My question should be simple. I am looking to remove nodes from a phylogenetic tree. The splice function in bioperl should presumably take both the node ids or the node pointers. I have tried to include or and not include the root, yet I cannot get this function work. At first I created an array of nodes that I wanted to keep, but I have since reverted to trying to keep all the nodes and just trying to get the splice function to work.

Any help would be greatly appreciated.
Thank you! 

#!/usr/bin/env perl                                                   
+                                                       

use strict;
use warnings;

use Bio::TreeIO;
use Bio::Tree::TreeFunctionsI;
use Bio::Tree::Tree;
use Data::Dumper;
use Bio::Seq;
use Bio::SeqIO;
use Bio::Tree::Node;

my $usage = "usage: $0 treeFile \n";
my $treeFile = $ARGV[0] or die $usage;

my @stored;

my $treeio = new Bio::TreeIO('-format' => 'newick',
                             '-file' => $treeFile);
my $tree = $treeio->next_tree();
my $root_node = $tree->get_root_node;
my @nodes = $tree->get_nodes();
#push (@nodes, $root_node);
$tree->splice(-keep_node => \@nodes);
exit(0);

[download]

I get the following error:
--------------------- WARNING ---------------------
MSG: Requested to remove everything except certain nodes, but those nodes were not found; doing nothing instead
---------------------------------------------------

When I just print the node ids, it works fine and I can get the node ids or the pointers: 

my $tree = $treeio->next_tree();
my $root_node = $tree->get_root_node;
my @nodes = $tree->get_nodes();
foreach my $my_node (@nodes){
    print $my_node->id();
    print "\n";
}

[download]

In reply to Splice Function for Bioperl Tree editing by xela07

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