[Gmod-gbrowse] gbrowse details

[Jason S. <jas...@du...>]

I'm confused about how aggregators should be behaving in  
gbrowse_details.

I have a feature with top-level mRNA and sub CDS features.

When I plug this into gbrowse_details, the mRNA doesn't ever seem to  
be part of the resulting aggregated coding feature so I can't get  
access to the tags/values that are stored in it, as well as the score  
which is in the score field of the mRNA.

In my track info I have this defined and this performs fine:
description  = sub {
             return "Probability ".shift->score;
            }
So the score is part of the aggregated feature at least for description.

I wanted to also try and draw different colors depending on the  
score.   I found that bgcolor shift->score returned null this is  
because bgcolor returns 'CDS' objects not the aggregated transcript  
obj - is there a good way for the sub-feature to get a handle on its  
parent object?

Here is some GFF3 that I load with the --gff3_munge option on:

##gff-version 3
ccin_1.131      GLEAN   mRNA    32937   34641   0.982957         
+       .       ID=Gene:GLEAN_gz_08241;transcriptSeq="ATGTAA"
ccin_1.131      GLEAN   CDS     32937   33245   .       +        
0       Parent=Gene:GLEAN_gz_08241
ccin_1.131      GLEAN   CDS     33311   33790   .       +        
0       Parent=Gene:GLEAN_gz_08241
ccin_1.131      GLEAN   CDS     33854   34042   .       +        
0       Parent=Gene:GLEAN_gz_08241
ccin_1.131      GLEAN   CDS     34110   34321   .       +        
0       Parent=Gene:GLEAN_gz_08241
ccin_1.131      GLEAN   CDS     34380   34641   .       +        
1       Parent=Gene:GLEAN_gz_08241


Thanks,
-jason
--
Jason Stajich
Duke University
http://www.duke.edu/~jes12