[Bioperl-l] Fascinating bug...

[Lincoln Stein]

This must be related to the handling of case-insensitive databases in 
Bio::DB::GFF.  Probably if you specify an aggregator with mixed-case, the 
config will work with the same name lower-cased.

	e.g.	aggregators = agg_WT_expression_1{expression_1:WT}
		[track]
		features = agg_wt_expression
		
I will fix this.

Lincoln


On Wednesday 19 March 2003 04:42 pm, Matthew Vaughn wrote:
> I've been working on implementing a generic microarray data viewer
> built on top of the Generic Genome Browser. This has required dealing a
> lot with aggregators, which, I have gathered from the documentation,
> are implemented via Bio::DB::GFF. Well, I found the most fascinating
> bug (or maybe it's a feature). In the configuration file for GGB, one
> can specify custom aggregators like so:
>
> aggregators = agg_wt_expression_1{expression_1:WT} transcript (and so
> on..)
>
> I was building names for these aggregators dynamically and the values
> used to build them contained capital letters. I discovered, after much
> gnashing of teeth, that while the above aggregator would work, this one
> will not.
>
> aggregators = agg_WT_expression_1{expression_1:WT}
>
> I assume this is some odd behavior inherited from the Bio::DB::GFF
> module, which is why I am mentioning it here.
>
> What is going on? Any enlightened opinions?

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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