Re: undefined sub-sequence with a single base

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: