[BioSQL-l] how to reconstruct the sequences placed on bioSQL?

[Hilmar Lapp]

It doesn't find the sequence. Note that bioentry2flat.pl is mostly for 
demonstration purposes and not necessarily a production quality script.

Having said that and observing that it hard-codes the namespace to 
sprot_hum, which is not the one you used when loading, it should be 
easy to either modify the script to use a different namespace, or to 
accept it as a command line, or alternatively to use the same namespace 
when loading.

Let me know if the script still doesn't work if you use the same 
namespace by any of the options above.

	-hilmar

On Nov 15, 2005, at 2:52 PM, Hrundi Barkshi wrote:

> Hi,
>
> I am a beginner to BioSQL and I upload (Using load_seqdatabase.pl) the
> example under the test folder ./t/data
>
> perl ~/tmp/biosql/load_seqdatabase.pl --dbname BioDB --namespace
> uniprot --debug --format swiss  swiss.da
>
> Now I would like to revert the sequence querying the db
>
> I have tried using bioentry2flat but I get the following error:
>
>
> $ perl  bioentry2flat.pl BioSQL3 Q07021Connecting with 
> mysql:BioSQL3:root:dbpass
>
> ------------- EXCEPTION  -------------
> MSG: Attempting to write with no seq!
> STACK Bio::SeqIO::embl::write_seq
> /usr/lib/perl5/site_perl/5.8.6/Bio/SeqIO/embl.pm:394
> STACK Bio::SeqIO::PRINT /usr/lib/perl5/site_perl/5.8.6/Bio/SeqIO.pm:661
> STACK toplevel bioentry2flat.pl:69
>
> -----------------------------------
>
> Any advise?
> Thanks in advance
> Hrundi
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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