[Bioperl-l] TreeIO and bootstrap values

[Lee Katz]

Very informative! Thanks! I also understand now why you have that method.
Now that I understand what to do, the extra method is not necessary for me.
However it might make bioperl easier to use for future users of treeio.
On Dec 28, 2013 9:16 PM, "Jason Stajich" <jason.stajich at gmail.com> wrote:

> Bootstrap is not a fixed newick field -
> best thing is to set the internal ID to the bootstrap value, that is where
> it is read from when writing a newick tee.
>
> replace $node->bootstrap( ... )
> with
> $node->id( ... );
>
> Or use NHX format which has separate fields for bootstrap and ID.
>
> There is also a connivence function which will copy IDs to the bootstrap
> field on the whole tree, (move_id_to_boostrap defined
> Bio::Tree::TreeFunctionsI) but there is not a corresponding reverse
> function that would move bootstrap to id at the moment, though it would be
> trivial to add this patch if you think it is useful enough.
>
>
> On Dec 23, 2013, at 2:44 PM, Lee Katz <lskatz at gmail.com> wrote:
>
> > Hi, I want to change the bootstrap values in my phylogeny to some
> > artificial Fst values I created earlier in the script.  This subroutine
> > seems to be doing the trick because Data::Dumper shows that the nodes and
> > the tree have the new bootstraps.  However, the resulting Newick tree
> does
> > not display them.  Can anyone help?  Thank you.
> >
> > http://pastie.org/private/wtn0pqgjwrmpdswodok4mw#
> >
> > sub printTree{
> >  my($fst,$tree,$settings)=@_;
> >  my $treeIn=new Bio::TreeIO(-file=>$tree)->next_tree;
> >  my $out=Bio::TreeIO->new(-format=>"newick");
> >  for my $node($treeIn->get_nodes){    # get all descendents of the
> > node and alpha-sort them    my @d=sort{$a->id cmp $b->id}
> > $node->each_Descendent;    next if(!@d);    # make a comma-separated
> > key    my $key; $key.=$_->id."," for(@d);    $key=~s/,$//;    # next
> > if that key isn't in $fst: not all $fst combos were calculated.
> > next if(!$$fst{$key});    # apply the Fst with that key
> > $node->bootstrap($$fst{$key});
> >  }
> >
> >  $out->write_tree($treeIn);
> > }
> >
> >
> > --
> > Lee Katz, Ph.D.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>