Re: MSG: Undefined sub-sequence
"Fields, Christopher J" <[email protected]>
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> http://mailman.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l