[Bioperl-l] loading data into bioperl-db

[Michael Thon]

Greetings - I've been tinkering with bioperl-db and I'm having trouble
loading data into the database.  Sequences that I download from genbank
in genbank format load ok but sequences in fasta format do not.  I
cannot load my own sequences in fasta format or genbank format. an
example session with load_seqdatabase.pl where I try to load my own data
in genbank format is shown below.  I first converted my sequences to
genbank format from fasta format priot ro running load_seqdatabase.pl. I
suspect that:

1) Fasta formated sequences are not supported.

2) my own genbank formatted files are not properly populated.

Is anyone else out there using bioperl-db in their research?

Thanks
Mike



$load_seqdatabase.pl --host localhost --format fasta --dbname myseqdb
--dbuser biosql N_crassa_3_protein.genbank
Loading N_crassa_3_protein.genbank ...
DBD::mysql::st execute failed: Duplicate entry 'unknown-1-0' for key 2
at /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm line 922,
<GEN0> line 1.

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("LOCUS","LOCUS","unknown","gnl|NCSU_FGL|NCU10032.1           31
aa            linear
UNK ","0","") FKs (1,<NULL>)
Duplicate entry 'unknown-1-0' for key 2
---------------------------------------------------
Could not store unknown:
------------- EXCEPTION  -------------
MSG: create: object (Bio::Seq) failed to insert or to be found by unique
key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:249
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) /home/mthon/bin/load_seqdatabase.pl:437
STACK toplevel /home/mthon/bin/load_seqdatabase.pl:421

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