[Bioperl-l] acc does not exist

[Brian Osborne]

Brent and Johnetta,

Perfectly appropriate question. Jason Stajich tracked down the actual bug in
Bio::DB::GenBank, it's now fixed in the bioperl-live version. If you don't
want to re-install you can simply change "protein" to "nucleotide" in
Genbank.pm as follows:

bioperl-live/Bio/DB GenBank.pm,1.48,1.49
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GenBank.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/bioperl/bioperl-live/Bio/DB/GenBank.pm	2003/05/12
15:03:37	1.48
+++ /home/repository/bioperl/bioperl-live/Bio/DB/GenBank.pm	2003/06/10
17:23:06	1.49
@@ -126,22 +126,22 @@
     $DEFAULTMODE   = 'single';
     $DEFAULTFORMAT = 'gp';
     %PARAMSTRING =

-		     'batch' => { 'db'     => 'protein',
+		     'batch' => { 'db'     => 'nucleotide',
 				  'usehistory' => 'n',
 				  'tool'   => 'bioperl',
 				  'retmode' => 'text'},
 		     'query' => { 'usehistory' => 'y',
 				  'tool'   => 'bioperl',
 				  'retmode' => 'text'},
-		     'gi' => { 'db'     => 'protein',
+		     'gi' => { 'db'     => 'nucleotide',
 			       'usehistory' => 'n',
 			       'tool'   => 'bioperl',
 			       'retmode' => 'text'},
-		     'version' => { 'db'     => 'protein',
+		     'version' => { 'db'     => 'nucleotide',
 				    'usehistory' => 'n',
 				    'tool'   => 'bioperl',
 				    'retmode' => 'text'},
-		     'single' => { 'db'     => 'protein',
+		     'single' => { 'db'     => 'nucleotide',
 				   'usehistory' => 'n',
 				   'tool'   => 'bioperl',
 				   'retmode' => 'text'},



Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Brent and
Johnetta Smith
Sent: Sunday, June 08, 2003 9:20 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] acc does not exist

I just recently installed BioPerl 1.2.1 on RedHat v9.0.  I'm trying to
execute the bptutorial script:

#!/usr/bin/perl

  use Bio::Perl;

  # this script will only work with an internet connection
  # on the computer it is run on

  $seq_object = get_sequence('genbank',"AF421111");

  write_sequence(">test.fasta", 'fasta', $seq_object) ;

and I receive the following error:

MSG: acc does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:176
STACK Bio::Perl::get_sequence
/usr/lib/perl5/site_perl/5.8.0/Bio/Perl.pm:510
STACK toplevel bpTest.pl:10

I am absolutely 100% certain that the accession number exists on GenBank
(I verified and re-verified several times by going directly to their web
site).  Also, when "genbank" is changed to "swissprot" and a valid
accession number for swissprot is put in place of the AF421111 then it
works perfectly.  I have installed BioPerl on another RedHat 9.0
computer and it was working with both swissprot and genbank last time I
checked (last Tuesday).

Any suggestions?

Thank you.

Also, if this question is not appropriate for this list then please let
me know where to go for a users list.

--
Brent and Johnetta Smith <bdsjls at qx.net>

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