[Bioperl-l] Bio::DB::GFF start/end coordinates

[Jason Stajich]

Lincoln -

One bug I'm still seeing in Bio::DB::GFF::Feature objects is start/ 
end are still returning start > end when strand < 0.   I know this is  
different expectation for Bioperl / Gbrowse but this causes a little  
problems, especially when you get an aggregated feature out from  
Bio::DB:GFF and then write it to a genbank file.  The locations looks  
like this:
complement(join(1031..975,676..501))

My workaround is just to create new Location objects and features  
from the Bio::DB::GFF obtained objects  (some of these aren't  
allowing write-back to overwrite the values).

Note on a slightly separate topic:
  I have patched my Bio::Location::Split to_FTstring to simplify the  
string, current behavior would be to output the location like this:
join(complement(1031..975),complement(676..501),))

I'm seeing about how applying the patch, I'm not sure whether or not  
it perfectly works.


-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/