[Bioperl-l] split location problems
jason at bioperl.org
Mon Oct 16 22:45:21 UTC 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.
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