R/write_ncbi.R

In fishsciences/metabarcode_utils: Meta-barcoding Utilities

##' Write tables extracted and possibly reduced to CSV files for
##' further analysis.
##' 
##' @title Write NCBI data to a CSV
##' @param x either a list or data.frame
##' @param outdir the directory to write CSVs to
##' @param out_prefix the common prefix for all files
##' @param combine logical, if TRUE the tables will be combined into a
##'     single CSV
##' @param out_names the unique name to use for each table
##' @param ... addtional args passed to write.csv
##' @return the file paths of the CSVs written
##' @author Matt Espe
##' @export
write_ncbi_tabs = function(x, outdir = ".", out_prefix = "NCBI_reduced_",
                           combine = FALSE,
                           out_names = if(is.data.frame(x)) "out" else names(x), ...)
{

    
    if(combine)
        x = combine_ncbi_tabs(x)

    full_out = file.path(outdir, paste0(out_prefix, out_names, ".csv"))

    if(is.data.frame(x) && is.null(out_names))
        stop("Please provide a name for the table")

    if(is.data.frame(x)){
        write.csv(x, full_out, row.names = FALSE, ...)
    } else {
        mapply(function(df, file) {write.csv(df, file, row.names = FALSE, ...)},
               df = x, file = full_out)
    }
    return(full_out)
}

combine_ncbi_tabs = function(x)
    # x is list of tables
{
    i = sapply(x, is.data.frame)
    if(any(i)) warning("Excluding tables without rows\n",
                       paste(names(x)[!i], "\n"))
    
    ans = do.call(rbind, x[i])
    ans$species = rep(names(x)[i], sapply(x[i], nrow))
    ans
}