Hello everyone!
I'm thinking of getting the KEGG/Koala/Kofamscan output of around 50 bacteria.
The output should be something like this:
gene_01 K?????
gene_02 K?????
gene_03 K?????
Usually I would get the genome from NCBI, annotate the genes using RAST or other gene annotation tools, then run the AA fasta into Kofamscan to get the final output.
I was just wondering if there is a way to get the KO output file directly.
Bioinformatics is not our strong suit so I usually try out things as I go about our research.
Thank you in advance!
-Adham
Edit: Deleted this part as I realized that you cannot get the htext for KOs from BRITE; and I manually edited the pathway htext:
I tried manually editing the htext files but it takes a bit of time...
I have old code that rips this using KEGGREST. Not guaranteed to be most efficient but should suit you.
library(KEGGREST)
res <- keggLink('pathway', 'hsa')
pathways <- data.frame(
kegg_gene_id=names(res),
kegg_pathway_id=as.character(res)
)
do.query <- function(id_lst) {
res <- list()
i <- 1
while ( i < length(id_lst) ) {
j <- min(length(id_lst), i+9)
qry <- keggGet(id_lst[i:j])
res <- c(res, qry)
i <- j + 1
}
res
}
ids <- unique(pathways$kegg_pathway_id)
res <- do.query(ids)
path2name <- data.frame(
kegg_pathway_id=ids,
pathway_name=sapply(res, function(x) { x$NAME})
)
ids <- unique(pathways$kegg_gene_id)
res <- do.query(ids)
gene2name <- data.frame(
kegg_gene_id=ids,
gene_name=sapply(res, function(x) { x$NAME }),
gene_symbol=sapply(res, function(x) { gsub('([^,]+).*', '\\1', x$SYMBOL) })
)
pathways <- merge(pathways, path2name, by='kegg_pathway_id')
pathways <- merge(pathways, gene2name, by='kegg_gene_id')
head(pathways)
Thank you for this!
Tried installing KEGGREST but kept running into problems during installation.
I'll try looking into it some more and will try to add updates.
-Adham
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