[Bioperl-l] Bio::TreeIO functions

Lucia Peixoto luciap at sas.upenn.edu
Tue Mar 7 09:01:46 EST 2006


Hi
so bad that there's no collapse function yet, If I come up with something
usefull I'll add it

On the other hand, the remove_nodes function, even if it removes the selected
nodes and its children, alters the newick format and the end results can't be
opened by any tree viewer, anyone has has a similar experience?

I guess I should post this in bugzilla

Lucia

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

>
> On Mar 6, 2006, at 3:43 PM, Lucia Peixoto wrote:
>
> > Hi
> > I am trying to colapse nodes bellow a certain bootstrap cutoff
> > value, so I just
> > work only with the most confident nodes on my trees.
> > After getting the nodes bellow my cutoff (70, and with newick
> > format the
> > bootstrap value is actually the _creation_id), I though that if I
> > just call
>
> The bootstrap value is not the _creation_id, but it will be the $node-
>  >id - you shouldn't be using methods that start with _
>
> You can move it to the bootstrap with $node->bootstrap($id) if you
> want but of course the newick format doesn't distinguish - you can
> set the flavor of your newick format bootstrap values for reading and
> writing when you init it with Bio::TreeIO.  If you use a format like
> NHX it will distinguish bootstrap from node Id although only ATV/
> Forester will reliably read this format.
>
> delete definitely removes a node completely to collapse nodes (and
> those remodel the parent/child relationship) you want to use the
> remove_Descendent and add_Descendent methods.
>
> Please feel free to submit a 'collapse' function if you end up
> writing something that works.
>
> -jason
>
> > $tree->remove_Node($node) I will just get rid of the nodes and
> > update the
> > ancestor relationships within the tree, however when I call it it
> > actually
> > deletes those nodes and all its children.
> > Anyone has any idea how can I just delete certain nodes so that the
> > children are
> > preserved and the relationships are collpased to polytomies on the
> > confident
> > nodes?
> >
> > thanks
> >
> >
> > 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
>
>
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>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


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