[Bioperl-l] RetrictionEnzyme.pm: a proposal

[Heikki Lehvaslaiho]

Paul-Christophe,

Please have a look at Bio::Variation::VariantI::restriction_changes,
too.
I would have prefered to use Bio::Tools::RestrictionEnzyme but decided
not to depend on it as I found it too complicated. It would be great
not to have to duplicate restriction enzyme lists and functionality.
If you come up with a solution I'd be happy to remove or modify the 
restriction_changes method.

	-Heikki

Paul-Christophe Varoutas wrote:
> 
> Yesterday I studied RestrictionEnzyme.pm more in depth. I haven't yet added
> the methods I wanted to, because in my opinion it is far more urgent for
> this module to get some redesigning.
> 
> The module somewhat suffers of poor design, and just adding methods to it
> will just worsen the situation.
> 
> RestrictionEnzyme has methods which are proper to the restriction enzymes:
>   - seq() is the accessor method to the enzyme's recognition sequence.
>   - cut_seq() "cuts" a Bio::Seq-derived object and generates an array of
> restriction site fragments.
>   - cuts_seq_at() does the same but this time generates an array of
> restriction site coordinates.
> 
> and methods which are proper to the list of enzymes:
>   - is_available() says if a particular enzyme is in the list.
>   - available_list() gives the list of all enzymes or list of n-base cutters.
> 
> Steve Chervitz already suggested in the module's documentation that
> is_available() "may be more appropriate for a REData.pm class", and I share
> his opinion. From a conceptual point of view, the existing
> RestrictionEnzyme.pm module corresponds to two object classes, not one.
> 
> Here is an outline of my proposal:
> 
> Separate RestrictionEnzyme in two classes:
> 
> RestrictionEnzymeDBase (or whatever more appropriate):
>   - members: the list of restriction enzymes.
>   - methods:
>        - constructor using hardwired list of enzymes OR user file OR URL.
>        - add/remove enzyme to/from list (adding will be the equivalent of
> _make_custom() ).
>        - member accessor methods: already existing methods: is_available(),
> available_list().
> 
> RestrictionEnzyme:
>    - members: the same as now (_name, _seq, _site, _cuts_after).
>    - methods:
>        - constructor (equivalent to the constructor calling the
> _make_standard() sub).
>        - already existing accessor methods.
>        - already existing methods: cut_seq, cuts_seq_at, etc.
> 
> This design, apart from being more "correct", will facilitate any future
> extensions of the two modules. The drawback in separating RestrictionEnzyme
> in two classes is that all code using RestrictionEnzyme.pm will have to be
> modified.
> 
> Perhaps we should take advantage of the imminent release of the 0.7 version
> and decide to proceed in the redesigning. If we change the design this will
> also be the opportunity to slightly change/extend its public interface to
> add small new functionalities such as being able to add and use asymmetric
> cutters and enzymes which cut outside the recognition site (perhaps just
> incorporating small changes now in order to be in time for the 0.7 release
> and leaving extensions for afterwards, especially if I do this alone based
> on what we decide).
> 
> Tell me what you think about it:
> - First of all, is redesigning possible or are we obliged to maintain
> compatibility ? In the latter case I will just add functionality,
> maintaining the poor design of the module.
> - If redesigning is possible, please make comments/suggestions.
> 
> Paul-Christophe
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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