https://github.com/cran/ape
Tip revision: c44657c7122de6f1ff126170a82fdac9211b53d5 authored by Emmanuel Paradis on 01 August 2012, 00:00:00 UTC
version 3.0-5
version 3.0-5
Tip revision: c44657c
write.dna.Rd
\name{write.dna}
\alias{write.dna}
\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)
}
\arguments{
\item{x}{a list or a matrix of DNA sequences.}
\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"').}
}
\description{
This function writes in a file a list of DNA sequences in sequential,
interleaved, or FASTA format.
}
\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
names 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.
}
\note{
Specifying a negative value for `nbcol' (meaning that the nucleotides
are printed on a single line) gives the same result for the
interleaved and sequential formats.
The names of the sequences may be truncated with the function
\code{\link{makeLabel}}. In particular, Clustal is limited to 30
characters, whereas PHYML seems limited to 99 characters.
The FASTA format may be used as input for Clustal.
}
\value{
None (invisible `NULL').
}
\author{Emmanuel Paradis}
\references{
Anonymous. FASTA format description.
\url{http://www.ncbi.nlm.nih.gov/BLAST/fasta.html}
Anonymous. IUPAC ambiguity codes.
\url{http://www.ncbi.nlm.nih.gov/SNP/iupac.html}
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}