-## clustal.R (2011-03-16)
+## clustal.R (2012-11-28)
## Multiple Sequence Alignment with External Applications
-## Copyright 2011 Emmanuel Paradis
+## Copyright 2011-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
clustal <- function(x, pw.gapopen = 10, pw.gapext = 0.1,
gapopen = 10, gapext = 0.2, exec = NULL,
- MoreArgs = "", quiet = TRUE)
+ MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
{
os <- Sys.info()[1]
if (is.null(exec)) {
if (os == "Linux") exec <- "clustalw"
if (os == "Darwin") exec <- "clustalw2"
- if (os == "Windows") exec <- "C:/Program Files/ClustalW2/clustalw2"
+ if (os == "Windows") shortPathName("C:/Program Files/ClustalW2/clustalw2.exe")
}
if (missing(x)) {
opts <- paste(prefix, suffix, sep = "=", collapse = " ")
opts <- paste(opts, MoreArgs)
system(paste(exec, opts), ignore.stdout = quiet)
- read.dna(outf, "clustal")
+ res <- read.dna(outf, "clustal")
+ if (original.ordering) res <- res[labels(x), ]
+ res
}
-muscle <- function(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
+muscle <- function(x, exec = "muscle", MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
{
if (missing(x)) {
system(exec)
if (quiet) opts <- paste(opts, "-quiet")
opts <- paste(opts, MoreArgs)
system(paste(exec, opts))
- read.dna(outf, "fasta")
+ res <- read.dna(outf, "fasta")
+ if (original.ordering) res <- res[labels(x), ]
+ res
}
-tcoffee <- function(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
+tcoffee <- function(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
{
if (missing(x)) {
system(exec)
opts <- paste(inf, MoreArgs)
if (quiet) opts <- paste(opts, "-quiet=nothing")
system(paste(exec, opts))
- read.dna("input_tcoffee.aln", "clustal")
+ res <- read.dna("input_tcoffee.aln", "clustal")
+ if (original.ordering) res <- res[labels(x), ]
+ res
}