[Bioperl-l] Restriction Enzymes

[Staffa, Nick (NIH/NIEHS) [C]]

The tutorial, I discovered, has an error.
a very bad experience for a trusting newby.
whereas the tutorial has these bold examples in the first box under
Identifying restriction enzyme sites (Bio::Restriction)

use Bio::Restriction::EnzymeCollection;
my $all_collection = Bio::Restriction::EnzymeCollection;

This is the form of the statement that seems to work:
my $all_collection = Bio::Restriction::EnzymeCollection->new();

All the other stuff necessary for my purpose of getting fragment lengths is there and seems to work
if the $enzyme database has the enzyme under the name you enter.
Updating the database with the file from NEB seems to be up to the user or his sysadmin.


On 5/24/10 11:55 AM, "Dave Messina" <David.Messina at sbc.su.se> wrote:

Hi Nick,

Now it's Bio::Restriction::Enzyme (and friends). Besides the perldoc for that module, see also:

http://www.bioperl.org/wiki/BioPerl_Tutorial#Identifying_restriction_enzyme_sites_.28Bio::Restriction.29


> How hard would it be to keep things backward compatible.
> Have I missed something here?

I don't know the history of the change, but the Bio::Tools::RestrictionEnzyme was deprecated in BioPerl 1.5.2 (2006?). According to the docs the new ones are intended to be at least partially backwards compatible.


Dave