[Bioperl-l] Bio::TreeIO functions
jason.stajich at duke.edu
Tue Mar 7 10:21:17 EST 2006
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.
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:
>> so bad that there's no collapse function yet, If I come up with
>> 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
>> Quoting Jason Stajich <jason.stajich at duke.edu>:
>>> On Mar 6, 2006, at 3:43 PM, Lucia Peixoto wrote:
>>>> 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
>>>> 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
>>> 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.
>>>> $tree->remove_Node($node) I will just get rid of the nodes and
>>>> update the
>>>> ancestor relationships within the tree, however when I call it it
>>>> 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
>>>> Lucia Peixoto
>>>> Department of Biology,SAS
>>>> University of Pennsylvania
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>> Jason Stajich
>>> Duke University
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Lucia Peixoto
>> Department of Biology,SAS
>> University of Pennsylvania
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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