[Bioperl-l] frac_aligned_query returning results >1.

Thiago Venancio thiago.venancio at gmail.com
Thu Mar 1 13:02:14 EST 2007

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"
I have just updated my SearhUtils.pm from:

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
STACK: Bio::Search::SearchUtils::_adjust_contigs
STACK: Bio::Search::SearchUtils::tile_hsps
STACK: Bio::Search::Hit::GenericHit::frac_aligned_query
STACK: ./geraStatGenome.pl:17

My code is pretty clean:

   while( my $hit = $result->next_hit ) {
'query' )."\n";



"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

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