[Bioperl-l] phyloxml and element order

Frédéric Romagné frederic.romagne at gmail.com
Fri Jul 30 00:59:35 EDT 2010


Hi,

I'm using bioperl to create phyloxml trees, after few tentatives, i got my
tree with all the element/attributes i want but when I write the tree,
element are not written following the order specified in the XSD Schema.

For example, i got :

<clade>
   <clade>
      <name>Loxosceles intermedia</name>
      <taxonomy>
         <scientific_name>Araneomorphae Sicariidae</scientific_name>
      </taxonomy>
      <sequence>
         <accession source="Arachnoserver">969</accession>
         <mol_seq>HAAERADSRKPIWDIAHMVNDLELVD</mol_seq>
      </sequence>
   </clade>
   <taxonomy>
      <scientific_name>Araneomorphae Sicariidae</scientific_name>
   </taxonomy>
</clade>

The program forester complains that <taxonomy> should be written before the
<clade> element.

According to
http://phyloxml.wordpress.com/2009/11/25/order-of-elements-in-phyloxml this
is what bioperl is supposed to do.

All my element/attributes are set before writing the tree using
'add_Annotation', 'add_tag_value' and 'sequence' methods from a
Bio::Tree::AnnotatableNode object, so i think the error comes from the
write_tree method.

Any help would be appreciated.

Thank you,
Fred


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