Thomas Sharpton | 26 Sep 23:54 2012
Picon

Re: Help connecting to Genbank...?

Damien,

It would be helpful to see the specific error. But, I'm guessing that Perl
can't find the BioPerl package (as opposed to an internal BioPerl error).
If that's the case, then check to make sure that you added the location of
the BioPerl root directory (it should contain Bio/) to your PERL5LIB system
variable.

Hope this helps,
Tom

On Wed, Sep 26, 2012 at 2:13 PM, shalabh sharma
<shalabh.sharma7 <at> gmail.com>wrote:

> You sure you installed bioperl ?
>
> On Wed, Sep 26, 2012 at 5:13 PM, shalabh sharma
> <shalabh.sharma7 <at> gmail.com>wrote:
>
> > Hey Damein,
> >                      Can you send the error you getting because this
> > should work fine.
> >
> > -Shalabh
> >
> >
> > On Wed, Sep 26, 2012 at 4:55 PM, Damien OHalloran <
> > damienmohalloran <at> yahoo.co.uk> wrote:
> >
> >>
> >> I'm a newbie trying to to download DNA sequences from Genbank. I used
> the
> >> script below but I get the error "cant locate Bio/SeqIO.pm" - help?
> >>
> >> #!/usr/bin/perl -w
> >> use Bio::SeqIO;
> >> use Bio::DB::GenBank;
> >> $genBank = new Bio::DB::GenBank;
> >> my $seq = $genBank->get_Seq_by_acc('AF060485');
> >> my $seqOut = new Bio::SeqIO(-format => 'genbank');
> >> $seqOut->write_seq($seq);
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l <at> lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics Specialist)
> > Department of Marine Sciences
> > University of Georgia
> > Athens, GA 30602-3636
> >
>
>
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Gmane