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#!/usr/bin/perl -w
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=head1 NAME
tree2pag - convert Bio::TreeIO parseable format trees to pagel format
=head1 SYNOPSIS
 tree2pag -if nexus -i file.nexus > file.pag
 # OR pipe in through STDIN, and use newick format instead
 cat file.newick | tree2pag -if newick > file.nh
 # OR specify an output and input
 tree2pag -o file.pag -i file.newick
=head1 DESCRIPTION
Convert TreeIO parseable files into Pagel format tree files.  Be
warned that pagel format only really supports a single tree per file
so.  Also Pagel parsing is not yet available in bioperl.
=cut
use strict;
use Bio::TreeIO;
use Getopt::Long;
my ($iformat,$oformat) = ('newick', 'pag');
my ($outfile,$infile);
GetOptions(
           'if|informat:s'    => \$iformat,
           'of|outformat:s'   => \$oformat,
           'i|in:s'           => \$infile,
           'o|out:s'          => \$outfile,
           'h|help'           => sub { exec('perldoc', $0);
                                       exit(0); },
           );
my $in;
if( ! $infile ) {
    $in = Bio::TreeIO->new(-format => $iformat,
                           -fh     => \*ARGV);
} else { 
    $in = Bio::TreeIO->new(-format => $iformat,
                           -file   => $infile);
}
my $out;
if( $outfile) {
    $out = Bio::TreeIO->new(-format => $oformat,
                            -file   => ">$outfile");
} else { 
    $out = Bio::TreeIO->new(-format => $oformat); #print to STDOUT instead
}
while( my $t = $in->next_tree ) {
    $out->write_tree($t);
}