[Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question

Scott Cain scott at scottcain.net
Thu Oct 28 23:41:09 EDT 2010

Hi Daniel,

It seems like the easiest thing to do would be to subclass
Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
(maybe only once), so subclassing and having it use your class instead
would probably be the easiest thing to do.

Also, about having it produce GFF3: make sure you're actually getting
valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
give it valid SeqFeature objects and get invalid GFF3 out in some


On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I am using the Bio::Tools::GFF parser to process and store GFF3 data
> in an application. Calls to next_feature() return
> Bio::SeqFeature::Generic objects. I have written a class that extends
> the Bio::SeqFeature::Generic class, but I still want to use the
> Bio::Tools::GFF class to do the initial parsing of the data.
> Is there a way for me to tell the Bio::Tools::GFF parser that I want
> it to give me objects from my custom class? Or should I just re-bless
> the objects it gives me? Will I run into garbage collection problems
> if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> (that extends the Bio::SeqFeature::Generic class)?
> Thanks!
> Daniel
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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