Open missuse opened 2 years 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'
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 Could it be that in the above link its simple an outdated prediction file which was removed from the server?
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'
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.
Yes I have the same error every time I use, I get the same error when I try (get_netGPI) as well. Thank you
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
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.
Ok I am trying it now thank you for your help
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.