[Bioperl-l] phyloxml and element order

Dave Messina David.Messina at sbc.su.se
Mon Aug 2 09:58:10 EDT 2010


Hi Fred,

Thanks for letting us know about this — definitely sounds like a bug.

Would you please submit this to our bug tracker?

    http://bugzilla.open-bio.org


(You can just copy and paste your previous email.)

Dave



On Jul 30, 2010, at 06:59, Frédéric Romagné wrote:

> 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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> Bioperl-l at lists.open-bio.org
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