[Bioperl-l] bioperl script error

[Andreo Beck]

Great Torsten. But I wonder where this function is being called. Also even if it is called when my code is supplying out of range coordinates?
I'm using BLASTP. 

Torsten Seemann <torsten.seemann at infotech.monash.edu.au> wrote: Andy,

> Any clue what may be the cause of this exception? The sub-sequence seems to be within the valid range.
>  ------------- EXCEPTION  -------------
> MSG: Undefined sub-sequence (75,77). Valid range = 17 - 77
> STACK Bio::Search::HSP::HSPI::matches /cmpchome/andyb/lib/perl/Bio/Search/HSP/HSPI.pm:711
> STACK (eval) /cmpchome/andyb/lib/perl/Bio/Search/SearchUtils.pm:365
> STACK Bio::Search::SearchUtils::_adjust_contigs /cmpchome/andyb/lib/perl/Bio/Search/SearchUtils.pm:364
> STACK Bio::Search::SearchUtils::tile_hsps /cmpchome/andyb/lib/perl/Bio/Search/SearchUtils.pm:176
> STACK Bio::Search::Hit::GenericHit::length_aln /cmpchome/andyb/lib/perl/Bio/Search/Hit/GenericHit.pm:740
> STACK toplevel /var/spool/slurmd/job01852/script:30

What type of report are you processing?
eg. [T]BLAST[NX], BLASTP, HMMER

Here's the problem causing function in bioperl-live:
http://doc.bioperl.org/bioperl-live/Bio/Search/HSP/HSPI.html#CODE22

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/



		
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