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## by KS
replace.single.quotes <- function(x, start = 1L)
{
z <- unlist(gregexpr("'", x))
if (length(z) %% 2) {
#warning("wrong number of single quotes around labels")
warning(paste0("odd number of single quotes (", length(z), "): label(s) unchanged"))
return(x)
}
i <- 1
while (i < length(z)) {
tmp <- substr(x, z[i], z[i + 1])
substr(x, z[i], z[i + 1]) <- gsub("\\s+", "_", tmp)
i <- i + 2
}
gsub("'", "", x)
}
"read.nexus.data" <- function (file)
{
# Simplified NEXUS data parser.
#
# Version: 09/13/2006 01:01:59 PM CEST
# (modified by EP 2011-06-01 and by TG 2019-06-25)
#
# By: Johan Nylander, nylander @ scs.fsu.edu
#
# WARNING: This is parser reads a restricted nexus format,
# see README for details.
#
# Argument (x) is a nexus formatted data file.
#
# Returns (Value) a list of data sequences each made of a single
# vector of mode character where each element is a character.
#
# TODO: Error checking, gap/missing, find.datatype, etc.
#------------------------------------------------------------------
"find.ntax" <- function (x)
{
for (i in 1:NROW(x)) {
if(any(f <- grep("\\bntax", x[i], ignore.case = TRUE))) {
ntax <- as.numeric(sub("(.+?)(ntax\\s*\\=\\s*)(\\d+)(.+)",
"\\3", x[i], perl = TRUE, ignore.case = TRUE))
break
}
}
ntax
}
"find.nchar" <- function (x)
{
for (i in 1:NROW(x)) {
if(any(f <- grep("\\bnchar", x[i], ignore.case = TRUE))) {
nchar <- as.numeric(sub("(.+?)(nchar\\s*\\=\\s*)(\\d+)(.+)",
"\\3", x[i], perl = TRUE, ignore.case = TRUE))
break
}
}
nchar
}
"find.matrix.line" <- function (x)
{
for (i in 1:NROW(x)) {
if(any(f <- grep("\\bmatrix\\b", x[i], ignore.case = TRUE))) {
matrix.line <- as.numeric(i)
break
}
}
matrix.line
}
"trim.whitespace" <- function (x)
{
gsub("\\s+", "", x)
}
"trim.semicolon" <- function (x)
{
gsub(";", "", x)
}
#TG: Added get polymorphism function
"get.polymorphism" <- function (x)
{
## Detect polymorphism function
is.poly.start <- function(x) {return("(" == x || "{" == x)}
is.poly.end <- function(x) {return(")" == x || "}" == x)}
## Position increment
position <- 1
## Check which position contains a polymorphism
while(position <= length(x)) {
## Check whether the position is polymorphic
if(is.poly.start(x[position])){
## Find the polymorphism end
poly_end <- position + 1
while(!is.poly.end(x[poly_end])) {
poly_end <- poly_end + 1
if(is.poly.start(x[poly_end]) || poly_end > length(x)) {
stop("missing closing bracket for a polymorphism at position ", position)
}
}
## Replace the position by what's in the middle of the polymorphism
x[position] <- paste0(x[(position+1):(poly_end-1)], collapse = "/")
## Remove the polymorphism
x <- x[-c((position+1):poly_end)]
}
## Increment the position
position <- position + 1
}
return(x)
}
X <- scan(file = file, what = character(), sep = "\n",
quiet = TRUE, comment.char = "[", strip.white = TRUE)
ntax <- find.ntax(X)
nchar <- find.nchar(X)
matrix.line <- find.matrix.line(X)
start.reading <- matrix.line + 1
Obj <- list()
length(Obj) <- ntax
i <- 1
pos <- 0
tot.nchar <- 0
tot.ntax <- 0
## by KS
single.quotes <- grepl("'", X)
if (any(single.quotes)) {
to.replace <- which(single.quotes)
for (j in to.replace) {
X[[j]] <- replace.single.quotes(X[[j]])
}
}
for (j in start.reading:NROW(X)) {
Xj <- trim.semicolon(X[j])
if(Xj == "") {
break
}
if(any(jtmp <- grep("\\bend\\b", X[j], perl = TRUE, ignore.case = TRUE))) {
break
}
ts <- unlist(strsplit(Xj, "(?<=\\S)(\\s+)(?=\\S)", perl = TRUE))
if (length(ts) > 2) {
stop("nexus parser does not handle spaces in sequences or taxon names (ts>2)")
}
if (length(ts) !=2) {
stop("nexus parser failed to read the sequences (ts!=2)")
}
Seq <- trim.whitespace(ts[2])
Name <- trim.whitespace(ts[1])
nAME <- paste(c("\\b", Name, "\\b"), collapse = "")
if (any(l <- grep(nAME, names(Obj)))) {
tsp <- strsplit(Seq, NULL)[[1]]
#TG: Convert polymorphisms
if(any("(" %in% tsp || "{" %in% tsp)) {
tsp <- get.polymorphism(tsp)
}
for (k in 1:length(tsp)) {
p <- k + pos
Obj[[l]][p] <- tsp[k]
chars.done <- k
}
}
else {
names(Obj)[i] <- Name
tsp <- strsplit(Seq, NULL)[[1]]
#TG: Convert polymorphisms
if(any("(" %in% tsp || "{" %in% tsp)) {
tsp <- get.polymorphism(tsp)
}
for (k in 1:length(tsp)) {
p <- k + pos
Obj[[i]][p] <- tsp[k]
chars.done <- k
}
}
tot.ntax <- tot.ntax + 1
if (tot.ntax == ntax) {
i <- 1
tot.ntax <- 0
tot.nchar <- tot.nchar + chars.done
if (tot.nchar == nchar*ntax) {
print("ntot was more than nchar*ntax")
break
}
pos <- tot.nchar
}
else {
i <- i + 1
}
}
if (tot.ntax != 0) {
cat("ntax:",ntax,"differ from actual number of taxa in file?\n")
stop("nexus parser did not read names correctly (tot.ntax!=0)")
}
for (i in 1:length(Obj)) {
if (length(Obj[[i]]) != nchar) {
cat(names(Obj[i]),"has",length(Obj[[i]]),"characters\n")
stop("nchar differ from sequence length (length(Obj[[i]])!=nchar)")
}
}
Obj <- lapply(Obj, tolower)
Obj
}
## by KS:
nexus2DNAbin <- function(x)
{
bs <- as.raw(._bs_)
cs <- ._cs_
fun <- function(x) {
res <- as.raw(0)
for (i in x) res <- res | bs[match(i, cs)]
res <- res & bs[15] # bs[15] == n
if (!(res %in% bs)) return(cs[17]) # return(?)
cs[match(res, bs)]
}
y <- unique(unlist(x))
y <- tolower(y)
y <- y[is.na(match(y, cs))]
if (length(y)) {
tmp <- strsplit(y, "/")
repl <- sapply(tmp, fun)
for (i in seq_along(x)) {
for (j in seq_along(y)) {
x[[i]] <- gsub(y[j], repl[j], x[[i]])
}
}
}
as.DNAbin(x)
}
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