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@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@ice.mpg.de 
Tel +493641571561