[Bioperl-l] 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 <thiago.venancio at gmail.com<mailto: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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