bioperl remove a node from newick tree

Question

I'm trying to remove a node from a newick tree using bioperl. The tree file contains this data :

(((A:5,B:5)90:2,C:4)25:3,D:10);

Below is the code:

use Bio::TreeIO;
use Bio::Tree::TreeFunctionsI;
use strict;
use warnings;
my $input = new Bio::TreeIO(-file   => "tree.newick", -format => "newick");
my $tree = $input->next_tree;
my $bool = $tree-> remove_Node('B');
print $bool;

output: 1;

So the remove_Node is working, but the problem is when I open the tree file I find the node is still present!... What is wrong with the code ? how to remove the node from the tree??

Thanks in advance.

Answer 1

use strict;
use warnings;
use Bio::TreeIO;
use Bio::Tree::TreeFunctionsI;

my $in  = Bio::TreeIO->new( -format => 'newick', 
                            -file   => 'tree.newick' );

my $out = Bio::TreeIO->new( -format => 'newick' );

while ( my $tree = $in->next_tree ) {
   $tree->remove_Node('B');
   $out->write_tree($tree);
}