Error with function to retrieve data from database

Question

I am trying to get a FASTA form file on the NCBI site, I am using the following function

getncbiseq <- function(accession){
  dbs <- c()
  for (i in 1:numdbs){
    db <- dbs[i]
    choosebank(db)
    resquery <- try(query(".tmpquery", paste("AC=", accession)),silent = TRUE)
    if (!(inherits(resquery, "try-error"))){
      queryname <- "query2"
      thequery <- paste("AC=",accession,sep="")
      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"))
}    

When I try to get a sequence

mydata <- getncbiseq("NC_001477")

Error in getSequence (query2 $ req [[1]]): object 'query2' not found

Is there a better way to shorten this loop function?

if i use

query('queryname','the query')
#or 
query("queryname","thequery")

I get another error

Error in the query ("queryname", "thequery"): invalid query: "unknown list in (^): \" (^) thequery \ ""

Answer 1

I think you intended to assign your call to a query()variable with a name query2, but you forgot to do it. Try the following:

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)
}

, , , , .

Update:

, sapply dbs (, R):

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"))
}

result , .

Answer 2

. . , , Windows 10 R3.4.0 (32 ): -

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"))
}