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

Lincoln Stein lstein at cshl.edu
Mon Aug 22 10:59:42 EDT 2005

On Sunday 21 August 2005 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 a legacy Perl global variable that was used to separate elements of 
multidimensional arrays in the perl 4 days. It contains an infrequently-used 
control character, and since nobody is likely to change it I adopted it for 
quick serialization (much faster than freeze/thaw I found in my benchmarks). 
Your warnings are probably coming from undefined values in the @a array, and 
I think the best thing to do is to localize $^W around this area. I'll do 

> $; 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.

This is badness on my part. I'll fix that. My old habits from AcePerl keep 
sneaking in.


> Thanks,
> -jason
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
SANDRA MICHELSEN, AT michelse at cshl.edu

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