[Biopython-dev] Fwd: contributing comparative genomics tools

Albert Krewinkel krewink at inb.uni-luebeck.de
Wed Aug 16 12:44:07 UTC 2006


I read Peter's SeqIO/__init__.py replacement and if I may say so: I
love it.  Thanks a lot for this!  Still, there are some things I'd
like to talk about.

The _parse_genbank_features function could also be used to parse embl
or ddjb features, therefore I think it should be named differently.

Since there is a lot of clean up effort right now: How about moving
the SeqRecord and SeqFeature objects into the Bio.Seq module?  They
are closely related and seperate modules only clutter the namespace.

To me, this seems to be a general problem. It's very difficult to find
a tool to use for a certain problem if one doesn't allready know what
to look for.  I'd pretty much favour to create modules like
Bio.structure to group modules like Bio.PDB and Bio.NMR etc.  This is
a very big change, and therefore I'd like to follow Marc's suggestion
of splitting off a branch.  In general, I pretty much agree with what
Marc said in his <rant />.

I cannot estimate how much work it would be to maintain two seperate
biopython distributions, so please forgive me if I re-suggest
something completely idiotic here.  I just don't believe there is much
that could be lost that way.


Albert Krewinkel <krewink at inb.uni-luebeck.de>
University of Luebeck, Institute for Neuro- and Bioinformatics

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