20 lines
546 B
R
20 lines
546 B
R
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testFastaData <- function(inFile) {
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# added by Lu Cheng, 11.11.2012
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if (!exists(inFile, 'file')) {
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stop('Fasta file ', inFile, ' does not exist!')
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}
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seqs <- load_fasta(inFile)
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heds <- colnames(seqs)
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ninds <- length(seqs)
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data <- as.matrix(seqs)
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newData <- ones(size(data)) * -9
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newData[toupper(data) == 'A'] <- 1
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newData[toupper(data) == 'C'] <- 2
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newData[toupper(data) == 'G'] <- 3
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newData[toupper(data) == 'T'] <- 4
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data <- c(newData, t(1:ninds))
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return(list("ninds" = ninds, "data" = data, "heds" = heds))
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}
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