[Bioperl-l] MSG: Undefined sub-sequence

[Thiago M. Venancio]

Hello again,

Please find below the code I used to parse a regular BLASTX report. I
confirm that the problem also happens with frac_aligned_hit().

Any help is appreciated.
Best,
Thiago

use strict;
use warnings;
use Bio::SearchIO;

my $searchio = Bio::SearchIO->new( -format => 'blast',
   -file   => shift );

while ( my $result = $searchio->next_result() ) {

    while( my $hit = $result->next_hit ) {
 print $hit->name."\t".$hit->frac_aligned_query."\n";
    }
}


On Wed, Dec 17, 2014 at 7:55 PM, Thiago M. Venancio <
thiago.venancio at gmail.com> wrote:
>
> Hi Chris,
> Thanks.
> I do not have the exact code rigth now, but it is very simple. The problem
> happens when I call the frac_aligned_query() on the hit object in
> Bio::SearchIO. I do not know a better way to get the coverage values.
> Best,
> Thiago
>
>
> On Wednesday, December 17, 2014, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
>
>>  Thiago,
>>
>>  Best thing would be to see your code to try to understand what you are
>> trying to do.  It seems to be triggering the older HSP tiling code for
>> BioPerl, and there may be better ways to get at the data (e.g. Mark
>> Jensen’s work on refactoring HSP tiling into a separate code base:
>> http://www.bioperl.org/wiki/HOWTO:Tiling).
>>
>>  chris
>>
>>  On Dec 17, 2014, at 12:04 PM, Thiago M. Venancio <
>> thiago.venancio at gmail.com> wrote:
>>
>>   Hi all,
>>  I am parsing a BLASTX report and got the following error for some
>> sequences.
>>  It always happen with sub-sequences of 1 base. I found some posts on
>> this issue, but they are old.
>>  I am use the latest version installed through cpan.
>>  *$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'*
>>  *1.006924*
>>
>>   Any help is appreciated.
>>  Thiago
>>
>>  ------------- EXCEPTION: Bio::Root::Exception -------------
>>  MSG: Undefined sub-sequence (241,242). Valid range = 96 - 242
>>  STACK: Error::throw
>>  STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
>>  STACK: Bio::Search::HSP::HSPI::matches
>> /usr/share/perl5/Bio/Search/HSP/HSPI.pm:716
>>  STACK: Bio::Search::SearchUtils::_adjust_contigs
>> /usr/share/perl5/Bio/Search/SearchUtils.pm:431
>>  STACK: Bio::Search::SearchUtils::tile_hsps
>> /usr/share/perl5/Bio/Search/SearchUtils.pm:201
>>  STACK: Bio::Search::Hit::GenericHit::frac_aligned_hit
>> /usr/share/perl5/Bio/Search/Hit/GenericHit.pm:1319
>>
>>  --
>> =================================
>> Thiago Motta Venancio, M.Sc., PhD
>> http://venancio.openwetware.org/
>> =================================
>>  _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
> --
> =================================
> Thiago Motta Venancio, M.Sc., PhD
> http://venancio.openwetware.org/
> =================================
>


-- 
=================================
Thiago Motta Venancio, M.Sc., PhD
http://venancio.openwetware.org/
=================================
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