R/kalign.R

In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

#######################################################################
# 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.

kalign <- 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="")
  
  writeXStringSet(x, infile, append=FALSE, format="fasta")
  
  ## call clustalw (needs to be installed and in the path!)
  system(paste(.findExecutable("kalign"), "-in", infile, "-out", outfile, 
    "-f fasta", "-quiet", param))
  
  if(is(x, "DNAStringSet")) 
    r <- readDNAMultipleAlignment(outfile, format="fasta")
  else  if(is(x, "RNAStringSet"))
    r <- readRNAMultipleAlignment(outfile, format="fasta")
  else stop("Type of XStringSet not supported!")
  
  r
}

kalign_help <- function() {
  system(paste(.findExecutable("kalign"), "-h"))
}