#!/usr/bin/perl -w
### remove_Node_bug.pl ###
# Created: Wed Sep 28 13:10:00 EDT 2005
# creator- Kevin Beckmann 

use strict;
use Bio::TreeIO;

my $file = "model_tree.phy";

my $treein = new Bio::TreeIO(-file => $file, -format => "newick");
my $tree = $treein->next_tree();
my $treestart = new Bio::TreeIO(-format => 'tabtree');
print "Starting tree:\n";
$treestart->write_tree($tree);

foreach my $node ( $tree->get_leaf_nodes() ) {
	my $leaf_id = $node->id();
	next if ($leaf_id ne "csa");
	
	$tree->remove_Node($node);
}

my $treeout = new Bio::TreeIO(-format => 'tabtree');
print "Tree w/ deleted node:\n";
$treeout->write_tree($tree);

$treeout = new Bio::TreeIO(-format => 'newick');
print "Extra set of parentheses:\n";
$treeout->write_tree($tree);
print "\n";
exit;