[Bioperl-l] load_seqdatabase.pl does not like fasta format

[Andy Hammer]

I used load_seqdatabase.pl just fine to load over
20,000 genbank sequences into a biosql database.  Then
I tried to load a fasta file into a new biosql
database and got the following:

postgres at westwater:/var/local/ucsc$
./load_seqdatabase.pl -dbname ucsc -dbuser postgres
-format fasta refMrna.fa 
Loading refMrna.fa ...
Processing NM_000367 at length 2742
Processing NM_000597 at length 1433
Could not store unknown: 
------------- EXCEPTION  -------------
MSG: You're trying to lie about the length: is 1433
but you say 2742
STACK Bio::PrimarySeq::length
/usr/local/share/perl/5.6.1/Bio/PrimarySeq.pm:419
STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD
/usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:541
STACK Bio::Seq::length
/usr/local/share/perl/5.6.1/Bio/Seq.pm:612
STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD
/usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:541
STACK
Bio::DB::BioSQL::BiosequenceAdaptor::populate_from_row
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BiosequenceAdaptor.pm:251
STACK
Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1300
STACK
Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:977
STACK
Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK
Bio::DB::BioSQL::PrimarySeqAdaptor::attach_children
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/PrimarySeqAdaptor.pm:284
STACK Bio::DB::BioSQL::SeqAdaptor::attach_children
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/SeqAdaptor.pm:279
STACK
Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1331
STACK
Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:977
STACK
Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:204
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval) ./load_seqdatabase.pl:521
STACK toplevel ./load_seqdatabase.pl:504


I added the Processing at length lines to see what was
going on.  Only the first entry actually makes it into
the db.  It seems to keep the last sequence in memory
for some reason.  I also tried destroying the $seq at
the end of the loop with a $seq->DESTROY; command but
got the same results.

Any ideas on this?
Thanks.


	
		
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