## write.dna.R (2009-05-10)
## Write DNA Sequences in a File
## Copyright 2003-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
write.dna <- function(x, file, format = "interleaved", append = FALSE,
nbcol = 6, colsep = " ", colw = 10, indent = NULL,
blocksep = 1)
{
format <- match.arg(format, c("interleaved", "sequential", "fasta"))
phylip <- if (format %in% c("interleaved", "sequential")) TRUE else FALSE
if (inherits(x, "DNAbin")) x <- as.character(x)
aligned <- TRUE
if (is.matrix(x)) {
N <- dim(x)
S <- N[2]
N <- N[1]
xx <- vector("list", N)
for (i in 1:N) xx[[i]] <- x[i, ]
names(xx) <- rownames(x)
x <- xx
rm(xx)
} else {
N <- length(x)
S <- unique(unlist(lapply(x, length)))
if (length(S) > 1) aligned <- FALSE
}
if (is.null(names(x))) names(x) <- as.character(1:N)
if (is.null(indent))
indent <- if (phylip) 10 else 0
if (is.numeric(indent))
indent <- paste(rep(" ", indent), collapse = "")
if (format == "interleaved") {
blocksep <- paste(rep("\n", blocksep), collapse = "")
if (nbcol < 0) format <- "sequential"
}
zz <- if (append) file(file, "a") else file(file, "w")
on.exit(close(zz))
if (phylip) {
if (!aligned)
stop("sequences must have the same length for
interleaved or sequential format.")
cat(N, " ", S, "\n", sep = "", file = zz)
if (nbcol < 0) {
nb.block <- 1
nbcol <- totalcol <- ceiling(S/colw)
} else {
nb.block <- ceiling(S/(colw * nbcol))
totalcol <- ceiling(S/colw)
}
## Prepare the sequences in a matrix whose elements are
## strings with `colw' characters.
SEQ <- matrix("", N, totalcol)
for (i in 1:N) {
X <- paste(x[[i]], collapse = "")
for (j in 1:totalcol)
SEQ[i, j] <- substr(X, 1 + (j - 1)*colw, colw + (j - 1)*colw)
}
## Prepare the names so that they all have the same nb of chars
max.nc <- max(nchar(names(x)))
## in case all names are 10 char long or less, sequences are
## always started on the 11th column of the file
if (max.nc < 11) max.nc <- 9
fmt <- paste("%-", max.nc + 1, "s", sep = "")
names(x) <- sprintf(fmt, names(x))
}
if (format == "interleaved") {
## Write the first block with the taxon names
colsel <- if (nb.block == 1) 1:totalcol else 1:nbcol
for (i in 1:N) {
cat(names(x)[i], file = zz)
cat(SEQ[i, colsel], sep = colsep, file = zz)
cat("\n", file = zz)
}
## Write eventually the other blocks
if (nb.block > 1) {
for (k in 2:nb.block) {
cat(blocksep, file = zz)
endcolsel <- if (k == nb.block) totalcol else nbcol + (k - 1)*nbcol
for (i in 1:N) {
cat(indent, file = zz)
cat(SEQ[i, (1 + (k - 1)*nbcol):endcolsel], sep = colsep, file = zz)
cat("\n", file = zz)
}
}
}
}
if (format == "sequential") {
if (nb.block == 1) {
for (i in 1:N) {
cat(names(x)[i], file = zz)
cat(SEQ[i, ], sep = colsep, file = zz)
cat("\n", file = zz)
}
} else {
for (i in 1:N) {
cat(names(x)[i], file = zz)
cat(SEQ[i, 1:nbcol], sep = colsep, file = zz)
cat("\n", file = zz)
for (k in 2:nb.block) {
endcolsel <- if (k == nb.block) totalcol else nbcol + (k - 1)*nbcol
cat(indent, file = zz)
cat(SEQ[i, (1 + (k - 1)*nbcol):endcolsel], sep = colsep, file = zz)
cat("\n", file = zz)
}
}
}
}
if (format == "fasta") {
for (i in 1:N) {
cat(">", names(x)[i], file = zz)
cat("\n", file = zz)
X <- paste(x[[i]], collapse = "")
S <- length(x[[i]])
totalcol <- ceiling(S/colw)
if (nbcol < 0) nbcol <- totalcol
nb.lines <- ceiling(totalcol/nbcol)
SEQ <- character(totalcol)
for (j in 1:totalcol)
SEQ[j] <- substr(X, 1 + (j - 1) * colw, colw + (j - 1) * colw)
for (k in 1:nb.lines) {
endsel <-
if (k == nb.lines) length(SEQ) else nbcol + (k - 1)*nbcol
cat(indent, file = zz)
cat(SEQ[(1 + (k - 1)*nbcol):endsel], sep = colsep, file = zz)
cat("\n", file = zz)
}
}
}
}
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