Is there any tool or script or package to download the KEGG gene sequence in fasta format by KO ids?
I have list of KO's.
It would help if you post some example KOs here. Use keggrest and user manual here. Sequence object is biostrings. You can write them to hdd in fasta format using biostrings package (writeXStringSet function). Try below example code and example kegg IDs are taken from manual::
test.seq=keggGet(c("hsa:10458", "ece:Z5100"), "ntseq")
writeXStringSet(test.seq,"temp.fa", format = "fasta")