[Bioperl-l] Bio::TreeIO functions

Jason Stajich jason.stajich at duke.edu
Tue Mar 7 10:01:46 EST 2006


On Mar 7, 2006, at 9:01 AM, Lucia Peixoto wrote:

> Hi
> so bad that there's no collapse function yet, If I come up with  
> something
> usefull I'll add it
Shouldn't be hard to do -  give it a shot - for the node you want to  
collapse N, get N's ancestor A, add the children of N as children of  
A instead, remove descendents of N, and then delete N.
  I'll add a note to the wiki Project priority list so that it is  
tracked.
>
> 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've not had a similar experience, myself and others have used it to  
prune trees successfully.  Are you using bioperl 1.5.1 or the latest  
code from CVS?

>
> I guess I should post this in bugzilla

please do and include a simple code sample that demonstrates the  
problem.
>
> 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
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/




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