https://github.com/cran/ape
Tip revision: 71a1c7f72dde13abe483316ea5fec16d2fd702fd authored by Emmanuel Paradis on 11 April 2024, 12:30:02 UTC
version 5.8
version 5.8
Tip revision: 71a1c7f
write.dna.Rd
\name{write.dna}
\alias{write.dna}
\alias{write.FASTA}
\title{Write DNA Sequences in a File}
\usage{
write.dna(x, file, format = "interleaved", append = FALSE,
nbcol = 6, colsep = " ", colw = 10, indent = NULL,
blocksep = 1)
write.FASTA(x, file, header = NULL, append = FALSE)
}
\arguments{
\item{x}{a list or a matrix of DNA sequences, or of AA sequences for
\code{write.FASTA}.}
\item{file}{a file name specified by either a variable of mode character,
or a double-quoted string.}
\item{format}{a character string specifying the format of the DNA
sequences. Three choices are possible: \code{"interleaved"},
\code{"sequential"}, or \code{"fasta"}, or any unambiguous
abbreviation of these.}
\item{append}{a logical, if \code{TRUE} the data are appended to the
file without erasing the data possibly existing in the file,
otherwise the file (if it exists) is overwritten (\code{FALSE} the
default).}
\item{nbcol}{a numeric specifying the number of columns per row (6 by
default); may be negative implying that the nucleotides are printed
on a single line.}
\item{colsep}{a character used to separate the columns (a single
space by default).}
\item{colw}{a numeric specifying the number of nucleotides per column
(10 by default).}
\item{indent}{a numeric or a character specifying how the blocks of
nucleotides are indented (see details).}
\item{blocksep}{a numeric specifying the number of lines between the
blocks of nucleotides (this has an effect only if `format =
"interleaved"').}
\item{header}{a vector of mode character giving the header to be
written in the FASTA file before the sequences. By default, there is
no header.}
}
\description{
These functions write in a file a list of DNA sequences in sequential,
interleaved, or FASTA format. \code{write.FASTA} can write either DNA
or AA sequences.
}
\details{
Three formats are supported in the present function: see the help page
of \code{\link{read.dna}} and the references below for a description.
If the sequences have no names, then they are given "1", "2", ... as
labels in the file.
With the interleaved and sequential formats, the sequences must be all
of the same length. The names of the sequences are not truncated.
The argument \code{indent} specifies how the rows of nucleotides are
indented. In the interleaved and sequential formats, the rows with
the taxon names are never indented; the subsequent rows are indented
with 10 spaces by default (i.e., if \code{indent = NULL}). In the FASTA
format, the rows are not indented by default. This default behaviour
can be modified by specifying a value to \code{indent}: the rows are then
indented with ``indent'' (if it is a character) or `indent' spaces (if
it is a numeric). For example, specifying \code{indent = " "} or
\code{indent = 3} will have the same effect (use \code{indent = "\\t"}
for a tabulation).
The different options are intended to give flexibility in formatting
the sequences. For instance, if the sequences are very long it may be
judicious to remove all the spaces beween columns (colsep = ""), in
the margins (indent = 0), and between the blocks (blocksep = 0) to
produce a smaller file.
\code{write.dna(, format = "fasta")} can be very slow if the sequences
are long (> 10 kb). \code{write.FASTA} is much faster in this
situation but the formatting is not flexible: each sequence is printed
on a single line, which is OK for big files that are not intended to
be open with a text editor.
}
\note{
Specifying a negative value for `nbcol' (meaning that the nucleotides
are printed on a single line) gives the same output for the
interleaved and sequential formats.
The names of the sequences can be truncated with the function
\code{\link{makeLabel}}. In particular, Clustal is limited to 30
characters, and PHYML seems limited to 99 characters.
}
\value{
None (invisible `NULL').
}
\author{Emmanuel Paradis}
\references{
Anonymous. FASTA format. \url{https://en.wikipedia.org/wiki/FASTA_format}
Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version
3.5c. Department of Genetics, University of Washington.
\url{http://evolution.genetics.washington.edu/phylip/phylip.html}
}
\seealso{
\code{\link{read.dna}}, \code{\link{read.GenBank}},
\code{\link{makeLabel}}
}
\keyword{IO}