[Bioperl-l] Bio::Restriction issues

[Heikki Lehvaslaiho]

Hi Rob,

Are you working on the Bio::Restriction bugs? It would be great to patch the 
Analysis module up for the 1.4 release. I had look but I do not want to 
duplicate what you are doing. Here are my current thoughts:

The main concerns seem to be:
1. MultiSite and MultiCut are not taken into account
2. sites in around start/end of circular molecules are cut.

These all problems have to do with  _new_cuts(). 
(_cuts() is now obsolete and could be removed?)

1. We have to change the IO modules so that only one Enzyme object is added 
into EnzymeCollection (the other versions can be accessed using others()). 
_new_cuts() then checks for enzyme type using isa() and loops over sequence 
for each Enzyme object. Instead of producing an array of fragments, it 
creates and array of cut sites and every Enzyme cuts the original sequence. 
In the end the cut site array is sorted and fragments created from the 
original sequence.

2. circular molecules need to be tested before cutting. To allow cuts across 
start.end boundary, the cut site needs to be analysed for each enzyme and the 
correct number of bases need to be added to the end (?) of the string from 
the start. When cut sites locations are converted into fragments, the 
locations are compared to the length of the original sequence and placed 
appropriately. 

Looks like the _new_cuts() code needs to be redistributed into smaller methods 
to make the logic of the code easier to follow. 

What do you think?

	-Heikki


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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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