[Bioperl-l] Bio::DB::GFF::Adaptor::berkeleydb

[Lincoln Stein]

On Monday 22 August 2005 08:31 am, Jason Stajich wrote:
> On Aug 21, 2005, at 10:04 PM, Jason Stajich wrote:
> > Lincoln -
> >
> > I'm getting these warning when using the memory or berkeleydb
> > adaptors:
> >
> > Use of uninitialized value in join or string at [MYPATH]/Bio/DB/GFF/
> > Adaptor/memory/feature_serializer.pm line 17.
> >
> > This the line
> > return join $;, at a;
> >
> > $; is not defined in my scripts, if I defining it warnings vanish,
> > but did you mean ';' or do you want to provide a particular
> > customizeable separator?
>
> Or perhaps the undef warnings are due to empty fields in @a, since
> features seem to be extracted out from the db later w/o incident.
>
> BTW - I think the 'memory' and 'berkeleydb' implementations
> effectively replace Bio::SeqFeature::Collection which also used a BDB
> Btree to store features/locations and make range queries, but not the
> full Bio::DB::GFF & DAS APIs.

Ouch! I apologize if I stepped on your (and anyone else's) foot!

Lincoln

>
> > Also I notice in the SYNOPSIS of berkeleydb you have this
> > # do queries
> >   my $segment  = $db->segment(Chromosome => '1R');
> >   my $subseg   = $segment->subseq(5000..6000);
> >   my @features = $subseg->features('gene');
> >
> >
> > Is there a reason to introduce a new subseq API since we already
> > have $seq->subseq($start,$end) for Bio::PrimarySeqI?  I didn't
> > check to see, but I assume this is a convention you are using
> > throughout Bio::DB::GFF? Hopefully start,end will work and I assume
> > your usual start => end works too.
> >
> > Thanks,
> > -jason
> > --
> > Jason Stajich
> > Duke University
> > http://www.duke.edu/~jes12
> >
> >
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> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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