[Bioperl-l] Bio::TreeIO functions

[Jason Stajich]

If you'd like some of those options off in the NEXUS trees just say  
so they are easily customizable to make write_tree - since there are  
so many flavors.  I only used the protml bootstrap flavor output by  
default because that was what I needed in nexus, but the newick  
writer is customized so that you can request where you want the  
bootstrap values ( removing the need for your s/\[\d+?\]//g;  
pattern).   This is pretty easy bit to add to the nexus writer as I  
would imagine it is preferrable to having to hack the output again  
when you get it out of the scripts.


I just use newick for treeview and I've never had a problem so I am  
confused what is causing the problems - I guess we'll just wait for  
bugs to be submitted to bugzilla.

-jason
On Mar 7, 2006, at 10:10 AM, Georgii A Bazykin wrote:

> I had similar experience... The attached script worked for me to
> covert the bioperl-generated nexus tree into treeview-readable - check
> if it helps you as a quick solution.
>
> Yegor Bazykin
>
>
> ------------------------------
> Tuesday, March 7, 2006, 9:01:46 AM, you wrote:
>
>> 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
>>>
>>>
>>> _______________________________________________
>>> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> <nexus_bioperl2nexus_treeview.pl>

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