate in the next few days and post my findings

missuse commented 1 month ago

I have checked the functions accessing different servers, the situation is:

get_phobius does not work due to server not being able to process requests. This happens in browser also: The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later. I expect this to be resolved server side at some point.

get_pred_gpi does not work due to server being replaced with another prediction server for TransMembrane β-Barrel (TMBB) detection. I will check if the server was moved to another address and if yes if its possible to communicate with it from R.

All others seem to work without issues.

MohamedBelal999 commented 1 month ago

Ok I am trying it now thank you for your help

missuse / ragp

cannot open the connection to NetGPI #11