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

Jason Stajich jason.stajich at duke.edu
Thu Aug 25 13:00:34 EDT 2005

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:

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:

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

Jason Stajich
jason.stajich at duke.edu

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