error with a function to retrieve data from a database

Question

I am trying to get a FASTA file form NCBI website, I use the following function

getncbiseq <- function(accession){
  dbs <- c()
  for (i in 1:numdbs){         


        

Answer 1

Thanks for great help. I was stuck at this point for a full day. I finally got the following code worked under windows 10 with R3.4.0(32bits):-

getncbiseq <- function(accession)
{
require("seqinr") # this function requires the SeqinR R package
# first find which ACNUC database the accession is stored in:
dbs <- c("genbank","refseq","refseqViruses","bacterial")
numdbs <- length(dbs)
for (i in 1:numdbs)
{
db <- dbs[i]
choosebank(db)
# check if the sequence is in ACNUC database 'db':
resquery <- try(query(".tmpquery", paste("AC=", accession)), silent = TRUE)

if (!(inherits(resquery, "try-error"))) {
  queryname <- "query2"
  thequery <- paste("AC=", accession, sep="")
  query2 <- query(queryname, thequery)
  # see if a sequence was retrieved:
  seq <- getSequence(query2$req[[1]])
  closebank()
  return(seq)
}
closebank()
}
print(paste("ERROR: accession",accession,"was not found"))
}