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fixup! Translated testFastaData() (#3)

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Waldir Leoncio 2023-02-07 10:37:00 +01:00
parent b5c70ac555
commit 3cfbe5bfe8
1 changed files with 5 additions and 4 deletions
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9
R/testFastaData.R
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@ -1,19 +1,20 @@
testFastaData <- function(inFile) {
# added by Lu Cheng, 11.11.2012
if (!exists(inFile, 'file')) {
if (!file.exists(inFile)) {
stop('Fasta file ', inFile, ' does not exist!')
}
seqs <- load_fasta(inFile)
heds <- colnames(seqs)
ninds <- length(seqs)
ninds <- nrow(seqs) # not sure if this should be nrow, ncols or length
data <- as.matrix(seqs)
newData <- ones(size(data)) * -9
newData <- matrix(-9, nrow = nrow(data), ncol = ncol(data))
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))
data <- cbind(newData, seq(1, ninds))
return(list("ninds" = ninds, "data" = data, "heds" = heds))
}