beast2newick

#!/bin/bash

## Convert beast mcmc-tree output to trees in newick format 
##
## 04/15/2009 13:37:35 AM CEST
## Johan Nylander
##
## Usage: beast2newick infile
##
## Notes: Requires the Perl script beast2phy.pl
##        Writes file <infile>.phy to cwd.
##

## Set globals
beast2phy="beast2phy.pl"
outputfileending='.phy'

## Check beast2phy.pl
beast2phy=`which $beast2phy`
if ! [ -x "$beast2phy" ]; then
    echo "beast2phy.pl can not be found in the PATH. Quitting."
    exit 1
fi

## Check arguments
if [ $# -gt 1  ] || [ ! $1 ] ; then
  echo
  echo "Usage: `basename $0` beast.tree.file"
  echo
  exit 1
fi

## Check input file
if [ -f "$1" ] ; then
      infile=$1
  else
      echo
      echo "File \"$1\" does not exist."
      echo "Usage: `basename $0` beast.tree.file"
      exit 1
fi

## Set output file
base=${infile%.*}
outfile=$base$outputfileending
if [ -e "$outfile" ] ; then
    echo
    echo "Outfile \"$outfile\" already exists. Quitting"
    echo
    exit 1
fi

## Try to convert
$beast2phy --decimals=6 --format=phy --outfile=$outfile $infile

## Finish
echo
echo "read $infile, wrote $outfile"
echo