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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: PhyloXML
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 13th February 2013 15:47:17 UTC (over 3 years ago)
On Feb 11, 2013, at 1:08 AM, S├ębastien MORETTI 
wrote:

>>> # Add annotation
>>> $treeio->add_phyloXML_annotation(-obj => $tree,
>>>                                -xml => 'SUMF family',
>>>                               );
>> 
>> 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 => 'SUMF family',
>                              );
> 
> Can't locate object method "add_phyloXML_annotation" via package
> 	"Bio::Tree::Tree" at ./add_annotation_to_phyloxml.pl line 40, 
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,  line
1.
> at ./add_annotation_to_phyloxml.pl line 40
> 
> 
> 
> -- 
> S├ębastien 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
 
CD: 3ms