[Bioperl-l] frac_aligned_query returning results >1.

Chris Fields cjfields at uiuc.edu
Thu Mar 1 13:27:10 EST 2007


This is related to a reported bug:

http://bugzilla.open-bio.org/show_bug.cgi?id=2193

The relevant code used to tile HSPs is a bit brittle and sometimes  
leads to errors like this.  The error (which is actually a thrown  
exception) is wrapped in an eval block and converted to a warn for  
that reason.  I'm not familiar with the tiling algorithm used, maybe  
Steve can add some input?

chris

On Mar 1, 2007, at 12:02 PM, Thiago Venancio wrote:

> Hi all,
>
> I have read a lot of threads regarding my issue, but still didn't  
> get any
> efficient answer yet.
>
> I am with problems with frac_aligned_query(). It is returning  "> 1"
> results.
> I have just updated my SearhUtils.pm from:
> http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
> Bio/Search/SearchUtils.pm
>
>
> The problem persists and, additionally, I get several warnings like:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Undefined sub-sequence (1507,1507) . Valid range = 1444 - 1507
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
> STACK: Bio::Search::HSP::HSPI::matches
> /usr/share/perl5/Bio/Search/HSP/HSPI.pm:711
> STACK: Bio::Search::SearchUtils::_adjust_contigs
> /usr/share/perl5/Bio/Search/SearchUtils.pm:489
> STACK: Bio::Search::SearchUtils::tile_hsps
> /usr/share/perl5/Bio/Search/SearchUtils.pm:200
> STACK: Bio::Search::Hit::GenericHit::frac_aligned_query
> /usr/share/perl5/Bio/Search/Hit/GenericHit.pm:1145
> STACK: ./geraStatGenome.pl:17
>
> My code is pretty clean:
>
>    while( my $hit = $result->next_hit ) {
>     print
> $result->query_name."\t".$hit->frac_aligned_query('query')."\t". 
> $hit->frac_identical(
> 'query' )."\n";
>     last;
>     }
>
>
> Thanks.
>
> Thiago
>
>
> -- 
> "The way to get started is to quit talking and begin doing."
>       Walt Disney
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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