[Bioperl-l] help with getgenbank.pl script

[Heikki Lehvaslaiho]

Pedro,

The first line points to the problem: "Can't locate IO/String.pm in @INC".
You need to install IO::String module into perl either as a root into
siteperl (recommended: ask your sysadmin), or into your local directory and
add the path into your PERL5LIB.


Note that even when you have all the modules you need, the NCBI Entrez
server sometimes returns nothing even on a legit request.

Yours,
	-Heikki





Pedro A Reche Gallardo wrote:
> 
> Hi All,  I have tried to execute the getgenbank.pl script deposited by
> Dr. Jason Stajich in the CVS depository (see script bellow),  but  I got
> the following error:
> 
> immbio 21% ./getgenbak.pl
> Can't locate IO/String.pm in @INC (@INC contains:
> /usr/freeware/lib/perl5/5.0050
> 3/irix-n32 /usr/freeware/lib/perl5/5.00503
> /usr/freeware/lib/perl5/site_perl/5.0
> 05/irix-n32 /usr/freeware/lib/perl5/site_perl/5.005
> /usr/freeware/lib/perl5/sgi_
> perl/irix-n32 /usr/freeware/lib/perl5/site_perl .) at
> /usr/freeware/lib/perl5/si
> te_perl/5.005/Bio/DB/WebDBSeqI.pm line 87.
> BEGIN failed--compilation aborted at
> /usr/freeware/lib/perl5/site_perl/5.005/Bio
> /DB/WebDBSeqI.pm line 87.
> BEGIN failed--compilation aborted at
> /usr/freeware/lib/perl5/site_perl/5.005/Bio
> /DB/NCBIHelper.pm line 81.
> BEGIN failed--compilation aborted at
> /usr/freeware/lib/perl5/site_perl/5.005/Bio
> /DB/GenBank.pm line 99.
> BEGIN failed--compilation aborted at ./getgenbak.pl line 7.
> 
> The script I am running is the following
> 
> #!/usr/sbin/perl -w
> #
> # How to retrieve GenBank entries over the Web
> #
> # by Jason Stajich
> #
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> my $gb = new Bio::DB::GenBank;
> 
> # the output stream for your seqs, this can be a file
> # instead or STDOUT, see the Bio::SeqIO module for info
> 
> my $seqout = new Bio::SeqIO(-fh => \*STDOUT, -format => 'fasta');
> $seq = $gb->get_Seq_by_acc('AF303112');
> 
> $seqout->write_seq($seq);
> 
> 
> Any help to make this script work will be great.
> Regards,
> 
> Pedro
> 
> --
> ***************************************************************************
> 
> PEDRO a. RECHE gallardo, pHD            TL: 617 632 3824
> Scientist, Mol.Immnunol.Foundation,     FX: 617 632 3351
> Dana-Farber Cancer Institute,           EM:
> reche@research.dfci.harvard.edu
> Harvard Medical School,                 EM: reche@mifoundation.org
> 44 Binney Street, D610C,                URL: http://www.reche.org
> Boston, MA 02115
> ***************************************************************************
> 
> 

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________