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

[Jason Stajich]

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.

> 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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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12