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[GuangchuangYu]

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[huerqiang]

Hi Nitesh, I don't know why you said our code was wrong. Have you try to download files from 'https://rest.kegg.jp/link/hsa/pathway' and 'https://rest.kegg.jp/link/pathway/hsa'? Best wishes, Erqiang Hu At 2022-08-11 04:44:00, "Nshriwash" ***@***.***> wrote: Hi GuangyuangYu, I am encountering an error in your code and found the bug. "Reading KEGG annotation online: fail to download KEGG data... Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... In addition: Warning message: In utils::download.file(url, quiet = TRUE, method = method, ...) : URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'Failure when receiving data from the peer' ..." I am getting this error while using enrichKEGG(). I trace it back into the source code and find that there is an error in source code of download.KEGG.Path() and kegg_link(). the argument passed in kegg_link in download.KEGG.Path function is different from what is required in source code of kegg_link(). Here is the piece of code with bugs: `download.KEGG.Path <- function(species) { keggpathid2extid.df <- kegg_link(species, "pathway") if (is.null(keggpathid2extid.df)) { message <- paste("Failed to download KEGG data.", "Wrong 'species' or the network is unreachable.", "The 'species' should be one of organisms listed in", "'https://www.genome.jp/kegg/catalog/org_list.html'") stop(message) } keggpathid2extid.df[,1] %<>% gsub("[^:]+:", "", .) keggpathid2extid.df[,2] %<>% gsub("[^:]+:", "", .) keggpathid2name.df <- kegg_list("pathway") keggpathid2name.df[,1] %<>% gsub("path:map", species, .) ## if 'species="ko"', ko and map path are duplicated, only keep ko path. ## ## https://www.kegg.jp/dbget-bin/www_bget?ko+ko00010 ## https://www.kegg.jp/dbget-bin/www_bget?ko+map0001 ## keggpathid2extid.df <- keggpathid2extid.df[keggpathid2extid.df[,1] %in% keggpathid2name.df[,1],] return(list(KEGGPATHID2EXTID=keggpathid2extid.df, KEGGPATHID2NAME=keggpathid2name.df)) } kegg_link <- function(target_db, source_db) { url <- paste0("https://rest.kegg.jp/link/", target_db, "/", source_db, collapse="") kegg_rest(url) }` here target_db must be "pathway" and source_db should be "species". But kegg_link in download.KEGG.Path giving "pathway" as a source_db and "species" as a target_db. right link = "https://rest.kegg.jp/link/<target_db>/<source_db>" resulting link from download.KEGG.Path = "https://rest.kegg.jp/link/<source_db>/<target_db>" which is wrong link. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>