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

[Lucia Peixoto]

Hi
Thanks
a couple more questions
why is the bootstrap value stored as the node id? Is that right?

also, in the add_descendant method, how do you set the $ignoreoverwrite
parameter to true?

Lucia

Quoting Jason Stajich <jason.stajich at duke.edu>:

> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania