R/readrdata.R

In jaredgk/megarwrapper:

#' MEGA data read-in
#' 
#' @param analysis_file Filename of MAO file generated by prototyper
#' @param data Data object
#' @param data_ext Datatype of input data, for writing
#' @param out_file Name of temporary output file
#' @param out_parse Datatype of MEGA output
#' 
#' @return Data from MEGA
#' 
#' @author Jared Knoblauch
#' 
#' @export
#' @import ape
#' 
#' 

runMegaOnData <- function(data,analysis_file,data_ext="",calib_file="",groups_file="",tree_file="",out_prefix="mega_out_",temp_input_prefix="mega_temp",keep_input=FALSE) {
  if (nchar(data_ext) == 0) {
    if (class(data) == 'DNAbin') { data_ext = 'fasta' }
    else if (class(data) == 'phylo') { data_ext = 'nwk' }
  }
  if (!is.element(data_ext,c("fasta","nwk"))) {
    stop("Input MEGA file format not supported, must be fasta or nwk")
  }
  temp_fn = paste(temp_input_prefix,'.',data_ext,sep="")
  print(temp_fn)
  if (data_ext == 'fasta') {
    write.FASTA(data,temp_fn)
  } else if (data_ext == 'nwk') {
    write.tree(data,temp_fn)
  }
  out_objects = runMega(analysis_file,temp_fn,out_prefix=out_prefix,calib_file=calib_file,groups_file=groups_file,tree_file=tree_file)
  if (keep_input == FALSE) {
    file.remove(temp_fn)
  }
  return(out_objects)
}