Re: undefined sub-sequence with a single base

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:
>
>
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Jason Stajich
jason <at> bioperl.org