[Bioperl-l] rebase file withrefm

Staffa, Nick (NIH/NIEHS) [C] staffa at niehs.nih.gov
Thu Jun 3 14:17:42 EDT 2010

Thanks Muchly.
I'll give it a try.

On 6/3/10 2:14 PM, "Dave Messina" <David.Messina at sbc.su.se> wrote:

> I was thinking about where the default restriction information is kept.

The default restriction information is embedded in Bio::Restriction::IO::Base, not downloaded. That is, look at the bottom of the file bioperl-live/Bio/Restriction/IO/base.pm, and you'll see the default set hardcoded there.

> I remember trying to use the withrefm file in the manner outlined below, and it didn't work.

It works in my hands. Here's example code


which should produce the output

(along with a trivial warning on STDERR)

If you absolutely want to work from the latest downloaded rebase file, you probably will want to download the file yourself and pass it directly to RestrictionIO, a la:

my $re_io = Bio::Restriction::IO->new(-file => 'mydownloadedREBASEfile', -format=>'withrefm');


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