Hi all,
I had a short look in the code and found some bits to speed the
read.nexus.data function up. I added Emmanuel on the list so he may
can put it into the next ape release if it does work.
Generally I agree with Johan that if speed matters fasta files are the
way to go. Nexus files are ugly to parse and contain many
inconsistencies, like parameters inside comments [].
Regards,
Klaus
On 4/9/13, Johan Nylander <johan.nylan...@abc.se> wrote:
> Dear All,
>
> Just to avoid confusion, the readNexus function is in the phylobase
> package. And as Ben pointed out, other packages have their own functions
> for reading the data part from a nexus-formatted file, see e.g., read.nex
> in phyloch.
>
> On a related note, I wrote read.nexus.data as a "temporary", crude parsing
> function while waiting for the phylobase project to take off (phylobase
> uses NCL by Lewis & Holder - _the_ nexus parser), so expect
> read.nexus.data to have it's limitations.
>
> Furthermore, if speed is the concern, it would perhaps be preferable to
> first convert the Nexus data to Fasta, and then use one of the many
> fast(er) parsers implemented in numerous R packages.
>
> Cheers
> Johan
>
>
> On 04/07/2013 02:59 PM, Ben Bolker wrote:> On 13-04-05 01:29 PM, Jessica
> Sabo wrote:
>>> Hi All,
>>>
>>> I am wondering if there is anyway to increase the speed of the
>>> read.nexus.data parser. Or if there is an alternative that is a
>>> faster nexus file data parser.
>>>
>>> THanks, Jess
>>>
>>
>> I don't know if it's faster or not, but there is ?readNexus in the
>> 'ape' package. Also see library("sos"); findFn("read {nexus format}")
>>
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--
Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
read.nexus.data <- function (file)
{
"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)
}
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 <- vector("list", ntax)
for(i in 1:ntax)Obj[[i]] = rep(NA, nchar)
i <- 1
pos <- 0
tot.nchar <- 0
tot.ntax <- 0
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))
# browser()
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]]
Obj[[l]][pos + c(1:length(tsp))] <- tsp
chars.done <- length(tsp)
}
else {
names(Obj)[i] <- Name
tsp <- strsplit(Seq, NULL)[[1]]
Obj[[i]][pos + c(1:length(tsp))] <- tsp
chars.done <- length(tsp)
}
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
}
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