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Gmane
From: =?ISO-8859-1?Q?Moretti_S=E9bastien?= <sebastien.moretti <at> unil.ch>
Subject: Re: PhyloXML
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 13th February 2013 16:21:23 UTC (over 3 years ago)
>>>> # 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
>
> 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

You mean that BioPerl 1.6.901 has not a full support of PhyloXML ?
The problem I have is "expected" ?

-- 
S├ębastien Moretti
 
CD: 4ms