[Bioperl-l] frac_aligned_query returning results >1.

Thiago Venancio thiago.venancio at gmail.com
Mon Mar 5 07:56:08 EST 2007


Hi all,

So I deduce the problem is in my end, but I have updated all the packages
through CPAN, using the command:

perl -MCPAN -e "install Bundle::BioPerl"

I think this should update all tthe essencial packages, no ?

Thanks,

Thiago


On 3/5/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> 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";
>
> exit;
> <---
>
>
> $ perl thiago.pl
> AEDES_05359.C   1.00
> $
>
>


-- 
"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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