https://github.com/cran/ape
Tip revision: 856dc17b51b415ee05514d54fb4ee6b7af8822ae authored by Emmanuel Paradis on 20 December 2004, 00:00:00 UTC
version 1.4
version 1.4
Tip revision: 856dc17
read.nexus.R
### read.nexus.R (2004-08-31)
###
### Read Tree File in Nexus Format
###
### Copyright 2004 Emmanuel Paradis <paradis@isem.univ-montp2.fr>
###
### This file is part of the `ape' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 2, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE. See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
clado.build <- function(tp) {
add.internal <- function() {
edge[j, 1] <<- current.node
node <<- node - 1
edge[j, 2] <<- current.node <<- node
j <<- j + 1
}
add.terminal <- function() {
edge[j, 1] <<- current.node
edge[j, 2] <<- tip
tip.label[tip] <<- tpc[k]
k <<- k + 1
tip <<- tip + 1
j <<- j + 1
}
go.down <- function() {
l <- which(edge[, 2] == current.node)
node.label[-current.node] <<- tpc[k]
k <<- k + 1
current.node <<- edge[l, 1]
}
tsp <- unlist(strsplit(tp, NULL))
tp <- gsub(")", ")NA", tp)
tp <- gsub(" ", "", tp)
tpc <- unlist(strsplit(tp, "[\\(\\),;]"))
tpc <- tpc[tpc != ""]
skeleton <- tsp[tsp == "(" | tsp == ")" | tsp == "," | tsp == ";"]
nsk <- length(skeleton)
nb.node <- length(skeleton[skeleton == ")"])
nb.tip <- length(skeleton[skeleton == ","]) + 1
## We will assume there is an edge at the root;
## if so, it will be removed and put in a vector
nb.edge <- nb.node + nb.tip
node.label <- character(nb.node)
tip.label <- character(nb.tip)
edge <- matrix(NA, nb.edge, 2)
edge[nb.edge, 1] <- 0 # see comment above
edge[nb.edge, 2] <- -1 #
node <- -1 # node number
current.node <- node
j <- 1 # index of the line number of edge
k <- 1 # index of the line number of tpc
tip <- 1 # tip number
for (i in 2:nsk) {
if (skeleton[i] == "(") add.internal() # add an internal branch (on top)
if (skeleton[i] == ",") {
if (skeleton[i - 1] != ")") add.terminal() # add a terminal branch
}
if (skeleton[i] == ")") {
if (skeleton[i - 1] == ",") { # add a terminal branch and go down one level
add.terminal()
go.down()
}
if (skeleton[i - 1] == ")") go.down() # go down one level
}
}
# if(node.label[1] == "NA") node.label[1] <- ""
edge <- edge[-nb.edge, ]
mode(edge) <- "character"
obj <- list(edge = edge,
tip.label = tip.label,
node.label = node.label)
obj$node.label <- if (all(obj$node.label == "NA")) NULL else gsub("^NA", "", obj$node.label)
class(obj) <- "phylo"
return(obj)
}
read.nexus <- function(file, tree.names = NULL)
{
X <- scan(file = file, what = character(), sep = "\n", quiet = TRUE)
## first remove all the comments
LEFT <- grep("\\[", X)
RIGHT <- grep("\\]", X)
for (i in length(LEFT):1) {
if (LEFT[i] == RIGHT[i]) {
X[LEFT[i]] <- gsub("\\[.*\\]", "", X[LEFT[i]])
} else {
X[LEFT[i]] <- gsub("\\[.*", "", X[LEFT[i]])
X[RIGHT[i]] <- gsub(".*\\]", "", X[RIGHT[i]])
if (LEFT[i] < RIGHT[i] - 1) X <- X[-((LEFT[i] + 1):(RIGHT[i] - 1))]
}
}
X <- gsub("[Ee][Nn][Dd][Bb][Ll][Oo][Cc][Kk];", "END;", X)
endblock <- grep("[Ee][Nn][Dd];", X)
semico <- grep(";", X)
i1 <- grep("[Bb][Ee][Gg][Ii][Nn] [Tt][Rr][Ee][Ee][Ss];", X)
i2 <- grep("[Tt][Rr][Aa][Nn][Ss][Ll][Aa][Tt][Ee]", X)
translation <- FALSE
if (length(i2) == 1) if (i2 > i1) translation <- TRUE
if (translation) {
end <- semico[semico > i2][1]
x <- paste(X[i2:end], sep = "", collapse = "")
x <- gsub("[Tt][Rr][Aa][Nn][Ss][Ll][Aa][Tt][Ee]", "", x)
x <- unlist(strsplit(x, "[,; \t]"))
x <- x[x != ""]
TRANS <- matrix(x, ncol = 2, byrow = TRUE)
TRANS[, 2] <- gsub("['\"]", "", TRANS[, 2])
}
start <- if (translation) semico[semico > i2][1] + 1 else semico[semico > i1][1]
end <- endblock[endblock > i1][1] - 1
tree <- paste(X[start:end], sep = "", collapse = "")
tree <- gsub(" ", "", tree)
tree <- unlist(strsplit(tree, "[=;]"))
tree <- tree[grep("[\\(\\)]", tree)]
nb.tree <- length(tree)
STRING <- as.list(tree)
trees <- list()
for (i in 1:nb.tree) {
obj <- if (length(grep(":", STRING[[i]]))) tree.build(STRING[[i]]) else clado.build(STRING[[i]])
if (translation) {
for (j in 1:length(obj$tip.label)) {
ind <- which(obj$tip.label[j] == TRANS[, 1])
obj$tip.label[j] <- TRANS[ind, 2]
}
if (!is.null(obj$node.label)) {
for (j in 1:length(obj$node.label)) {
ind <- which(obj$node.label[j] == TRANS[, 1])
obj$node.label[j] <- TRANS[ind, 2]
}
}
}
trees[[i]] <- obj
## Check here that the root edge is not incorrectly represented
## in the object of class "phylo" by simply checking that there
## is a bifurcation at the root (node "-1")
if(sum(trees[[i]]$edge[, 1] == "-1") == 1) {
warning("The root edge is apparently not correctly represented\nin your tree: this may be due to an extra pair of\nparentheses in your file; the returned object has been\ncorrected but your file may not be in a valid Newick\nformat")
ind <- which(trees[[i]]$edge[, 1] == "-1")
trees[[i]]$root.edge <- trees[[i]]$edge.length[ind]
trees[[i]]$edge.length <- trees[[i]]$edge.length[-ind]
trees[[i]]$edge <- trees[[i]]$edge[-ind, ]
for (j in 1:length(trees[[i]]$edge))
if (as.numeric(trees[[i]]$edge[j]) < 0)
trees[[i]]$edge[j] <- as.character(as.numeric(trees[[i]]$edge[j]) + 1)
## Check a second time and if there is still a problem...!!!
if(sum(trees[[i]]$edge[, 1] == "-1") == 1)
stop("There is apparently two root edges in your file:\cannot read tree file")
}
}
if (nb.tree == 1) trees <- trees[[1]] else {
names(trees) <- if (is.null(tree.names)) paste("tree", 1:nb.tree, sep = "") else tree.names
class(trees) <- c("phylo", "multi.tree")
}
if (length(grep("[\\/]", file)) == 1) attr(trees, "origin") <- file
else attr(trees, "origin") <- paste(getwd(), file, sep = "/")
trees
}