[Bioperl-l] suggestions for suitable 'taxon' object
cjfields at uiuc.edu
Wed Dec 20 01:16:47 EST 2006
On Dec 19, 2006, at 10:23 PM, Rutger Vos wrote:
> Hi all,
> I am looking for a bioperl object that can be abused to function as a
> suitable 'taxon' object, where I mean 'taxon' as understood by the
> file format (i.e. not strictly an entity from a taxonomy, but more
> an OTU).
> The object would primarily function as a way to relate nodes in
> trees to
> sequences in an alignment (a foreign key that both nodes and
> sequences refer
> to), and secondarily as the keeper of the canonical name of the
> OTU, such
> that a sequence named 'Homo_sapiens|EF177447.1/12-56' and a node
> named 'Homo
> sapiens (constrained monophyly)' can still be understood to refer
> to the
> same thing - the OTU 'Homo sapiens sapiens' (for example).
Alignment (SimpleAlign) objects contain Bio::LocatableSeq sequence
objects; at the moment LocatableSeqs don't store their own annotation
but they could easily be made or subclassed to be AnnotatableI (i.e.
they can store annotation collections). I recently made SimpleAlign
Annotatable; Jason has also made SimpleAlign implement
FeatureHolderI, so alignments can store SeqFeatures as well; he may
have his own designs here.
There may be a wide variety of ways to go about this. I would
probably do the following (bear in mind I'm a microbiologist, not a
computer scientist). If one could add trees as annotation to the
alignment (i.e. if trees could be Annotation objects and kept in the
SimpleAlign's annotation collection), and each sequence in the
alignment contained reference to a node object of the tree (i.e. if
Bio::Taxon/Bio::Species objects could also be Annotation objects, but
kept in a LocatableSeq annotation collection), both could refer to
the same node object. This may not be exactly what you want, but
maybe it's close?
I suppose this could also be done with Seqfeatures...
> I was thinking that a (possibly expanded) Bio::Species might work
> if there
> was some sensible way of appending references to node and sequence
> to it (or otherwise associate them with each other), but I am
> writing *to
> solicit any and all suggestions*. I am looking for something
> similar to
> Any and all comments and suggestions greatly appreciated!
> Best wishes,
> Rutger Vos
Sendu would be the best one to speak about Bio::Taxon and
Bio::Species and may have some ideas on the above. The current plan
was to deprecate Bio::Species, but who knows?
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