#######################################################################
# BiostringsTools - Interfaces to several sequence alignment and
# classification tools
# Copyright (C) 2012 Michael Hahsler and Anurag Nagar
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# any later version.
#
# 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.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
clustal <- function(x, param=NULL) {
## get temp files and change working directory
wd <- tempdir()
dir <- getwd()
temp_file <- basename(tempfile(tmpdir = wd))
on.exit({
file.remove(Sys.glob(paste(temp_file, ".*", sep="")))
setwd(dir)
})
setwd(wd)
infile <- paste(temp_file, ".in", sep="")
outfile <- paste(temp_file, ".aln", sep="")
reader <- if(is(x, "RNAStringSet")) readRNAMultipleAlignment
else if(is(x, "DNAStringSet")) readDNAMultipleAlignment
else if(is(x, "AAStringSet")) readAAMultipleAlignment
else stop("Unknown sequence type!")
writeXStringSet(x, infile, append=FALSE, format="fasta")
## call clustalw (needs to be installed and in the path!)
system(paste(.findExecutable(c("clustalw", "clustalw2")),
infile, param))
reader(outfile, format="clustal")
}
clustal_help <- function() {
system(paste(.findExecutable(c("clustalw", "clustalw2")),
"-help"))
}
clustal_profile <- function(x, y, param=NULL) {
if(is(y, "DNAMultipleAlignment")) {
profileprofile <- TRUE
param2 <- "-profile"
} else {
profileprofile <- FALSE
param2 <- "-sequence"
}
## get temp files and change working directory
wd <- tempdir()
dir <- getwd()
temp_file <- basename(tempfile(tmpdir = wd))
on.exit({
file.remove(Sys.glob(paste(temp_file, ".*", sep="")))
setwd(dir)
})
setwd(wd)
prof1 <- paste(temp_file, ".in1", sep="")
prof2 <- paste(temp_file, ".in2", sep="")
outfile <- paste(temp_file, ".aln", sep="")
write.phylip(x, prof1)
if(profileprofile) write.phylip(y, prof2)
else writeXStringSet(y, prof2, append=FALSE, format="fasta")
## call clustalw (needs to be installed and in the path!)
system(paste(.findExecutable(c("clustalw", "clustalw2")),
" -profile1=", prof1,
" -profile2=", prof2,
" ", param2, " ", param, sep=""))
readDNAMultipleAlignment(paste(temp_file, ".aln", sep=""),
format="clustal")
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.