R/savelist.R

In seqinr: Biological Sequences Retrieval and Analysis

# ==>  savelist&lrank=xx{&type=[N|A]}
# <==  code=0\n
# list element names or acc nos on successive lines
# savelist END.\n
# To obtain names of all elements of a bit list sent on socket on successive lines;
# for sequence lists, option &type=A, will give accession numbers instead of seq names;
# end of series of lines is when savelist END.\n appears
# lrank : rank of bitlist
# type: A gives accession numbers, N (default) gives seq names; useful for seq lists only

savelist <- function(lrank, type = c("N", "A"),
                     filename = paste(gln(lrank), ifelse(type == "N", "mne", "acc"), sep = "."),
                     socket = autosocket(), warnme = TRUE){
    #
    # Check argument:
    #
    if(!is.finite(lrank)) stop("wrong lrank argument")
    if(getliststate(lrank)$type != "SQ") stop("wrong ACNUC list type, should be SQ for sequences")
    #
    # Default is "N":
    #
    type <- type[1]
    if( !(type %in% c("N", "A"))) stop("wrong type argument")
    #
    # Build request:
    #
    request <- paste("savelist&lrank=", lrank, "&type=", type, sep = "")
    writeLines(request, socket, sep = "\n")
    answerFromServer <- readLines(socket)
    #
    # Check that there is an answer from server:
    #
    if(length(answerFromServer) == 0){
        warning("Empty answer from server")
        return(NA)
    }
    #
    # Check that no error is returned:
    #
    if(parser.socket(answerFromServer[1])[1] != "0"){
        warning(paste("error code from server:", answerFromServer[1]))
        return(NA)
    }
    #
    # Remove first line (code=0):
    #
    answerFromServer <- answerFromServer[-1]
    #
    # Check completness of answer:
    #
    if( answerFromServer[length(answerFromServer)] != "savelist END."){
        warning("incomplete answer from server")
        return(NA)
    }
    #
    # Remove last line and dump to file:
    #
    answerFromServer <- answerFromServer[-length(answerFromServer)]
    writeLines(answerFromServer, con = filename)
    #
    # Say it's over
    #
    if(warnme){
        if(type == "N"){
            cat(paste(length(answerFromServer), "sequence mnemonics written into file:", filename), sep = "\n")
        } else {
            cat(paste(length(answerFromServer), "sequence accession numbers written into file:", filename), sep = "\n")
        }
    }
}