[Bioperl-l] Bio::DB::SeqFeature::Store::berkeleydb

Jason Stajich jason at bioperl.org
Wed May 13 23:57:52 UTC 2009

Lincoln -

Looks like there have been a change to the berkeleydb.pm Store module  
which force the 'create' bit to 0 when doing reindex_gfffiles . This  
means an empty DB cannot be created.

So I get these errors:
  -------------------- EXCEPTION --------------------
MSG: Couldn't tie: ../gff/indexes/features.bdb No such file or directory
STACK Bio::DB::SeqFeature::Store::berkeleydb::_open_databases /usr/ 
STACK Bio::DB::SeqFeature::Store::berkeleydb::reindex_gfffiles /usr/ 
STACK Bio::DB::SeqFeature::Store::berkeleydb::auto_reindex /usr/local/ 
STACK Bio::DB::SeqFeature::Store::berkeleydb::init /usr/local/lib/ 
STACK Bio::DB::SeqFeature::Store::new /usr/local/lib/perl5/Bio/DB/ 
STACK toplevel scripts/haplotype_block_association.pl:12

This stems from Line 374 of berkeleydb.pm in the redindex_gfffiles ?

371    warn "Reindexing GFF files...\n" if $self->verbose;
372   $self->_permissions(1,1);
373    $self->_close_databases();
374    $self->_open_databases(1,0);

*Could* be changed to this:
374    $self->_open_databases(1,1);

But I'm not sure do you want the CREATE bit always set to on when  
reindexing?  Maybe yes since the DB was typically erased beforehand  
whenever a reindex (or initial index) is applied?


Jason Stajich
jason at bioperl.org

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