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

Jason Stajich jason.stajich at duke.edu
Sun Aug 21 22:04:28 EDT 2005

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?

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.

Jason Stajich
Duke University

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