Re: undefined sub-sequence with a single base

I agree completely with everything Jason says.  Not to mention this is  
also very similar to a filed bug, which I have no clue on how to fix:

http://bugzilla.open-bio.org/show_bug.cgi?id=2476

chris

On Nov 17, 2008, at 12:16 PM, Jason Stajich wrote:

> Personally - I'm not sure I trust tile_hsps on a translated search -  
> or at all - really - you may want to compute the "dominant" strand  
> yourself by iterating through the HSPs or using WU-BLAST to get  
> logical groups of HSPs which is a better tiling HSP algorithm (the -- 
> links option in WU-BLAST).
>
> -jason
> On Nov 17, 2008, at 9:43 AM, Alexie Papanicolaou wrote:
>
>> Hi Chris
>>
>> Sorry, I got the new SVN build today and still get the same error...
>>
>> Could it be because the subseq is not divisible by 3 (due to blastx)?
>>
>> a
>>
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Undefined sub-sequence (2,2). Valid range = 2 - 190
>> STACK: Error::throw
>> STACK:
>> Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm: 
>> 357
>> STACK:
>> Bio::Search::HSP::HSPI::matches /usr/local/share/perl/5.8.8/Bio/ 
>> Search/HSP/HSPI.pm:691
>> STACK:
>> Bio::Search::SearchUtils::_adjust_contigs /usr/local/share/perl/ 
>> 5.8.8/Bio/Search/SearchUtils.pm:460
>> STACK:
>> Bio::Search::SearchUtils::tile_hsps /usr/local/share/perl/5.8.8/Bio/ 
>> Search/SearchUtils.pm:200
>> STACK:
>> Bio::Search::Hit::GenericHit::strand /usr/local/share/perl/5.8.8/ 
>> Bio/Search/Hit/GenericHit.pm:1455
>>
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Undefined sub-sequence (3,4). Valid range = 3 - 44
>> STACK: Error::throw
>> STACK:
>> Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm: 
>> 357
>> STACK:
>> Bio::Search::HSP::HSPI::matches /usr/local/share/perl/5.8.8/Bio/ 
>> Search/HSP/HSPI.pm:691
>> STACK:
>> Bio::Search::SearchUtils::_adjust_contigs /usr/local/share/perl/ 
>> 5.8.8/Bio/Search/SearchUtils.pm:404
>> STACK:
>> Bio::Search::SearchUtils::tile_hsps /usr/local/share/perl/5.8.8/Bio/ 
>> Search/SearchUtils.pm:200
>> STACK:
>> Bio::Search::Hit::GenericHit::strand /usr/local/share/perl/5.8.8/ 
>> Bio/Search/Hit/GenericHit.pm:1455
>>
>>
>>
>>
>>
>>
>> On Fri, 2008-11-14 at 11:08 -0600, Chris Fields wrote:
>>
>>> We've switched to subversion a while ago.  Could you try updating  
>>> from
>>> there, or using one of our nightly builds?
>>>
>>> http://www.bioperl.org/DIST/nightly_builds/
>>>
>>> chris
>>>
>>> On Nov 14, 2008, at 8:59 AM, Alexie Papanicolaou wrote:
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l <at> lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Jason Stajich
> jason <at> bioperl.org
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign