[Bioperl-l] Restriction Enzymes

[Chris Fields]

On May 24, 2010, at 9:32 AM, Staffa, Nick (NIH/NIEHS) [C] wrote:

> So, back in 2007 I wrote a script using
> 
> use Bio::Tools::RestrictionEnzyme;
> 
> and generated some useful restriction maps for a client.
> 
> This year he comes back to me with some very new enzymes
> that RestrictionEnzyme did not recognize. I erroneously thought that I
> needed an update of BioPerl, which I requested of SysAdmin.
> They did this across the board, there is no going back.
> (I did learn about the NEB file that needed to be installed)
> 
> Now it appears that I must re-write my scripts because RestrictionEnzyme is
> not known to the latest version of bioperl.  Is this true?
> How hard would it be to keep things backward compatible.
> Have I missed something here?

Bio::Tools::RestrictionEnyzme was deprecated quite a while ago,around v. 1.5, with removal at 1.6 (an announcement was made to the list regarding this, with no respondents, prior to the 1.6.0 release).  The live version of the DEPRECATED docs are here:

http://github.com/bioperl/bioperl-live/blob/master/DEPRECATED

If I understand correctly, the main reason was most development was put into Bio::Restriction modules, with very little change occurring in Bio::Tools::RestrictionEnzyme.  We did similar changes with some of the older BLAST parsers (BPLite).  You could just download Bio::Tools::RestrictionEnyzme and call it via a 'use lib' directive (or local::lib) or package it with your script, it should still work.

However, from my perspective, if the older module wasn't recognizing specific enzyme cut sites, and the supported one did, wouldn't it be easier to modify your script to use the newer supported one instead?  If the supported Bio::Restriction modules don't recognize the new sites I would consider that a bug.  

> Nick Staffa 
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Enterprise-Wide Information Technology Support Contract
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina



chris