[Bioperl-l] Project suggestion: Restriction Enzyme Analysis

[Neill White]

> I had been playing with REBASE for a little while, and was in the middle of a 
> script to parse one of the rebase files, so I munged that, broke all Steve's 
> code, and came up with something to start with.
> 
> All of the hard work was already done by Steve and I just moved things around 
> enough so that nothing works now (not quite), and plastered my name all over 
> the place.
> 
> I have added more comments to the bugzilla page 
> (http://bugzilla.bioperl.org/show_bug.cgi?id=1422) that describe the changes 
> in more detail.
> 
> Anyway, take a look and send me comments.
> 
> http://www.salmonella.org/bioperl/
> 
> Rob

It looks good.  

I'm especially interested in getting support for non-blunt cutters - the 
digest fragments that are returned are for the 5' sequence only and I'd
like to see fragment collections of the 3' sequence as well.  Does
anyone have a strong preference as to how this should be implemented?
i.e., 
RestrictionEnzymeAnalysisObj->{'enz'}->{'five_prime_fragments'} = @frags_5p;
RestrictionEnzymeAnalysisObj->{'enz'}->{'three_prime_fragments'} = @frags_3p;

I'm anxious to get started on this and the partial digests - but 
want to see if the new classes that Rob has created are going
to take hold.  What do others think of the new RestrictionEnzyme classes?

-neill

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