[Bioperl-l] frac_aligned_query returning results >1.

Sendu Bala bix at sendu.me.uk
Mon Mar 5 07:41:19 EST 2007

Thiago Venancio wrote:
> Hi all.
> Sorry about this, but the bug persists. Although the number of 
> problematic cases is too low (3 out of 35139), they are present.
> Please find attached an example buggy blast report.
> The line I use to call the function is:
> print $result->query_name."\t".$hit->frac_aligned_query."\n";
> The warning bellow is still appearing a lot of times during processing 
> reports, so I think it is not due to the same bug.
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Undefined sub-sequence (821,821). Valid range = 778 - 821
> 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:421
> 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:34
> -----------------------------------------------------------
> I have checked the code, but I have no idea about what is happening in 
> this case. the attached file produced the ">1" result and pops the 
> exception error, so it could be useful.

Are you sure you attached the correct file? Are you sure you're using 
the latest version of all relevant modules (GenericHit, SearchUtils, 
HSPI, SearchIO, SearchIO::blast, possibly others)? What is the exact 
code you're using when you generate the problems?

I see nothing wrong on my end: correct answer and no exception warning.

---> thiago.pl

#!/usr/bin/perl -w
use warnings;
use strict;

use Bio::SearchIO;

my $sin = Bio::SearchIO->new(-format => 'blast',
                              -file => 'buggyBlast.txt');
my $result = $sin->next_result;
my $hit = $result->next_hit;

print $result->query_name."\t".$hit->frac_aligned_query."\n";


$ perl thiago.pl
AEDES_05359.C   1.00

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