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

[Mark A. Jensen]

I think we're (Dave, Chris, and I) are  making progress on the subsequence 
boundary issues. The fix should propagate through everything having this 
issue...we hope--stay tuned...
----- Original Message ----- 
From: "Steve Chervitz" <sac at bioperl.org>
To: "Jason Stajich" <jason at bioperl.org>
Cc: "Chris Fields" <cjfields at illinois.edu>; <bioperl-l at lists.open-bio.org>; 
"Alexie Papanicolaou" <apapanicolaou at ice.mpg.de>
Sent: Sunday, November 30, 2008 12:50 PM
Subject: Re: [Bioperl-l] undefined sub-sequence with a single base


> 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
>>
>>
>>
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>>
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