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

Chris Fields cjfields at uiuc.edu
Tue Jun 12 21:20:41 EDT 2007


It will be interesting to see if bioperl handles wrap-around split  
locations via spliced_seq() and other methods.  I can't see why it  
wouldn't but one never knows.  Might be something to add to location  
tests at some point...

chris

On Jun 12, 2007, at 7:57 PM, Hilmar Lapp wrote:

> 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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>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
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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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