[Bioperl-l] retreive GenBank Seq - the same script always worked before but now ...

[Heikki Lehvaslaiho]

Qunfeng,

NCBI has changed the URL for the servise. This has been fixed in the 
CVS but but we have not had time to make a fix release of bioperl.

You can copy latest Bio::DB::{GenBank&NCBIHelper&WebDBSeqI}  from WebCVS
and replace the older ones:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/DB/?cvsroot=bioperl


For your script to work, you need to remove '-format=>genbank' which
then defaults to the right format. This is in my opinion a bug in
Bio::DB::GenBank. 

Jason, shouldn't the format string be bioperlish 'genbank' rather than
'gb' required by NCBI eutils ?

	-Heikki



On Thu, 2003-06-12 at 21:52, Qunfeng Dong wrote:
> Hello, 
> 
> I have this simple perl script that takes a GenBank Acc# as input and retrieve 
> the GB format record from NCBI. However, it suddenly stop working and gave me 
> the following error msg when I tried to retrieve sequence U89959.
> 
> ------------- EXCEPTION  -------------
> MSG: WebDBSeqI Error - check query sequences!
> 
> STACK 
> Bio::DB::WebDBSeqI::get_seq_stream /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBS
> eqI.pm:443
> STACK 
> Bio::DB::WebDBSeqI::get_Stream_by_id /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebD
> BSeqI.pm:259
> STACK toplevel ./getGB:16
> 
> --------------------------------------
> 
> Any idea what might go wrong?
> 
> ---my script starts here--------------
> #!/usr/bin/perl -w
> #script: getGB
> use Bio::SeqIO;
> use Bio::Seq;
> use Bio::DB::GenBank();
> 
> @ARGV==1 or die("usage: $0 <Accession Number>\n");
> my $ac = shift @ARGV;
> my $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format 
> => 'Genbank');
> my $seqio = $gb->get_Stream_by_id([$ac]);
> my $out = Bio::SeqIO->new(-format => 'Genbank');
> while ( my $seq = $seqio->next_seq() ) {
>     $out->write_seq($seq);
> }
> 
> 
> 
> 
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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