[Bioperl-l] game xml SeqIO

Brian Osborne osborne1 at optonline.net
Tue Feb 14 16:32:42 EST 2006


Robert,

It looks like you're right that this data isn't handled by SeqIO/game. If
you'd like to add this then feel free to do it, the modified files or
patches can be submitted to bugzilla.bioperl.org. If you take this on then
please add a test or 2 to t/game.t as well.

Yes, Bio::SeqFeature::Computation sounds right - does it match the data
you're trying to parse? SeqFeature::Generic is the most commonly used, and
it's flexible, but if another type of SeqFeature fits your data more
precisely then that's the one you should use.

Brian O.


On 2/13/06 5:12 PM, "Robert Buels" <rmb32 at cornell.edu> wrote:

> Hi all,
> 
> Currently, the SeqIO for doing GAME XML does not seem to support writing
> (or reading?) <computational_analysis> elements.  Am I correct?
> 
> If I am, are there any plans to add this functionality?  Can I help / do it?
> 
> If there are plans to add this, how would one distinguish SeqFeatures
> that should be rendered as <computational_analysis> from SeqFeatures
> that should be rendered as <annotation>?  Would we do that with
> Bio::SeqFeature::Computation?  I assume that a given Seq can have
> SeqFeatures of different types associated with it (I don't know, I'm a
> bioperl newb).
> 
> Rob




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