[Bioperl-l] split location problems

Jason Stajich jason at bioperl.org
Mon Oct 16 18:45:21 EDT 2006


The whole point of split locations is to represent genes with introns  
so that is not the "rare" case.

I'm confused where the problem is.  The locations that I get out with  
to_FTstring on the location object are exactly the same as those input.

I have processed the genbank fungal genomes into GFF3 and have had no  
problems so I'm confused where you are breaking down.  If I write  
them out as embl I also get the correct thing.  This is using the CVS  
version of bioperl from the HEAD.

I've added code to test this to bug 2101 including a C.glabrata  
chromsome downloaded from genbank.  Perhaps the problem is on the  
EMBL parsing side, I didn't test that.

On the technical side, I still am not sure I fully know where the  
strand information should be stored - the top level container or the  
sub-features.  I'll try and stay up on the discussion if anything has  
been decided that I should know about.

-jason





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