[Bioperl-l] Re: [BioSQL-l] tigr.pm

[Josh Lauricha Hi]

The problem with setting strand in tigr.pm is that, for simplicity, I've
already reversed the strands to the positive oriantation. So while their
not "unknown" they are neither positive nor negative. Marking a positive
strand as positive is fine, but marking a negative strand as negative is
not, since it has been reversed already. It might be misinterpreted (by
code or people) that a negative strand must be reversed again.

On Fri 12/10/04 09:34, Hilmar Lapp wrote:
> Strand is NOT NULLable in all three (MySQL, Pg, Oracle) versions of the 
> schema.
> 
> This constraint could be relaxed, as Strand is not part of any unique 
> key constraint.
> 
> OTOH the designated value for an unknown strand is 0 in bioperl, not 
> NULL or undef.
> 
> Furthermore, the schema defines 0 as the default value for the Strand 
> column. Unfortunately, this doesn't help if the column is explicitly 
> inserted as NULL.
> 
> I could add a fix to the LocationAdapter to default a null strand to 0.
> 
> Any opinions? I'm leaning towards adding a fix to LocationAdapter to 
> fix this problem immediately and forever.
> 
> 	-hilmar
> 
> On Dec 10, 2004, at 2:49 AM, matthieu CONTE wrote:
> 
> >I am trying to load tigr rice data in my biosql db with the 
> >load_seqdatabase.pl using the lastest tigr parser on the CVS.
> >I still have the same problem with null field
> >
> >Thanks
> >
> >perl load_seqdatabase.pl --dbuser biosql --dbpass biosql --namespace 
> >tigr_arath --format tigr 
> >/home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml
> >Loading 
> >/home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml 
> >...
> >
> >-------------------- WARNING ---------------------
> >MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, 
> >values were ("130","2000","","1") FKs (16962,<NULL>)
> >Column 'strand' cannot be null
> >---------------------------------------------------
> >
> >**************************************
> >m_conte at hotmail.com
> >CIRAD
> >**************************************
> >
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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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