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

[Hrundi Barkshi]

I changed that and make
 $biodbname = 'bioperl'; according to the entry in the database
 mysql> select * from biodatabase;
+----------------+---------+-----------+-------------+
| biodatabase_id | name | authority | description |
+----------------+---------+-----------+-------------+
| 3 | bioperl | NULL | NULL |
+----------------+---------+-----------+-------------+
1 row in set (0.01 sec)

Now works perfect.

Thanks
Hrundi


On 16/11/05, Hilmar Lapp <hlapp at gnf.org> wrote:
> 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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> > BioSQL-l at open-bio.org
> > http://open-bio.org/mailman/listinfo/biosql-l
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org <http://gnf.org>
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>