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

Chris Fields cjfields at uiuc.edu
Fri Jun 15 16:55:06 EDT 2007

I'll try getting to that in tonight.  Been pretty tied up lately...


On Jun 15, 2007, at 2:37 PM, Mark Johnson wrote:

> 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
> point.
> 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 ../ 
>>>> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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