[Bioperl-l] Help connecting to Genbank...?

[Alexey Morozov]

2012/9/27 Thomas Sharpton <thomas.sharpton at gmail.com>

> 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
> >
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>

Why not type into terminal 'sudo apt-get install bioperl' just in case you
haven't installed bioperl properly? It will also drag along a lot of useful
tools like blast and muscle.

Alexey Morozov
Limnological institute SB RAS
Irkutsk, Russia.