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- library("seqinr")
- 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"))
- }
- dengueseq <- getncbiseq("NC_001477")
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