[Bioperl-l] help with getgenbank.pl script

Pedro A Reche Gallardo reche@research.dfci.harvard.edu
Mon, 12 Nov 2001 11:38:40 -0500


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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
***************************************************************************



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

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