[Bioperl-l] Bio::Restriction

[Rob Edwards]

I have just added the latest version of Bio::Restriction to cvs. The 
changes here are mainly to Restriction::Analysis, and should speed up 
looking at longer sequences, and adding functionality suggested by 
Peter.

Restriction::Analysis should correctly handle the following:

- overlapping sites
- sites at or near the join points of circular sequences
- non-palindromic restriction enzymes
- enzymes that cut at more than one site
- enzymes that cut more than once per site

Restriction::Analysis should be more suitable for handling much larger 
sequences, using less memory and (hopefully) being faster than previous 
versions, especially for collections of non-ambiguous enzymes.

The only thing that is stored for all enzymes are the cut positions 
(integers), and some statistics about how frequently each enzyme cuts 
and so forth. You can still get fragments and fragment maps out, 
they're just generated each time they are requested for each enzyme.

The code should be cleaner and more readable too, now!

I also fixed the tests that were failing with RestrictionIO.

I removed the dependency on the caret (^) in the cut site, and now 
Analysis.pm just uses the values returned by cut and complementary_cut. 
Next on the list is to clean up Enzyme.pm and remove the caret unless 
it is essential.

I also submitted the beginnings of a bairoch format rebase IO filter. 
This is barely limping in at the moment so use with caution, but this 
is the format that MacVector, VectorNTI, and PC/Gene support so I 
wanted to add this in.

Rob