Question

uniprot.ws select error

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Apoorva ▴ 10

@apoorva-24217

Last seen 3.2 years ago

Hello, i am trying to recreate the example on uniprot.ws documentation but i am getting an error. Both the code and error are shown below. Can someone please help where am i going wrong?


f (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("UniProt.ws")
library(UniProt.ws)
up <- UniProt.ws(taxId=9606)
select(up, keys=c("P31946","P62258"), columns=c("PDB","SEQUENCE"),
       keytype="UNIPROTKB")

error: Getting mapping data for P31946 ... and PDB_ID error while trying to retrieve data in chunk 1: no results after 5 attempts; please try again later continuing to try Getting extra data for P31946, P62258 Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column

UniProt.ws • 1.3k views

ADD COMMENT • link 3.4 years ago Apoorva ▴ 10

score 0 · Answer 1 · 2020-11-23

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 hour ago

United States

That is apparently a problem with the Windows version of RCurl, which seems to be due to being built against an old version of OpenSSL. Unfortunately, RCurl is a CRAN package, so we will have to interface with the maintainer over there. It does work on Linux fwiw, so if you have access to a different OS (or you could use a docker image).

ADD COMMENT • link 3.4 years ago James W. MacDonald 65k

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Thank you Mr. James for your reply. Rstudio was showing me that i have updates available for certain packages. I updated those and the code works now.

ADD REPLY • link 3.4 years ago Apoorva ▴ 10

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Really? Will you provide the output from running sessionInfo() after running the code?

ADD REPLY • link 3.4 years ago James W. MacDonald 65k

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sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 10586)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] parallel stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] bio3d_2.4-1 UniProt.ws_2.30.0 BiocGenerics_0.36.0 [4] RCurl_1.98-1.2 RSQLite_2.2.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.5 compiler_4.0.3 pillar_1.4.7
[4] BiocManager_1.30.10 dbplyr_2.0.0 bitops_1.0-6
[7] tools_4.0.3 digest_0.6.27 bit_4.0.4
[10] BiocFileCache_1.14.0 memoise_1.1.0 lifecycle_0.2.0
[13] tibble_3.0.4 pkgconfig_2.0.3 rlang_0.4.8
[16] DBI_1.1.0 curl_4.3 dplyr_1.0.2
[19] httr_1.4.2 generics_0.1.0 S4Vectors_0.28.0
[22] vctrs_0.3.5 IRanges_2.24.0 rappdirs_0.3.1
[25] grid_4.0.3 stats4_4.0.3 bit64_4.0.5
[28] tidyselect_1.1.0 glue_1.4.2 Biobase_2.50.0
[31] R6_2.5.0 AnnotationDbi_1.52.0 purrr_0.3.4
[34] blob_1.2.1 magrittr_2.0.1 ellipsis_0.3.1
[37] assertthat_0.2.1 crayon_1.3.4

and this is the code :

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("UniProt.ws")
suppressPackageStartupMessages(library(UniProt.ws))
up <- UniProt.ws(taxId=9606)
info<-select(up, keys=c("Q5S007"), columns=c("PDB","LENGTH"),
             keytype="UNIPROT")

But I feel this is too tricky. Like in some trials the code works and in some it does not. When I tried using functions from Bio3d in this code, it did not work. So, I really don't know what is making the code work. Basically it is not reproducible.

ADD REPLY • link 3.4 years ago Apoorva ▴ 10