[Biopython-dev] Fwd: contributing comparative genomics tools

Marc Colosimo mcolosimo at mitre.org
Thu Aug 17 12:24:24 UTC 2006

On Aug 16, 2006, at 8:44 AM, Albert Krewinkel wrote:
> Hello,
> 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.
The top namespace is sort of a mess of things.
> 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.

I second this.
> 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.
I've done this for my internal work, but I never went back to see how  
to check out the other branch (I had not need). CVS is sometimes a  
bear to work with. SVN is suppose to handle branches much better, but  
I can't access SVN repositories that are not through HTTPS (SSL).  
Stupid corporate proxy is  currently not set up to handle external  

This might be a pain for a little while until the next full version  
is released, but I think the benfits of doing this now far out weigh  
the short term pain (of course I'm not an admin who has to build the  


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