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## write.dna.R (2020-11-08)
## Write DNA Sequences in a File
## Copyright 2003-2020 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(lengths(x, use.names = FALSE))
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)))
## always put a space between the sequences and the taxa names
fmt <- paste("%-", max.nc + 1, "s", sep = "")
names(x) <- sprintf(fmt, names(x))
}
switch(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)
}
}
}
}, "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)
}
}
}
}, "fasta" = {
for (i in 1:N) {
cat(">", names(x)[i], file = zz, sep = "")
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)
}
}
})
}
write.FASTA <- function(x, file, header = NULL, append = FALSE)
{
dna <- inherits(x, "DNAbin")
if (!dna && !inherits(x, "AAbin"))
stop("data are apparently neither DNA nor AA sequences")
if (!is.null(header)) {
header <- as.character(header)
if (!length(header) || !sum(nchar(header)) || is.na(header)) {
warning("header cannot be coerced as character; was ignored")
header <- NULL
}
}
labs <- labels(x)
if (is.matrix(x)) {
s <- ncol(x) # always integer
n <- nrow(x) #
} else {
s <- -1L
n <- length(x)
}
if (is.null(labs)) labs <- as.character(1:n)
labs <- lapply(labs, charToRaw)
if (!is.null(header)) {
cat(header, sep = "\n", file = file, append = append)
} else {
fileExists <- file.exists(file)
if (append) {
if (!fileExists) stop(paste("cannot access FASTA file", file))
} else {
if (fileExists) file.remove(file)
o <- file.create(file)
if (!o) stop(paste("cannot create FASTA file", file))
}
}
## 'file' should always exist now
file <- normalizePath(file)
if (dna) .Call(writeDNAbinToFASTA, x, file, n, s, labs)
else .Call(writeAAbinToFASTA, x, file, n, s, labs)
invisible(NULL)
}
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