[Bioperl-l] MSG: Undefined sub-sequence

[Thiago M. 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 <
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
> <javascript:_e(%7B%7D,'cvml','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/
> =================================
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>

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