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

[Steve Chervitz]

Apologies for the trouble my tile_hsps method has caused. My original
intent for it was to provide approximate answers at the level of the
Hit object, providing a means of summing over all HSPs in a reasonable
way. I don't think it has ever gone through extensive testing with
different blast flavors and edge cases.

What to do with it? Maybe provide warnings to it's limitations with
advice on other ways to proceed. Or bite the bullet and make it more
robust.

As for the specific exception reported in this thread, it looks like
there's a bug causing it to not properly handle zero-length ranges:

"Undefined sub-sequence (548,548). Valid range = 51 - 548"

Patching this might be fairly straightforward and could help in the
short term. I'll take a look.

Steve


On Mon, Nov 17, 2008 at 10:16 AM, Jason Stajich <jason at bioperl.org> 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
>