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

I think you intended to assign your call to query() to a variable called query2, but you forgot to do it. Try this:

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)
}

As you mentioned, the rest of your code also has some quirks and kinks which could probably be improved upon.

Update:

Here is a refactor of your code using sapply on the dbs vector instead of an explicit for loop (the latter which is usually frowned upon by R people):

processdbs <- function(x, y) {
    choosebank(x)
    resquery <- try(query(".tmpquery", paste("AC=", y)), silent = TRUE)
    if (!(inherits(resquery, "try-error"))) {
      queryname <- "query2"
      thequery  <- paste("AC=", y, sep="")
      query2 <- query(queryname, thequery)

      # see if a sequence was retrieved:
      seq <- getSequence(query2$req[[1]])
      closebank()
      return(seq)
    }
    closebank()
}

getncbiseq <- function(accession) {
   dbs <- c("genbank","refseq","refseqViruses","bacterial")
   result <- sapply(dbs, processdbs, y=accession)
   closebank()

   print(paste("ERROR: accession",accession,"was not found"))
}

You may have to do a slight amount of additional work to inspect the result vector and determine whether a sequence was retrieved anywhere.