From 8ce9f3af04cf6beae319663113c7d6724b5bb79a Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 23 Jan 2023 11:21:16 +0100
Subject: [PATCH] Translated testFastaData() (#3)

---
 R/testFastaData.R | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 R/testFastaData.R

diff --git a/R/testFastaData.R b/R/testFastaData.R
new file mode 100644
index 0000000..ad88256
--- /dev/null
+++ b/R/testFastaData.R
@@ -0,0 +1,19 @@
+testFastaData <- function(inFile) {
+  #  added by Lu Cheng, 11.11.2012
+  if (!exists(inFile, 'file')) {
+    stop('Fasta file ', inFile, ' does not exist!')
+  }
+
+  seqs <- load_fasta(inFile)
+  heds <- colnames(seqs)
+  ninds <- length(seqs)
+
+  data <- as.matrix(seqs)
+  newData <- ones(size(data)) * -9
+  newData[toupper(data) == 'A'] <- 1
+  newData[toupper(data) == 'C'] <- 2
+  newData[toupper(data) == 'G'] <- 3
+  newData[toupper(data) == 'T'] <- 4
+  data <- c(newData, t(1:ninds))
+  return(list("ninds" = ninds, "data" = data, "heds" = heds))
+}