[Bioperl-l] Bio::SeqFeature::Gene::Exon throws exception when encountering split location (Bio::Location::Split)

Hilmar Lapp hlapp at gmx.net
Tue Jun 12 20:57:06 EDT 2007


I like that. Don't force a model to do what you want if it doesn't  
really apply anyway.

	-hilmar

On Jun 12, 2007, at 12:59 PM, Mark Johnson wrote:

>     That's a good point.  Both Bio::Tools::Glimmer and
> Bio::Tools::Genemark produce Bio::SeqFeature::Gene objects, each with
> a single Bio::SeqFeature::Gene::Exon, when parsing predictions for
> prokaryotic sequence (multiple exons for eukaryotic).  There are
> eukaryotic and prokaryotic versions of both predictor families.  Maybe
> the most elegant solution would be to simply modify both modules to
> only emit Bio::SeqFeature::Generic features when operating on
> prokaryotic mode output?  Fix the data model and the problem goes
> away.  8)
>
> On 6/12/07, Chris Fields <cjfields at uiuc.edu> wrote:
>>
>> On Jun 12, 2007, at 11:10 AM, Mark Johnson wrote:
>>
>>> On 6/12/07, Torsten Seemann
>>> <torsten.seemann at infotech.monash.edu.au> wrote:
>>>> Can you use the ->spliced_seq() method to do this?
>>>>
>>>> http://doc.bioperl.org/releases/bioperl-1.5.2/Bio/
>>>> SeqFeatureI.html#POD11
>>>>
>>>> --
>>>> --Torsten Seemann
>>>> --Victorian Bioinformatics Consortium, Monash University
>>>> --Tel +61 3 9905 9010
>>>
>>>     Actually, I'd forgotten about spliced_seq().  That seems like it
>>> will Do The Right Thing.  It's just up to the invoker to call
>>> spliced_seq() instead of seq() as appropriate.
>>>     So, is there any other code that will break if I modify
>>> Bio::SeqFeature::Gene::Exon::location to not throw an exception when
>>> encountering Bio::Location::SplitLocationI?  I'm wondering if it's
>>> just a paranoid check or if it's there to guard against  
>>> something.  If
>>> the latter, I need to know what code to fix.  I'll dig and look, but
>>> if anybody knows or has an idea, save me some time.  I suppose I can
>>> just change it and see what tests start failing. 8)
>>
>> I'm wondering why you want to use Bio::SeqFeature::Gene::Exon to
>> describe the 'wrap-around' genes.  The SeqFeature::Gene::Exon docs
>> state that the Exon class is used to specifically describe exons, as
>> the name implies.  Exons are primarily eukaryotic in origin, so you
>> shouldn't encounter wraparounds, and should not have split locations
>> by definition (which likely explains the exception).
>>
>> Wouldn't a SeqFeature::Generic work just as well using a split  
>> location?
>>
>> chris
>>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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