## read.dna.R (2010-05-17)
## Read DNA Sequences in a File
## Copyright 2003-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
read.dna <- function(file, format = "interleaved", skip = 0,
nlines = 0, comment.char = "#", seq.names = NULL,
as.character = FALSE, as.matrix = NULL)
{
getTaxaNames <- function(x) {
x <- sub("^['\" ]+", "", x) # remove the leading quotes and spaces
x <- sub("['\" ]+$", "", x) # " " trailing " " "
x
}
getNucleotide <- function(x) {
x <- gsub(" ", "", x)
x <- strsplit(x, NULL)
unlist(x)
}
formats <- c("interleaved", "sequential", "fasta", "clustal")
format <- match.arg(format, formats)
phylip <- if (format %in% formats[1:2]) TRUE else FALSE
X <- scan(file = file, what = "", sep = "\n", quiet = TRUE,
skip = skip, nlines = nlines, comment.char = comment.char)
pat.base <- "[-AaCcGgTtUuMmRrWwSsYyKkVvHhDdBbNn?]{10}"
if (phylip) {
## need to remove the possible leading spaces in the first line
fl <- gsub("^ +", "", X[1])
fl <- as.numeric(unlist(strsplit(fl, " +")))
if (length(fl) != 2 || any(is.na(fl)))
stop("the first line of the file must contain the dimensions of the data")
n <- fl[1]
s <- fl[2]
obj <- matrix("", n, s)
X <- X[-1]
}
if (format == "interleaved") {
start.seq <- regexpr(pat.base, X[1])[1]
if (is.null(seq.names))
seq.names <- getTaxaNames(substr(X[1:n], 1, start.seq - 1))
X[1:n] <- substr(X[1:n], start.seq, nchar(X[1:n]))
nl <- length(X)
for (i in 1:n)
obj[i, ] <- getNucleotide(X[seq(i, nl, n)])
}
if (format == "sequential") {
taxa <- character(n)
j <- 1
for (i in 1:n) {
start.seq <- regexpr(pat.base, X[j])[1]
taxa[i] <- substr(X[j], 1, start.seq - 1)
sequ <- getNucleotide(substr(X[j], start.seq, nchar(X[j])))
j <- j + 1
while (length(sequ) < s) {
sequ <- c(sequ, getNucleotide(X[j]))
j <- j + 1
}
obj[i, ] <- sequ
}
if (is.null(seq.names)) seq.names <- getTaxaNames(taxa)
}
if (format == "fasta") {
start <- grep("^ {0,}>", X)
taxa <- X[start]
n <- length(taxa)
obj <- vector("list", n)
if (is.null(seq.names)) {
taxa <- sub("^ {0,}>", "", taxa) # remove the hook and the spaces before
seq.names <- getTaxaNames(taxa)
}
start <- c(start, length(X) + 1) # this avoids the following to crash when `i = n'
for (i in 1:n)
obj[[i]] <- getNucleotide(X[(start[i] + 1):(start[i + 1] - 1)])
}
if (format == "clustal") {
X <- X[-1]
## find where the 1st sequence starts
start.seq <- regexpr(pat.base, X[1])[1]
## find the lines with *********....
nspaces <- paste("^ {", start.seq - 1, "}", sep = "", collapse = "")
stars <- grep(nspaces, X)
## we now know how many sequences in the file:
n <- stars[1] - 1
## get the sequence names in the same way than "interleaved":
if (is.null(seq.names))
seq.names <- getTaxaNames(substr(X[1:n], 1, start.seq - 1))
## need to remove the sequence names before getting the sequences:
X <- substr(X, start.seq, nchar(X))
nl <- length(X)
## find the length of the 1st sequence:
tmp <- getNucleotide(X[seq(1, nl, n + 1)])
s <- length(tmp)
obj <- matrix("", n, s)
obj[1, ] <- tmp
for (i in 2:n)
obj[i, ] <- getNucleotide(X[seq(i, nl, n + 1)])
}
if (format != "fasta") {
rownames(obj) <- seq.names
obj <- tolower(obj)
} else {
names(obj) <- seq.names
obj <- lapply(obj, tolower)
LENGTHS <- unique(unlist(lapply(obj, length)))
allSameLength <- length(LENGTHS) == 1
if (is.logical(as.matrix) && as.matrix && !allSameLength)
stop("sequences in FASTA file not of the same length")
if (is.null(as.matrix) && allSameLength)
as.matrix <- TRUE
if (as.matrix) {
obj <- matrix(unlist(obj), ncol = LENGTHS, byrow = TRUE)
rownames(obj) <- seq.names
}
}
if (!as.character) obj <- as.DNAbin(obj)
obj
}
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