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

Jason Stajich jason.stajich at duke.edu
Tue May 30 16:30:56 EDT 2006


you need to special case the root - it won't have an ancestor.  just  
protect the my $parent = $node->ancestor with an if statement as I  
did below

On May 30, 2006, at 4:11 PM, Lucia Peixoto wrote:

> 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 ){
>    >>> if(        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
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




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