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

[Lincoln Stein]

Hi Jason,

Could you send me the script the elicits the problem? I am unsure of the
create/write logic because -- unfortunately -- the berkeleydb implementation
has this dual use of supporting conventional loading as well as
autoindexing.

I have to redo the autoindexing in any case so that it doesn't need to
reload every file whenever one file changes.

Lincoln

On Wed, May 13, 2009 at 7:57 PM, Jason Stajich <jason at bioperl.org> wrote:

> 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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>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>