restriction enzymes overhang missing

[fgvieira]

Dear all,

I've been looking using the restriction modules in Bioperl and I think that, for some enzymes, it is not properly calculating the overhang sequence. For example, with EcoRI it looks fine and gives AATT:

$ perl -e 'use Bio::Restriction::Enzyme; $re = Bio::Restriction::Enzyme->new(-name=>"EcoRI",-site=>"GAATTC", -cut=>1); print $re->overhang_seq()."\n"'
AATT

But, (e.g.) if you use TasI, Bioperl cannot identify any overhang:

$ perl -e 'use Bio::Restriction::Enzyme; $re = Bio::Restriction::Enzyme->new(-name=>"TasI",-site=>"AATT", -cut=>0); print $re->overhang_seq()."\n"'

As I see it, both should give the same overhang, no?
cheers,

[hyphaltip]

There are a few places in the code where
if( $cut ) ... or if ( $self->{_cut} )
needs to be rewritten
if ( defined $cut ) {}
I have a fix I can patch in - not sure what branch we are working on any more though - help? @cjfields .

[hyphaltip]

See bioperl/bioperl-live#254 but we need to probably also push this to any release branches as this is only on master. Can a current release developer take a look?

[cjfields]

@hyphaltip we're running off master for the latest releases. I'm in Africa but will be back this weekend, can take a look when I have a bit better internet (it's been reeaaaaaaally inconsistent).