[Bioperl-l] Why does Bio::DB::GFF::Feature::gff3_string swap start and stop coordinates??

Mark Johnson johnsonm at gmail.com
Fri Jun 15 15:37:26 EDT 2007

Patches waiting in Bugzilla (Bug #2299).  Changes:

-Bio::Tools::Glimmer now emits Bio::SeqFeature::Generic features for
prokaryotic reports (Glimmer2/Glimmer3)
-Bio::Tools::Glimmer now produces features with Fuzzy or Split
locations as appropriate (partial or circular/wraparound predictions)
-Bio::Tools:Glimmer goes through the Glimmer3 .detail file to pull out
sequence lengths
-Bio::Tools::Run::Glimmer passes along the sequence length to
Bio::Tools::Glimmer for Glimmer2

I should probably modify Bio::Tools::Genemark to use
Bio::SeqFeature::Generic features for prokaryotic reports, to be
consistent, but this is more likely to surprise people.  If nobody
screams about the change to Bio::Tools::Glimmer, I'll do it at some

On 5/21/07, Chris Fields <cjfields at uiuc.edu> wrote:
> On May 21, 2007, at 7:29 PM, Torsten Seemann wrote:
> >> glimmer2/3 both assume the genome is circular by default (I'm
> >> assuming since Glimmer2/3 are used for bacterial genomes).  Acc. to
> >> the Glimmer3 release notes the detail file has the information in the
> >> header; from the Glimmer3 data used for tests:
> >
> > You beat me to the reply Chris - yes, Glimmer2/3 assume circular
> > chromosome by default. I had forgotten about this in earlier
> > discussions of the new Glimmer parsers as I normally run it in
> > --linear / -L mode (even if I know it is circular) because it is
> > easier to handle, and our sequencer/assembler team usually gets the
> > origin of replication right.
> >
> >> Command:  /bio/sw/glimmer3/bin/glimmer3 -o 50 -g 110 -t 30 ../BCTDNA
> >> Glimmer3.icm Glimmer3
> >
> > I did a double-take here - that's the path to my Glimmer3
> > installation! It took me a couple of minutes to realise that you got
> > it from the bioperl test data I created. D'oh! :-)
> Yep, I forgot about that!
> >> There are options available for glimmer3 (-L, -X) that specify a
> >> linear sequence or allow ORFs to extend past the end of the sequence
> >> analyzed (the latter assumes a linear sequence).
> >
> > If the -L mode should produce Bio::Location::Split objects, I guess if
> > -X is used
> > it should produce Bio::Location::Fuzzy objects too...
> >
> > --Torsten
> True, didn't think about that one.  Def. something to consider adding
> in.
> chris

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