[Bioperl-l] undefined sub-sequence with a single base

[Chris Fields]

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:

> Ah, I should add this is a BLASTX.
>
>
> On Fri, 2008-11-14 at 14:56 +0000, Alexie Papanicolaou wrote:
>
>> Dear all,
>>
>> Would anyone have an insight into this error while parsing a BLAST
>> report (bioperl from CVS on 28th of August)?
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Undefined sub-sequence (548,548). Valid range = 51 - 548
>> 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:421
>> 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
>>
>> This is using HSPI.pm with the patch starting
>> ## ML: START fix for substr out of range error
>>
>> many thanks for any pointers
>> a
>>
>> Alexie Papanicolaou
>> Entomology
>> Max Planck Institute for Chemical Ecology
>> Hans Knoell Str 8
>> Jena 07745
>> Germany
>> Email apapanicolaou at ice.mpg.de
>> Tel +493641571561
>>
>>
>>
>
> -- 
> -- 
> "Eppur si evolve" ("And yet it evolves")
> -Galileo Jr (ca 21st century)
>
> "One Galileo in two thousand years is enough." -Pope Pius XII
> -- 
> Alexie Papanicolaou
> Entomology
> Max Planck Institute for Chemical Ecology
> Hans Knoell Str 8
> Jena 07745
> Germany
> Email apapanicolaou at ice.mpg.de
> Tel +493641571561
>
>
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