[Bioperl-l] Bio::Location::Split question

Chris Fields cjfields at uiuc.edu
Mon Sep 18 21:04:08 EDT 2006


I'll take a look at it.  There's a related bug report already in  
Bugzilla that's related to this but I'll add a new one that's more  
directly related to the issue here.

I'll give your test a try to see if it makes a difference.

Chris

On Sep 18, 2006, at 5:26 PM, Hilmar Lapp wrote:

> On Sep 18, 2006, at 5:55 PM, Chris Fields wrote:
>
>> However, if I take the two examples above, run them through
>> FTLocationFactory, then use to_FTstring() to get the feature  
>> string, this is
>> what I get:
>>
>> complement(join(2691..4571,4918..5163))
>>
>> complement(join(4918..5163,2691..4571))
>
> So this looks like a bug, right? The correct result would be if  
> both yielded the same strings, or syntactically equivalent strings.  
> The two above are neither identical nor syntactically equivalent.
>
> Another test is if you set a feature location from either string  
> and then request the sub-sequence, the resulting sequence should be  
> identical given syntactically equivalent location specifications.
>
> Do you want to file (and possibly address?) this?
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

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





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