MSG: Undefined sub-sequence

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MSG: Undefined sub-sequence

Thiago Venancio
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/
=================================

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Re: MSG: Undefined sub-sequence

Fields, Christopher J
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 <[hidden email]> 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/
=================================
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Bioperl-l mailing list
[hidden email]
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Re: MSG: Undefined sub-sequence

Thiago Venancio
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 <[hidden email]> 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 <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;thiago.venancio@gmail.com&#39;);" target="_blank">thiago.venancio@...> 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/
=================================
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--
=================================
Thiago Motta Venancio, M.Sc., PhD
http://venancio.openwetware.org/
=================================

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Re: MSG: Undefined sub-sequence

Thiago 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
[hidden email]
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/
=================================

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l