[Bioperl-l] frac_aligned_query returning results >1.

[Thiago Venancio]

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
========================