[Bioperl-l] loading yeast data failing...

[Hilmar Lapp]

You could do that but first that puts you out of sync with the
official schema, and second if you look at the value it isn't really
an accession number anyway that's causing the problem but rather a
concatenation of identifiers, accession numbers, and namespace
acronyms. Since you're using a custom SeqProcessor anyway already why
don't you just add a line or two of code that parses the display_id
value into the accession and identifier? (for instance, the token
between two '|' characters following the token 'gb')

   -hilmar

On 1/3/06, Angshu Kar <angshu96 at gmail.com> wrote:
> Hi,
>
> Could you please help me resolve the follwoing error?
>
> I run:
>
> ./load_seqdatabase.pl --dbname=USBA --dbuser=postgres --format=fasta
> --driver=Pg --pipeline="SeqProcessor::Accession" yeast_nrpep.fasta
>
> The error:
>
> Loading yeast_nrpep.fasta ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
> ("gi|4261605|gb|AAD13905.1|S58126_11111111111111","gi|4261605|gb|AAD13905.1|S58126_11111111111111","gi|4261605|gb|AAD13905.1|S58126_11111111111111","Unknown
> [Saccharomyces cerevisiae]","0","") FKs (19,<NULL>)
> ERROR:  value too long for type character varying(40)
> ---------------------------------------------------
> Could not store gi|4261605|gb|AAD13905.1|S58126_11111111111111:
> ------------- EXCEPTION  -------------
> MSG: error while executing statement in
> Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: ERROR:  current transaction
> is aborted, commands ignored until end of transaction block
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
> /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
> /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
> STACK Bio::DB::Persistent::PersistentObject::store
> /home/akar/local/perl//Bio/DB/Persistent/PersistentObject.pm:272
> STACK (eval) ./load_seqdatabase.pl:621
> STACK toplevel ./load_seqdatabase.pl:604
>
> --------------------------------------
>
>  at ./load_seqdatabase.pl line 634
>
> Should I change the field lengths for accession, name and identifier to some
> value >40 in the bioentry table?  What  should I change it to?
>
> Thanks,
> Angshu
>
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>


--
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: Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
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