[Bioperl-l] Bio::*Taxonomy* changes (Chris Fields)

Sendu Bala bix at sendu.me.uk
Fri Jul 28 14:38:20 UTC 2006

Gabriel Valiente wrote:
>> Would be nice to know how you use Bio::Taxonomy.  You are the first  
>> here who
>> seems to have a use for it.
> I'm using it to obtain a reference taxonomy for a set of organisms,  
> against which to assess a phylogeny obtained by the usual protocol  
> (fetch rRNA sequences, align them, obtain a distance matrix,  
> cluster). Roughly:
> use Bio::DB::Taxonomy;

Ah, we were specifically wondering if you had used Bio/Taxonomy.pm, not 
Taxonomy modules in general. Again, DB::Taxonomy usage will be unaffected.

> Here, get_lineage_nodes could be added as a method to  
> Bio::Taxonomy::Node or equivalent:
> sub get_lineage_nodes{
>    my $node = shift;
>    my @lineage;
>    while ($node->node_name ne "root") {
>      $node = $node->get_Parent_Node;
>      unshift @lineage, $node;
>    }
>    return @lineage;
> }

I think you must have an older version of bioperl. Bio::Taxonomy::Node 
has a method get_Lineage_Nodes() which more or less does exactly that.

> I've also written a method to merge the full lineages of a set of  
> Bio::Taxonomy::Node object into a Bio::Tree::Tree object. I'd be glad  
> to contribute it as well, but I'm not sure where it would fit.

Post it and I'll see if it will fit anywhere :)

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