[Bioperl-l] TreeIO question/problem
Simon K. Chan
skchan at cs.usask.ca
Wed Mar 10 00:56:24 EST 2004
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';
# 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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