[Bioperl-l] Problems getting sequence with Bio::DB::GenBank

[hilmar.lapp@pharma.Novartis.com]

Have you recently upgraded your BioPerl installation from the CVS
repository? If so, there is then a change effective in DB::GenBank that
causes entries to be retrieved in GenBank format by default. This may or
may not cause a problem, but if it does, calling $gb->request_format
('fasta') after object creation should make the problem go away. I'd like
to hear of it if this is indeed the case.

If the above does not apply, you may want to check whether or not your
accession is really a valid (i.e., existing) entry, which you can check
through the NCBI website. You can even copy and paste the URL from the
source code (method get_Seq_by_id()), and append the acc to it, and check
whether it works (replace $fmt by g or f, depending on GenBank and Fasta
format, respectively).

     Hilmar





gert thijs <gert.thijs@esat.kuleuven.ac.be>@bioperl.org on 16.08.2000
12:19:17

Sent by:  bioperl-l-admin@bioperl.org


To:
cc:   Bioperl <bioperl-l@bioperl.org>
Subject:  [Bioperl-l] Problems getting sequence with Bio::DB::GenBank


Hi,

I have used Bio::DB::GenBank to download sequences for quite some time now,
but recently those scripts cannot do their job anymore.
I have been using the following code a lot and it worked fine:
   $accn = 'ab013396';
   $gb = new Bio::DB::GenBank;
   $seq = $gb->get_Seq_by_acc($accn);

This throws the following exception:
-------------------- EXCEPTION --------------------
MSG: Unable to get seq for id ab013396, is it really a genbank id?

CONTEXT: Error in uNKNOWN CONTEXT
SCRIPT: ./my_getseq.pl
STACK:
Bio::DB::GenBank::get_Seq_by_id(121)
Bio::DB::GenBank::get_Seq_by_acc(142)
main::./my_getseq.pl(26)
---------------------------------------------------

Can anybody help me out here?

Gert Thijs


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