Open kijavko opened 2 years ago
Nice find, I was not aware Signalp6 was out.
I checked the speed of the fast method with five test sequences. It finished in 30s which is not that bad. The mirror https://dtu.biolib.com/SignalP-6 doesn't seem to work.
It seems the group changed the way the server code is presented.
The link: https://services.healthtech.dtu.dk/services/SignalP-6.0/1-Submission.php
seems to contain the familiar web form.
@kijavko could you try to make a get_signalp6
using get_signalp5
code as template? If any problems arise I can take a look.
Key code:
url <- "https://services.healthtech.dtu.dk/cgi-bin/webface2.fcgi"
cfg <- "/var/www/html/services/SignalP-6.0/webface.cf"
file_up <- httr::upload_file("test.fa")
res <- httr::POST(
url = url,
encode = "multipart",
body = list(
`configfile` = cfg,
`uploadfile` = file_up,
`organism` = "Eukarya",
`format` = "short",
`mode` = "fast"
))
Hi @missuse,
I really love this package and I really wish I had the capacity to contribute to it....this is at the top of my list when I have time! In the mean time, I don't suppose you have any capacity to look at this issue? get_signalp is returning a server error when I try to run it and I think it might be related to this issue. I recently published a paper that uses this package (I did cite you!) and now I realise my code is broken. Kind regards, Phil
Hi @PhilPlantMan,
glad you are still using the package! Thanks for the citation.
Your contributions will be welcome when ever you have time.
I have sketched a direction with some issues https://github.com/missuse/ragp/issues, but haven't had the time to implement these functionalities yet.
If you have ideas please open a issue or a PR.
The current issue is about implementing a function that queries Signalp version 6 based on the transformer protein language. It is not related to your problem simply because this is not yet implemented in ragp.
Regarding the current problem you are experiencing. I have installed the last version of ragp and run this:
library(ragp)
#> This is ragp >= 0.3.5 which adds several new features and consequently breaking changes.
#> Please read the NEWS: https://github.com/missuse/ragp/blob/master/NEWS.md.
#> If you encounter any problems please report them:
#> https://github.com/missuse/ragp/issues
data(at_nsp)
get_signalp(data = at_nsp[1:13,],
sequence,
Transcript.id,
progress = TRUE)
#> | | | 0% | |======================================================================| 100%
#> id Cmax Cmax.pos Ymax Ymax.pos Smax Smax.pos Smean Dmean is.sp
#> 1 ATCG00660.1 0.210 30 0.162 30 0.260 2 0.146 0.154 N
#> 2 AT2G43600.1 0.860 23 0.894 23 0.984 13 0.930 0.913 Y
#> 3 AT2G28410.1 0.779 23 0.826 23 0.940 15 0.877 0.853 Y
#> 4 AT2G22960.1 0.701 23 0.790 23 0.948 15 0.891 0.844 Y
#> 5 AT2G19580.1 0.422 26 0.586 26 0.885 17 0.798 0.671 Y
#> 6 AT2G19690.2 0.797 29 0.870 29 0.987 18 0.952 0.914 Y
#> 7 AT2G19690.1 0.797 29 0.870 29 0.987 18 0.952 0.914 Y
#> 8 AT2G33130.1 0.318 33 0.530 27 0.990 16 0.933 0.748 Y
#> 9 AT2G05520.1 0.633 24 0.782 24 0.990 16 0.966 0.881 Y
#> 10 AT2G05520.2 0.633 24 0.782 24 0.990 16 0.966 0.881 Y
#> 11 AT2G05520.3 0.633 24 0.782 24 0.989 16 0.965 0.881 Y
#> 12 AT2G05520.4 0.633 24 0.782 24 0.989 16 0.965 0.881 Y
#> 13 AT2G05520.6 0.633 24 0.782 24 0.989 16 0.965 0.881 Y
#> Dmaxcut Networks.used is.signalp sp.length
#> 1 0.450 SignalP-noTM FALSE 30
#> 2 0.450 SignalP-noTM TRUE 23
#> 3 0.450 SignalP-noTM TRUE 23
#> 4 0.450 SignalP-noTM TRUE 23
#> 5 0.500 SignalP-TM TRUE 26
#> 6 0.450 SignalP-noTM TRUE 29
#> 7 0.450 SignalP-noTM TRUE 29
#> 8 0.450 SignalP-noTM TRUE 27
#> 9 0.450 SignalP-noTM TRUE 24
#> 10 0.450 SignalP-noTM TRUE 24
#> 11 0.450 SignalP-noTM TRUE 24
#> 12 0.450 SignalP-noTM TRUE 24
#> 13 0.450 SignalP-noTM TRUE 24
get_signalp5(data = at_nsp[1:13,],
sequence,
Transcript.id,
progress = TRUE)
#> batch 1 jobid is: 62B46991000058867DBE69D3
#> id Prediction SP.Sec.SPI Other CS_pos Pr cleave.site
#> 1 ATCG00660.1 OTHER 0.000375 0.999625 NA
#> 2 AT2G43600.1 SP(Sec/SPI) 0.999802 0.000198 22-23 0.9639 VFS-QN
#> 3 AT2G28410.1 SP(Sec/SPI) 0.990424 0.009576 22-23 0.8897 ALA-QD
#> 4 AT2G22960.1 SP(Sec/SPI) 0.998142 0.001858 22-23 0.9424 AES-GS
#> 5 AT2G19580.1 OTHER 0.264792 0.735208 NA
#> 6 AT2G19690.2 SP(Sec/SPI) 0.989540 0.010460 28-29 0.9030 ARS-EE
#> 7 AT2G19690.1 SP(Sec/SPI) 0.989540 0.010460 28-29 0.9030 ARS-EE
#> 8 AT2G33130.1 SP(Sec/SPI) 0.959278 0.040722 26-27 0.5119 VVG-SR
#> 9 AT2G05520.1 SP(Sec/SPI) 0.999493 0.000507 23-24 0.5666 VAA-AS
#> 10 AT2G05520.2 SP(Sec/SPI) 0.999493 0.000507 23-24 0.5666 VAA-AS
#> 11 AT2G05520.3 SP(Sec/SPI) 0.999416 0.000584 23-24 0.5699 VAA-AS
#> 12 AT2G05520.4 SP(Sec/SPI) 0.999419 0.000581 23-24 0.5677 VAA-AS
#> 13 AT2G05520.6 SP(Sec/SPI) 0.999419 0.000581 23-24 0.5677 VAA-AS
#> is.signalp sp.length
#> 1 FALSE NA
#> 2 TRUE 22
#> 3 TRUE 22
#> 4 TRUE 22
#> 5 FALSE NA
#> 6 TRUE 28
#> 7 TRUE 28
#> 8 TRUE 26
#> 9 TRUE 23
#> 10 TRUE 23
#> 11 TRUE 23
#> 12 TRUE 23
#> 13 TRUE 23
Created on 2022-06-23 by the reprex package (v2.0.1)
As far as I can tell it is working normally.
Potential causes of your problem:
Hi @PhilPlantMan,
glad you are still using the package! Thanks for the citation.
Your contributions will be welcome when ever you have time.
I have sketched a direction with some issues https://github.com/missuse/ragp/issues, but haven't had the time to implement these functionalities yet.
If you have ideas please open a issue or a PR.
The current issue is about implementing a function that queries Signalp version 6 based on the transformer protein language. It is not related to your problem simply because this is not yet implemented in ragp.
Regarding the current problem you are experiencing. I have installed the last version of ragp and run this:
library(ragp) #> This is ragp >= 0.3.5 which adds several new features and consequently breaking changes. #> Please read the NEWS: https://github.com/missuse/ragp/blob/master/NEWS.md. #> If you encounter any problems please report them: #> https://github.com/missuse/ragp/issues data(at_nsp) get_signalp(data = at_nsp[1:13,], sequence, Transcript.id, progress = TRUE) #> | | | 0% | |======================================================================| 100% #> id Cmax Cmax.pos Ymax Ymax.pos Smax Smax.pos Smean Dmean is.sp #> 1 ATCG00660.1 0.210 30 0.162 30 0.260 2 0.146 0.154 N #> 2 AT2G43600.1 0.860 23 0.894 23 0.984 13 0.930 0.913 Y #> 3 AT2G28410.1 0.779 23 0.826 23 0.940 15 0.877 0.853 Y #> 4 AT2G22960.1 0.701 23 0.790 23 0.948 15 0.891 0.844 Y #> 5 AT2G19580.1 0.422 26 0.586 26 0.885 17 0.798 0.671 Y #> 6 AT2G19690.2 0.797 29 0.870 29 0.987 18 0.952 0.914 Y #> 7 AT2G19690.1 0.797 29 0.870 29 0.987 18 0.952 0.914 Y #> 8 AT2G33130.1 0.318 33 0.530 27 0.990 16 0.933 0.748 Y #> 9 AT2G05520.1 0.633 24 0.782 24 0.990 16 0.966 0.881 Y #> 10 AT2G05520.2 0.633 24 0.782 24 0.990 16 0.966 0.881 Y #> 11 AT2G05520.3 0.633 24 0.782 24 0.989 16 0.965 0.881 Y #> 12 AT2G05520.4 0.633 24 0.782 24 0.989 16 0.965 0.881 Y #> 13 AT2G05520.6 0.633 24 0.782 24 0.989 16 0.965 0.881 Y #> Dmaxcut Networks.used is.signalp sp.length #> 1 0.450 SignalP-noTM FALSE 30 #> 2 0.450 SignalP-noTM TRUE 23 #> 3 0.450 SignalP-noTM TRUE 23 #> 4 0.450 SignalP-noTM TRUE 23 #> 5 0.500 SignalP-TM TRUE 26 #> 6 0.450 SignalP-noTM TRUE 29 #> 7 0.450 SignalP-noTM TRUE 29 #> 8 0.450 SignalP-noTM TRUE 27 #> 9 0.450 SignalP-noTM TRUE 24 #> 10 0.450 SignalP-noTM TRUE 24 #> 11 0.450 SignalP-noTM TRUE 24 #> 12 0.450 SignalP-noTM TRUE 24 #> 13 0.450 SignalP-noTM TRUE 24 get_signalp5(data = at_nsp[1:13,], sequence, Transcript.id, progress = TRUE) #> batch 1 jobid is: 62B46991000058867DBE69D3 #> id Prediction SP.Sec.SPI Other CS_pos Pr cleave.site #> 1 ATCG00660.1 OTHER 0.000375 0.999625 NA #> 2 AT2G43600.1 SP(Sec/SPI) 0.999802 0.000198 22-23 0.9639 VFS-QN #> 3 AT2G28410.1 SP(Sec/SPI) 0.990424 0.009576 22-23 0.8897 ALA-QD #> 4 AT2G22960.1 SP(Sec/SPI) 0.998142 0.001858 22-23 0.9424 AES-GS #> 5 AT2G19580.1 OTHER 0.264792 0.735208 NA #> 6 AT2G19690.2 SP(Sec/SPI) 0.989540 0.010460 28-29 0.9030 ARS-EE #> 7 AT2G19690.1 SP(Sec/SPI) 0.989540 0.010460 28-29 0.9030 ARS-EE #> 8 AT2G33130.1 SP(Sec/SPI) 0.959278 0.040722 26-27 0.5119 VVG-SR #> 9 AT2G05520.1 SP(Sec/SPI) 0.999493 0.000507 23-24 0.5666 VAA-AS #> 10 AT2G05520.2 SP(Sec/SPI) 0.999493 0.000507 23-24 0.5666 VAA-AS #> 11 AT2G05520.3 SP(Sec/SPI) 0.999416 0.000584 23-24 0.5699 VAA-AS #> 12 AT2G05520.4 SP(Sec/SPI) 0.999419 0.000581 23-24 0.5677 VAA-AS #> 13 AT2G05520.6 SP(Sec/SPI) 0.999419 0.000581 23-24 0.5677 VAA-AS #> is.signalp sp.length #> 1 FALSE NA #> 2 TRUE 22 #> 3 TRUE 22 #> 4 TRUE 22 #> 5 FALSE NA #> 6 TRUE 28 #> 7 TRUE 28 #> 8 TRUE 26 #> 9 TRUE 23 #> 10 TRUE 23 #> 11 TRUE 23 #> 12 TRUE 23 #> 13 TRUE 23
Created on 2022-06-23 by the reprex package (v2.0.1)
As far as I can tell it is working normally.
Potential causes of your problem:
- outdated ragp version - previous version used parallel queries to the server, this is no longer permitted.
- SignalP allows one concurrent job per ip, if a job hangs, or takes a long time and you press stop while running the R function the server will not permit the next job to be run. Try to run the query directly on the server, if you get the error also there then it means you must change your ip or wait it out.
Thank you so much for your reply! I shall try out what you suggested now. All the best, Phil
I also tried:
get_signalp5(data = at_nsp[1:200,],
sequence,
Transcript.id,
progress = TRUE,
splitter = 100)
so that the data gets split into batches and processed, and it works as expected also. If you can provide a reproducible example of the problem I will give it a look.
Hi @missuse Updating the package did the trick; I feel foolish not trying this first! I'm very grateful for your help (and the creation of this great tool!) All the best Phil
SignalP6 is available https://www.biorxiv.org/content/10.1101/2021.06.09.447770v1.full, https://services.healthtech.dtu.dk/service.php?SignalP. It seems slow currently but it would be nice if ragp supported communication with it.