[Bioperl-l] Bio::Tree::IO "Collapse" function

[Lucia Peixoto]

Hi
OK that was silly, but what I have in my code is what you just wrote
But the problem is that if I write

$parent->add_Descendent($child)

it tells me that I am calling  the method "ass_Descendent" on an undefined value
(but I did define $parent before??)

So here it goes the code so far:

use Bio::TreeIO;
 my $in = new Bio::TreeIO(-file => 'Test2.tre',
                          -format => 'newick');
 my $out = new Bio::TreeIO(-file => '>mytree.out',
                           -format => 'newick');
 while( my $tree = $in->next_tree ) {
    foreach my $node ( grep { ! $_->is_Leaf() } $tree->get_nodes() ) {
    my $bootstrap=$node->_creation_id;

    if ($bootstrap < 70 ){
            my $parent = $node->ancestor;
            my @children=$node->get_all_Descendents;
            foreach my $child (@children){
                $parent->add_Descendent($child);
            }

........

eventually I'll add (once I assigned the children to the parent succesfully):
$tree->remove_Node($node);

        }
    }
    $out->write_tree($tree);
}

Quoting aaron.j.mackey at gsk.com:

> > foreach $child (@children){
> >          $parent=add_Descendent->$child;
> > }
>
> I think what you want is $parent->add_Descendent($child)
>
> -Aaron
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania