[Bioperl-l] rebase file withrefm

Staffa, Nick (NIH/NIEHS) [C] staffa at niehs.nih.gov
Thu Jun 3 13:59:20 EDT 2010

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

I remember trying to use the withrefm file in the manner outlined below, and it didn't work.
I did not know about File::Temp.
I must find out about this.

On 6/3/10 1:45 PM, "Dave Messina" <David.Messina at sbc.su.se> wrote:

Hi Nick,

> Could someone please tell me where in a normal bioperl installation the
> rebase file withrefm  downlaoded from NEB goes.

Are you talking about when using the (apparently undocumented) invocation of Bio::Restriction::IO to have BioPerl grab the latest rebase file itself via FTP?

my $io = Bio::Restriction::IO->new('-format' => 'withrefm',
                                   '-current' => 1);

If so, it's written to a temporary file via File::Temp, so the location is OS-dependent and determined at runtime.

If you're not talking about that, though, could you please clarify?


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