8 Feb 2013 17:19
PhyloXML
Moretti Sébastien <sebastien.moretti <at> unil.ch>
2013-02-08 16:19:29 GMT
2013-02-08 16:19:29 GMT
Hi I would like to add some XML to an existing PhyloXML tree. No problem to read and write it. I would like to add <name>smthg</name> after the <phylogeny> tag as in http://www.phyloxml.org/examples_syntax/phyloxml_syntax_example_1.html but get problems with add_phyloXML_annotation() : Can't locate object method "annotation" via package "Bio::Tree::Tree" at /software/share/perl5/vendor_perl/Bio/TreeIO/phyloxml.pm line 984, <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 "annotation" via package "Bio::Tree::Tree" at /software/share/perl5/vendor_perl/Bio/TreeIO/phyloxml.pm line 984, <GEN0> line 1. at /software/share/perl5/vendor_perl/Bio/TreeIO/phyloxml.pm line 984 Bio::TreeIO::phyloxml::element_default('Bio::TreeIO::phyloxml=HASH(0x134b1268)') called at /software/share/perl5/vendor_perl/Bio/TreeIO/phyloxml.pm line 670 Bio::TreeIO::phyloxml::processXMLNode('Bio::TreeIO::phyloxml=HASH(0x134b1268)') called at /software/share/perl5/vendor_perl/Bio/TreeIO/phyloxml.pm line 309 Bio::TreeIO::phyloxml::add_phyloXML_annotation('Bio::TreeIO::phyloxml=HASH(0x134b1268)', '-obj', 'Bio::Tree::Tree=HASH(0x13525258)', '-xml', '<name>SUMF family</name>') called at ./add_annotation_to_phyloxml.pl line 40 I think I do something wrong but what ? Here is the code my $treeio = new Bio::TreeIO(-file => "$infile", -format => 'phyloxml', ); my $tree = $treeio->next_tree; # Add annotation $treeio->add_phyloXML_annotation(-obj => $tree, -xml => '<name>SUMF family</name>', ); -- -- Sébastien Moretti
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