R/knowndbs.R

In seqinr: Biological Sequences Retrieval and Analysis

# ==>  knowndbs{&tag=xx}
# <== nl=.. \n
# dbname | on/off | db description \n      nl such lines
# Returns, for each database known by the server, its name (a valid value for the db= argument 
# of the acnucopen command), availability (off means temporarily unavailable), and description.
# When the optional tag= argument is used, only databases tagged with the given string are listed;
# without this argument, only untagged databases are listed.
# The tag argument thus allows to identify series of special purpose (tagged) databases, 
# in addition to default (untagged) ones. The full list of untagged and tagged databases is here.

knowndbs <- function(tag = c(NA, "TP", "TEST", "DEV"), socket = autosocket()){
    #
    # Use default tag:
    #
    tag <- tag[1]
    #
    # Build request:
    #
    if( !is.na(tag) ){
        askforbank <- paste("knowndbs&tag=", tag, sep = "")
    } else {
        askforbank <- "knowndbs"
    }
    writeLines(askforbank, socket, sep = "\n")
    rep <- readLines(socket, n = 1)
    nbank <- as.numeric(parser.socket(rep))  
    #
    # Read bank infos from server:
    #
    res <- readLines(socket, n = nbank)
    #
    # Build result:
    #
    resdf <- as.data.frame(list(bank = I(rep("NAbank", nbank)), 
                                status = I(rep("NAstatus", nbank)), 
                                info = I(rep("NAinfo", nbank))))
    for(i in seq_len(nbank))
        resdf[i, ] <- unlist(strsplit(res[i], split = "\\|"))[1:3]
    for(i in seq_len(nbank))
        for(j in seq_len(3))
            resdf[i, j] <- trimSpace(resdf[i, j])   
    #
    # Return result:
    #
    return(resdf)
}

kdb <- knowndbs