Part 2: [Bioperl-l] TreeIO question/problem

[Simon K. Chan]

My apologies, but there was a mistake in my first email.  My code is actually
the following:  


use lib '/home/skchan/bioperl/bioperl-1.4';
use Bio::Tree::Node;
use Bio::TreeIO;
use Bio::Tree::Tree;
use Bio::Tree::TreeI;
                     
# obtained code from bioperl documentation:                                    
                      
my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree");
my $tree = $treeio->next_tree;
                                                                                
print "tree: $tree\n";

$treeio->next_tree does not return anything, thus, I cannot run get_nodes.

Many thanks again.

Simon


----- Forwarded message from "Simon K. Chan" <skchan at cs.usask.ca> -----
    Date: Tue, 09 Mar 2004 23:56:24 -0600
    From: "Simon K. Chan" <skchan at cs.usask.ca>
Reply-To: "Simon K. Chan" <skchan at cs.usask.ca>
 Subject: [Bioperl-l] TreeIO question/problem
      To: bioperl-l at bioperl.org

Hi,

I wish to parse a tree in newick format.

I attempted to use the TreeIO module to do so:

My problem is that $treeio->next_tree does not return anything, thus I cannot
call the get_nodes method to get all the nodes in my tree.

My code follows.  Many thanks for your time.

use lib '/home/skchan/bioperl/bioperl-1.4';
use Bio::Tree::Node;
use Bio::TreeIO;
use Bio::Tree::Tree;
use Bio::Tree::TreeI;
                     
# obtained code from bioperl documentation:                                    
                      
my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree");
my $tree = $treeio->next_tree;
                                                                                
print "tree: $tree\n";
                                                                                
my @nodes = $treeIO->get_nodes;
                                                                                
print "nodes: @nodes\n";




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