[Bioperl-l] bioperl-db: exporting data

[Johan Viklund]

Thanks for the help, it works now (it was a small programming error).


(sending this so someone else in a similar predicament can find help)
On 7/6/05, Hilmar Lapp <hlapp at gmx.net> wrote:
> The way you're describing doesn't sound too far off. The rank is an
> ordering index as well as a component of the unique key constraint,
> i.e.,  you can't have two seqfeature qualifier values for the same
> feature and tag name unless the rank is different.
> 
> Have you convinced yourself that you con log in to the database and
> retrieve those additions by hand (using SQL)?
> 
> Can you reduce this to a test case where you load a single sequence
> record, then issue SQL to add your custom annotation, and then retrieve
> the record again. Email me the entry you loaded, the SQL statements you
> issued, and the entry you got out.
> 
>          -hilmar
> 
> On Jul 5, 2005, at 8:01 AM, Johan Viklund wrote:
> 
> > Hi
> >
> > I'm trying to add COG annotations from Entrez Gene to sequences (from
> > refseq in genbank format) I have in a biosql database (on mysql). The
> > problem is I can't get them out again with the bioentry2flat.pl script
> > (the bioentries appears without what i've added).
> >
> > I don't use bioperl for this (i've got ~40000 COG annotations (linked
> > to GeneIDs)). Instead I add it to the seqfeature_qualifer_value table
> > similar to the way GeneID:s are represented (as far as i've figured),
> > with term_id corresponding to db_xref, the same seqfeature_id as the
> > GeneID had and rank i've tried a few different variations but none
> > seem to work (the first free that's larger than GeneID and 1).
> >
> > How should I add this annotation to the database so it gets exported
> > when I use bioperl?
> >
> > I've also got another question: What is rank for?
> >
> > --
> > Johan Viklund
> > E-mail: <johan.viklund.0705 at student.uu.se>
> >         <johan.viklund at gmail.com>
> >
> > _______________________________________________
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> > Bioperl-l at portal.open-bio.org
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> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> 
> 


-- 
Johan Viklund
E-post: <johan.viklund at gmail.com>