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

gert thijs gert.thijs@esat.kuleuven.ac.be
Thu, 17 Aug 2000 15:54:05 +0200

It was an internal problem. It seems that our sysads have updated perl
recently and this new installation was conflicting with some of the modules I
installed myself, like IO::Socket. I managed to fix that problem by
reinstalling most of the modules. 
I also managed to use LWP to download GenBank entries instead of IO::Socket.
So now getting GenBank files is working fine again, although I still have
problems using Boulder::Genbank to get and parse genbank entries.


hilmar.lapp@pharma.novartis.com wrote:
> 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