[Bioperl-l] Bio::Restriction::Analysis feature merge

[Rob Edwards]

Peter,

I have a few comments on these revised modules:

1. Does circularity work OK? It fails the tests I devised at the moment 
(there is an MwoI site near the 0 point on t/data/dna1.fa)
2. It doesn't seem to handle multiple digests - did you add this in and 
am I missing it?
3. Do you have other test scripts that you have run on these so I can 
compare?
4. I don't like the idea of reverse complementing the target sequence. 
If you are using a large target sequence (e.g. 1 Mbp or more) this will 
be horrible. It would be a lot better to reverse the enzyme and should 
be the same (of course, you'd have to reverse the complementary strand 
of the non-palindroimic enzyme).
5. The newer version of Enzyme.pm (in cvs) doesn't require Storable.pm, 
and this is better than demanding it be there.

If you are done working on this I'll fix it up and alter the method 
that gets the cut site to move that into Enzyme.pm so that Analysis 
just works with the integers, and add the changed modules into cvs 
before the weekend. If you have made any other changes can you email 
them to me so I can incorporate them too?

Thanks

Rob



On Sunday, December 7, 2003, at 08:32  PM, Peter Blaiklock wrote:

> Hi
>
>    I modified my new Bio::Restriction::Analysis module to incorporate 
> Rob's
> changes, including the use of index to locate nonambiguous sites and a
> digestion method that can handle multiple enzymes.  Please let me know 
> about
> any problems, suggestions, bugs, etc. I should have tests ready in a 
> day or
> two.
>
>  http://www.restrictionmapper.org/bioperl/Analysis.pm
>  http://www.restrictionmapper.org/bioperl/Enzyme.pm
>  http://www.restrictionmapper.org/bioperl/base.pm
>
>  Peter Blaiklock
>
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