about a year ago I wrote a simple wrapper for
KEGGREST to generate a collection of modules and pathways for a particular organism in the form of
.gmt file, which is very useful for gene set enrichment tools like
fgsea. Coming back to use the code a year later, I discovered that
keggGet command started to fail when trying to retrieve modules (but not pathways).
For example, for Salmonella Typhimurium LT2 (KEGG organism code
stm), modules are named something like
md:stm_M00841, and pathways have a format like
path:stm03440. Running the two commands produces very different outputs though:
keggGet("path:stm00550")` > [] []$ENTRY Pathway "stm00550" > > []$NAME  "Peptidoglycan biosynthesis - Salmonella enterica > subsp. enterica serovar Typhimurium LT2" > .................................. keggGet("md:stm_M00841")` >Error in .getUrl(url, .flatFileParser) : Not Found (HTTP 404).
Any ideas why this would happen? Thank you in advance. Below is the output of
> sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8.1 x64 (build 9600) > Matrix products: default > > locale:  LC_COLLATE=Russian_Russia.1251 > LC_CTYPE=Russian_Russia.1251 LC_MONETARY=Russian_Russia.1251 > LC_NUMERIC=C LC_TIME=Russian_Russia.1251 > > attached base packages:  stats graphics grDevices utils > datasets methods base > > other attached packages:  KEGGREST_1.24.1 > > loaded via a namespace (and not attached):  zlibbioc_1.30.0 > httr_1.4.1 compiler_3.6.1 R6_2.4.1 > IRanges_2.18.3 XVector_0.24.0 parallel_3.6.1 > tools_3.6.1  curl_4.2 Biostrings_2.52.0 > S4Vectors_0.22.1 BiocGenerics_0.30.0 stats4_3.6.1 png_0.1-7