search

bioperl / Bio-Restriction

BioPerl distribution for restriction enzymes
0 stars 1 forks source link

restriction enzymes overhang missing #3

Open fgvieira opened 6 years ago

fgvieira commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

See https://github.com/bioperl/bioperl-live/pull/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 commented 6 years ago

@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).