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Translated testFastaData() (#3)

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Waldir Leoncio 2023-01-23 11:21:16 +01:00
parent 71c8e98e55
commit 8ce9f3af04
1 changed files with 19 additions and 0 deletions
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R/testFastaData.R Normal file
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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))
}