Package: ape
Version: 3.0-4
-Date: 2012-04-30
+Date: 2012-05-03
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
BUG FIXES
- o read.dna() failed to read interleaved files if the first line
- uses tabulations instead of white spaces.
+ o read.dna() failed to read Phylip files if the first line used
+ tabulations instead of white spaces.
+
+ o read.dna() failed to read Phylip or Clustal files with less than
+ 10 nucleotides failed. (See other changes in this function
+ below.)
OTHER CHANGES
+ o read.dna() now requires at least one space (or tab) between the
+ taxa names and the sequences (whatever the length of taxa
+ names). write.dna() now follows the same rule.
+
o The files ape-defunct.R and ape-defunct.Rd, which have not been
modified for almost two years, have been removed.
o The C code of bionj() has been reworked: it is more stable (by
avoiding passing character strings), slightly faster (by about
- 20%), and more accurate numerically.
+ 20%), and numerically more accurate.
o The C code of fastme.*() has been slightly modified and should
be more stable by avoiding passing character strings (the
if (!pairwise.deletion) {
keep <- .C("GlobalDeletionDNA", x, n, s,
rep(1L, s), PACKAGE = "ape")[[4]]
- x <- x[, as.logical(keep)]
+ x <- x[, as.logical(keep)]
s <- dim(x)[2]
}
Ndist <- if (imod == 11) n*n else n*(n - 1)/2
-## read.dna.R (2012-04-26)
+## read.dna.R (2012-05-03)
## Read DNA Sequences in a File
## See the file ../COPYING for licensing issues.
read.dna <- function(file, format = "interleaved", skip = 0,
- nlines = 0, comment.char = "#", seq.names = NULL,
+ nlines = 0, comment.char = "#",
as.character = FALSE, as.matrix = NULL)
{
+ findFirstNucleotide <- function(x) {
+ ## actually find the 1st non-blank character
+ ## just in case: pat.base <- "[-AaCcGgTtUuMmRrWwSsYyKkVvHhDdBbNn?]{10}"
+ tmp <- regexpr("[[:blank:]]+", x[1]) # consider only a single string
+ tmp[1] + attr(tmp, "match.length")
+ }
getTaxaNames <- function(x) {
x <- sub("^['\" ]+", "", x) # remove the leading quotes and spaces
x <- sub("['\" ]+$", "", x) # " " trailing " " "
getNucleotide <- function(x) {
x <- gsub(" ", "", x)
x <- strsplit(x, NULL)
- unlist(x)
+ tolower(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 and/or tabs in the first line
fl <- gsub("^[[:blank:]]+", "", X[1])
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]))
+ switch(format,
+ "interleaved" = {
+ start.seq <- findFirstNucleotide(X[1])
+ one2n <- 1:n
+ taxa <- getTaxaNames(substr(X[one2n], 1, start.seq - 1))
+ X[one2n] <- substr(X[one2n], start.seq, nchar(X[one2n]))
nl <- length(X)
- for (i in 1:n)
+ for (i in one2n)
obj[i, ] <- getNucleotide(X[seq(i, nl, n)])
- }
- if (format == "sequential") {
+ },
+ "sequential" = {
taxa <- character(n)
- j <- 1
+ j <- 1L # line number
for (i in 1:n) {
- start.seq <- regexpr(pat.base, X[j])[1]
- taxa[i] <- substr(X[j], 1, start.seq - 1)
+ start.seq <- findFirstNucleotide(X[j])
+ taxa[i] <- getTaxaNames(substr(X[j], 1, start.seq - 1))
sequ <- getNucleotide(substr(X[j], start.seq, nchar(X[j])))
- j <- j + 1
+ j <- j + 1L
while (length(sequ) < s) {
sequ <- c(sequ, getNucleotide(X[j]))
- j <- j + 1
+ j <- j + 1L
}
obj[i, ] <- sequ
}
- if (is.null(seq.names)) seq.names <- getTaxaNames(taxa)
- }
- if (format == "fasta") {
+ taxa <- getTaxaNames(taxa)
+ },
+ "fasta" = {
start <- grep("^ {0,}>", X)
taxa <- X[start]
+ taxa <- sub("^ {0,}>", "", taxa) # remove the hook and the spaces before
+ taxa <- getTaxaNames(taxa)
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]
+ },
+ "clustal" = {
+ X <- X[-1] # drop the line with "Clustal bla bla..."
## find where the 1st sequence starts
- start.seq <- regexpr(pat.base, X[1])[1]
+ start.seq <- findFirstNucleotide(X[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))
+ taxa <- 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)
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)
+ rownames(obj) <- taxa
} else {
- names(obj) <- seq.names
- obj <- lapply(obj, tolower)
+ names(obj) <- taxa
LENGTHS <- unique(unlist(lapply(obj, length)))
allSameLength <- length(LENGTHS) == 1
if (is.logical(as.matrix)) {
}
if (as.matrix) {
obj <- matrix(unlist(obj), ncol = LENGTHS, byrow = TRUE)
- rownames(obj) <- seq.names
+ rownames(obj) <- taxa
}
}
if (!as.character) obj <- as.DNAbin(obj)
-## write.dna.R (2009-05-10)
+## write.dna.R (2012-05-03)
## Write DNA Sequences in a File
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
}
## 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
+ ## always put a space between the sequences and the taxa names
fmt <- paste("%-", max.nc + 1, "s", sep = "")
names(x) <- sprintf(fmt, names(x))
}
variables: geometric interpretations. \emph{Evolution}, \bold{55},
2143--2160.
- Harvey, P. H. and Pagel, M. D. (1991) \emph{The comparative method in
- evolutionary biology}. Oxford University Press.
+ Harvey, P. H. and Pagel, M. D. (1991) \emph{The Comparative Method in
+ Evolutionary Biology}. Oxford University Press.
}
\author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
\seealso{\code{\link{compar.lynch}}}
phylogeny algorithms under equal and unequal evolutionary rates.
\emph{Molecular Biology and Evolution}, \bold{11}, 459--468.
- Nei, M. and Kumar, S. (2000) \emph{Molecular evolution and
- phylogenetics}. Oxford: Oxford University Press.
+ Nei, M. and Kumar, S. (2000) \emph{Molecular Evolution and
+ Phylogenetics}. Oxford: Oxford University Press.
Penny, D. and Hendy, M. D. (1985) The use of tree comparison
metrics. \emph{Systemetic Zoology}, \bold{34}, 75--82.
used, a named vector or matrix.
}
\references{
- Felsenstein, J. (2004) \emph{Inferring phylogenies}. Sunderland:
+ Felsenstein, J. (2004) \emph{Inferring Phylogenies}. Sunderland:
Sinauer Associates.
}
\author{Emmanuel Paradis}
Legendre, P. and Gallagher, E. D. (2001) Ecologically meaningful transformations for ordination of species data. \emph{Oecologia}, \bold{129}, 271--280.
-Legendre, P. and Legendre, L. (1998) \emph{Numerical ecology, 2nd English
+Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology, 2nd English
edition.} Amsterdam: Elsevier Science BV.
Lingoes, J. C. (1971) Some boundary conditions for a monotone analysis of symmetric matrices. \emph{Psychometrika}, \bold{36}, 195--203.
\title{Read DNA Sequences in a File}
\usage{
read.dna(file, format = "interleaved", skip = 0,
- nlines = 0, comment.char = "#", seq.names = NULL,
+ nlines = 0, comment.char = "#",
as.character = FALSE, as.matrix = NULL)
}
\arguments{
read untill its end).}
\item{comment.char}{a single character, the remaining of the line
after this character is ignored.}
- \item{seq.names}{the names to give to each sequence; by default the
- names read in the file are used.}
\item{as.character}{a logical controlling whether to return the
sequences as an object of class \code{"DNAbin"} (the default).}
\item{as.matrix}{(used if \code{format = "fasta"}) one of the three
way with blanks and line-breaks inside (with the restriction that the
first ten nucleotides must be contiguous for the interleaved and
sequential formats, see below). The names of the sequences are read in
- the file unless the `seq.names' option is used. Particularities for
- each format are detailed below.
+ the file. Particularities for each format are detailed below.
\itemize{
- \item{Interleaved:}{the function starts to read the sequences when it
- finds 10 contiguous characters belonging to the ambiguity code of
- the IUPAC (namely A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, and
- N, upper- or lowercase, so you might run into trouble if you have a
- taxa name with 10 contiguous letters among these!) All characters
- before the sequences are taken as the taxa names after removing the
- leading and trailing spaces (so spaces in a taxa name are
- allowed). It is assumed that the taxa names are not repeated in the
- subsequent blocks of nucleotides.}
+ \item{Interleaved:}{the function starts to read the sequences after it
+ finds one or more spaces (or tabulations). All characters before the
+ sequences are taken as the taxa names after removing the leading and
+ trailing spaces (so spaces in taxa names are allowed). It is assumed
+ that the taxa names are not repeated in the subsequent blocks of
+ nucleotides.}
\item{Sequential:}{the same criterion than for the interleaved format
is used to start reading the sequences and the taxa names; the
\item{cum}{Send cumulative variance components.}
}
\details{
- Variance computations is done as in Venables and Ripley's book.
+ Variance computations is done as in Venables and Ripley (2002).
}
\value{
A named vector of class \code{varcomp} with estimated variance components.
}
\references{
- Venables, W. N. and Ripley, B. D. (2002) \emph{Modern applied statistics
- with S (fourth edition)}. New York: Springer-Verlag.
+ Venables, W. N. and Ripley, B. D. (2002) \emph{Modern Applied Statistics
+ with S (Fourth Edition)}. New York: Springer-Verlag.
}
\author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
\seealso{\code{\link[nlme]{lme}}}
projects / ape.git / commitdiff