[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/
local/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm:576
STACK Bio::DB::SeqFeature::Store::berkeleydb::reindex_gfffiles /usr/
local/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm:374
STACK Bio::DB::SeqFeature::Store::berkeleydb::auto_reindex /usr/local/
lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm:314
STACK Bio::DB::SeqFeature::Store::berkeleydb::init /usr/local/lib/
perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm:293
STACK Bio::DB::SeqFeature::Store::new /usr/local/lib/perl5/Bio/DB/
SeqFeature/Store.pm:360
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?
Thanks,
-jason
--
Jason Stajich
jason at bioperl.org
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