Added function to convert from FASTA to BAPS (#24)

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(convert_FASTA_to_BAPS)
 export(greedyMix)
 export(handleData)
 export(importFile)

R/convert_FASTA_to_BAPS.R

@@ -0,0 +1,15 @@
+#' @title Convert from FASTA to BAPS
+#' @description Converts a file (not an R object) from FASTA to BAPS format
+#' @param file filename of FASTA file
+#' @return `data` in BAPS format
+#' @author Waldir Leoncio
+#' @export
+#' @examples
+#' file <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
+#' convert_FASTA_to_BAPS(file)
+convert_FASTA_to_BAPS <- function(file) {
+  data <- load_fasta(file) # Processing data
+  data <- cbind(data, seq_len(nrow(data))) # Add IDs of individuals (sequential)
+  data[data == 0] <- -9 # Because zeros (missing) in BAPS are coded as -9
+  return(data)
+}

R/greedyMix.R

@@ -28,7 +28,8 @@ greedyMix <- function(
 ) {
   # Importing and handling data ================================================
   if (tolower(format) %in% "fasta") {
-    stop("FASTA format not yet supported on greedyMix")
+    data <- load_fasta(data)
+    data <- handleData(data, "FASTA")
   }
   if (tolower(format) %in% "baps") {
     data <- process_BAPS_data(data, NULL)

R/handleData.R

@@ -30,6 +30,7 @@ handleData <- function(raw_data, format = "Genepop") {
     "bam"     = stop("BAM format not supported for processing yet")
   )
   data <- as.matrix(raw_data)
+
   dataApu <- data[, seq_len(nloci)]
   nollat <- matlab2r::find(dataApu == 0)
   if (!isempty(nollat)) {
@@ -54,6 +55,7 @@ handleData <- function(raw_data, format = "Genepop") {
     alleleCodes[, i] <- as.matrix(c(alleelitLokuksessaI, zeros(puuttuvia, 1)))
   }
 
+  # This is where data gets converted to {1, 2, 3, 4} for {A, C, G, T}
   for (loc in seq_len(nloci)) {
     for (all in seq_len(noalle[loc])) {
       data[matlab2r::find(data[, loc] == alleleCodes[all, loc]), loc] <- all

man/convert_FASTA_to_BAPS.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convert_FASTA_to_BAPS.R
+\name{convert_FASTA_to_BAPS}
+\alias{convert_FASTA_to_BAPS}
+\title{Convert an R object from FASTA to BAPS format}
+\usage{
+convert_FASTA_to_BAPS(data)
+}
+\arguments{
+\item{data}{dataset to be converted}
+}
+\value{
+`data` in BAPS format
+}
+\description{
+Converts an R object from FASTA to BAPS format
+}
+\examples{
+data <- system.file("extdata", "FASTA_clustering_diploid.fasta", package = "rBAPS")
+convert_FASTA_to_BAPS(data)
+}
+\author{
+Waldir Leoncio
+}