[Biopython-dev] reusable code in Genbank

Brad Chapman chapmanb at arches.uga.edu
Wed Mar 14 05:33:21 EST 2001

> .   Since this post, I've noticed more opportunities to reuse code.  I think
> the class Referennce.py in Genbank is close enough to the Kabat references
> to use as a base class.

For reusing representations of common objects like this, I think the
best way to go is to the use the Seq, SeqRecord and SeqFeature
stuff. In my mind, these are supposed to represent common reusable
objects, like references. On the other hand, the Reference.py is
GenBank is meant to be an "exactly like GenBank" representation of a
reference, for people who only care about GenBank. Because of this,
this class will change if GenBank changes.

So, if you want to reuse a reference object, I think the best thing to 
do would be to use the Reference class in Bio/SeqFeature.py. This is
what this class (and everything else in SeqFeature was designed
for). Let me know if this doesn't work for what you need.


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