[Bioperl-l] Can protein glyph tracks interfere with other tracks?

Scott Cain scott at scottcain.net
Thu Mar 11 11:11:04 EST 2010

Hi Nathan,

Well, it certainly shouldn't!  The tracks are supposed to be
calculated independently without reusing anything.  Debugging should
be fun though.  Does it matter if you change the adaptor (for
instance, if you are using the memory adaptor for
Bio::DB::SeqFeature::Store, try putting it in a mysql database (or
vice versa) to help narrow down where the bug is.


On Wed, Mar 10, 2010 at 5:52 PM, Nathan Liles <nml5566 at gmail.com> wrote:
> I'm trying to patch Gbrowse to properly display circular segments.
> Currently, I'm working on getting the protein glyphs to display properly
> beyond the end of the track.
> I noticed when I turn on the protein track, it can sometimes affect another
> track. Specifically, turning on the protein track can either cause the gene
> glyphs to disappear or be duplicated.
> This only happens for features with two subfeatures that appear on the panel
> at opposite ends.
> This seems strange since I can't imagine how one track could affect another.
> Has anyone noticed this behavior before?
> Can anybody think of a way that the protein glyph module can affect other
> glyphs?
> Thanks,
> Nathan Liles
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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