[Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes
Greg Baillie
gb7 at sanger.ac.uk
Thu Jul 8 14:24:14 UTC 2010
Hi Jason.
I'm trying to get access to the posterior probability value, rate, etc,
that are stored within open-square-bracket-ampersand and
close-square-bracket ([&<here>]) blocks in the tree string. It appears
that this information is stripped out during the parsing of the tree
string (I have tried to get it from the $node->bootstrap()).
I'm having trouble identifying the module that parses the tree string -
I thought I might be able to modify that. Any suggestions where I might
find the appropriate code?
In the meantime, I'll look at the Bio::Phylo modules (as per Chris'
suggestion) to see if they have a way of handling that info.
Thanks.
Greg.
Jason Stajich wrote:
> Hi -
>
> Is this just that you have internal nodes labeled with the
> bootstrap/posterior value? If so you just want the node ids for the
> internal nodes then. The semantics of what is encoded in the internal
> nodes is not forced by the nexus format so it assumes they are ids by
> default.
> You can call $tree->move_id_to_bootstrap
> to migrate the ids of internal nodes to the bootstrap option.
>
> you can also use the -internal_node_id => 'bootstrap' option when
> initializing TreeIO objects too:
>
> =head2 new
>
> Title : new
> Usage : my $obj = Bio::TreeIO->new();
> Function: Builds a new Bio::TreeIO object
> Returns : Bio::TreeIO
> Args : a hash. useful keys:
> -format : Specify the format of the file. Supported formats:
>
> newick Newick tree format
> nexus Nexus tree format
> nhx NHX tree format
> svggraph SVG graphical representation of tree
> tabtree ASCII text representation of tree
> lintree lintree output format
> -internal_node_id : what is stored in the internal node ids,
> bootstrap values or ids, coded as
> 'bootstrap' or 'id'
>
> -jason
> Greg Baillie wrote, On 7/7/10 7:41 AM:
>> Hi.
>>
>> I'm trying to extract information (eg. posterior values) from nodes
>> of trees generated using BEAST/treeannotator/FigTree.
>>
>> The trees, which are in nexus format, seem to load OK, but when I
>> iterate through the nodes looking for posterior values (/if (
>> $node->has_tag('posterior') ) {.../), none of the nodes seem to have
>> posteriors.
>>
>> In fact, none of the nodes have any tags (/my @tags =
>> $node->get_all_tags(); print join ',', @tags/). And when I dump an
>> entire tree using Data::Dumper, there is no sign of any of the node
>> values.
>>
>> Does TreeIO handle these values? If so, should I be looking somewhere
>> other than the tags for the values?
>>
>> Thanks.
>>
>> Greg.
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