[Bioperl-l] Re: Bio ::seqIO ::tigr

Hilmar Lapp hlapp at gnf.org
Fri Feb 27 19:45:13 EST 2004

On Thursday, February 26, 2004, at 09:45  AM, Josh Lauricha wrote:

> Does the source_term_id refer to the source_tag()?


> On Feb 26, 2004, at 9:08 AM, matthieu CONTE wrote:
>> [conte at bearn biosql]$ perl load_seqdatabase.pl --dbuser biosql 
>> --dbpass biosql --namespace orysa_tigr --format tigr 
>> /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml
>> Loading /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml ...
>> -------------------- WARNING ---------------------
>> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed, 
>> values were ("","1") FKs (26216,37,<NULL>)
>> Column 'source_term_id' cannot be null
>> ---------------------------------------------------

What this means is that there was no $feat->source_tag set, and looking 
up undef resulted in undef for the foreign key :-)

While bioperl doesn't enforce it, for biosql the source_tag() as well 
as the primary_tag() of a feature are mandatory and cannot be undef. 
Most SeqIO parsers set source_tag() to a static default if there is no 
value, e.g. 'EMBL/GenBank/SwissProt' if you're using FTHelper.pm.

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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