[Bioperl-l] Bio::Species, Bio::Taxonomy::Node overhaul

Chris Fields cjfields at uiuc.edu
Mon Aug 7 15:10:48 EDT 2006

On Aug 7, 2006, at 1:09 PM, Sendu Bala wrote:

> The other point of contention was with what Bio::Species::species  
> should
> return, and again since its debatable I'll go with the old expected
> behaviour (guess badly what the specific name is).

This 'guessing badly' already occurs in SeqIO, so you wouldn't have  
to do anything about it.  My initial idea was to snip out all  
dependencies that SeqIO has on Bio::Species, replacing them with  
streamlined dependencies (i.e. no 'guessing') using  
Bio::Taxonomy::Node.  You can do the same with Bio::Taxon,  
Bio::DB::Taxonomy::list, and the RichSeq organelle() method for I/O.   
Although redundant, this would allow for the gradual transition  
Hilmar suggested (and the data is small; not like you're storing a  
copy of the sequence or features).  Therefore you wouldn't have to  
worry about weird API issues with species() etc.

1)  Make the critical replacement allowing read/write using  
Bio::Taxon instead of Bio::Species
2)  Notify the group about changes, but indicate that Bio::Species  
will be supported until v 1.6.
3)  At bioperl v1.6, add warnings but continue allowing use of  
4)  Remove Bio::Species, have the RichSeq species() throw or make it  
act as an alias of taxon().

# lineage stored here or in a separate Bio::DB::Taxonomy::list
$taxon = $seq->taxon;  # get Bio::Taxon object
# use Bio::Taxon specific methods here

$species = $seq->species; # get Bio::Species object
# use Bio::Species methods here
# eventually add warnings then deprecate

#both the below return the same info; latter will be deprecated
$seq->organelle();  # new
$seq->species->organelle(); #old

#eventually deprecate Bio::Species and species()


> I'll wait till this weekend for any more comments and then commit and
> add to the wiki.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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