[Bioperl-l] PhyloXML

[Fields, Christopher J]

On Feb 11, 2013, at 1:08 AM, Sébastien MORETTI <sebastien.moretti at unil.ch> wrote:

>>> # Add annotation
>>> $treeio->add_phyloXML_annotation(-obj => $tree,
>>>                                -xml => '<name>SUMF family</name>',
>>>                               );
>> 
>> If you really have $treeio in your script in this line and not $tree, then that's at least one problem. But the stack suggests that the above isn't the exact line in your script - can you confirm that?
>> 
>> 	-hilmar
> 
> I replaced $treeio by $tree in the above line but still get an error.
> Don't see what you mean by "the stack suggests that the above isn't the exact line in your script"
> 
> The only think I changed is the length of the xml string I try to insert. But get the same error with an empty xml string.
> 
> 
> 
> my $treeio = new Bio::TreeIO(-file   => "$infile",
>                             -format => 'phyloxml',
>                            );
> my $tree = $treeio->next_tree;
> 
> # Add annotation
> $tree->add_phyloXML_annotation(-obj => $tree,
>                               -xml => '<name>SUMF family</name>',
>                              );
> 
> Can't locate object method "add_phyloXML_annotation" via package
> 	"Bio::Tree::Tree" at ./add_annotation_to_phyloxml.pl line 40, <GEN0> line 1 (#1)
>    (F) You called a method correctly, and it correctly indicated a package
>    functioning as a class, but that package doesn't define that particular
>    method, nor does any of its base classes.  See perlobj.
> 
> Uncaught exception from user code:
> 	Can't locate object method "add_phyloXML_annotation" via package "Bio::Tree::Tree" at ./add_annotation_to_phyloxml.pl line 40, <GEN0> line 1.
> at ./add_annotation_to_phyloxml.pl line 40
> 
> 
> 
> -- 
> Sébastien Moretti
> Department of Ecology and Evolution,
> Biophore, University of Lausanne,
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4221/4079
> http://bioinfo.unil.ch/\

Will have to look into this.  One problem we have is that phyloXML support has dwindled, so if anyone wants to take this on I would be more than happy to help them get started.

chris