[Biopython-dev] GenBank parser -- first go

Jeffrey Chang jchang at SMI.Stanford.EDU
Thu Dec 7 19:24:23 EST 2000

> [SeqFeature classes]
> > Yes, I definitely agree with needing a general class.  However, I've been
> > purposefully shying away from proposing a general framework for
> > annotations for two main reasons.
> > [Blah blah]

> Agreed. I think our chances of getting it perfect are pretty slim
> :-). However, I think it would really help writing "applications that
> use Biopython" to have some kind of general class to work off of (even 
> if it is imperfect). It is just too much work to have to support
> Genbank record classes and EMBL record classes and whatever record
> classes.

That sounds reasonable.  Yes, having specific classes for every format is
a lot of work.  It's fine to map directly into a general class, since
bioperl shows that it's still useful for people.

> I'm not sure if my SeqFeature classes are the best thing ever, but it
> is just meant as a bit of a start. I am definately willing to throw
> out/ammend lots of what I wrote if people have got ideas for changing
> them to be better.

A good test of its generality is to see whether you can map the data from
other classes, e.g. Fasta.Record, SwissProt.SProt.Record, or
Medline.Record into it.

> from Bio.Feature import SeqFeature
> Either way is fine, though (or I'm very open to additional
> suggestions), so whatever you think.

Are there going to be other Features not applied to sequences, such as

I don't think there should be a separate package for Feature.  The
SeqFeature stuff should be close to the Seq class.


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