R/where.is.this.acc.R

In seqinr: Biological Sequences Retrieval and Analysis

where.is.this.acc <- function(acc, stopAtFirst = TRUE, ...){
    #
    # Argument check:
    #
    if(!is.character(acc)) stop("string expected for argument acc")
    #
    result <- character(0)
    #
    cat("Looking for available databases\n")  
    banks <- choosebank(...)
    nbanks <- length(banks)
    cat(paste("Looking for sequence with accession number", acc,
              "in the following ACNUC databases:\n"))
    print(banks)
    #
    # Looping over banks:
    #
    for(i in seq_len(nbanks)){
        cat(paste("\nTrying to open bank with name --->", banks[i], 
                  "<--- ...", sep = ""))
        bkopenres <- try(choosebank(banks[i]))
        if(inherits(bkopenres, "try-error")){
            cat("... opening not OK, skipping this bank.\n")
        } else {
            cat("... and opening was OK.\n")
            cat(paste("==> Trying to find sequence", acc, "in bank", 
                      banks[i], "..."))
            resquery <- try(query(".tmpquery", paste("AC=", acc)), silent = TRUE)
            if(inherits(resquery, "try-error")){
                cat("... not found here.\n")
            } else {
                cat("... *** FOUND *** here.\n")
                result <- c(result, banks[i])
            }
            closebank()
            if(length(result) != 0 && stopAtFirst){
                return(invisible(result))
            }
        }
    }
    #
    # Print result summary:
    #
    cat("\n\n")
    if(length(result) == 0){
        cat(paste("Sequence with accesion number", acc, 
                  "was not found in available databases.\n Are you sure this is an accession number and not a sequence name?"))
    } else {
        cat(paste("Sequence with accesion number", acc, 
                  "was found in the following database(s):\n"))
        print(result)
    }
    invisible(result)
}