[Bioperl-l] bioperl script error

Jason Stajich jason.stajich at duke.edu
Wed Jan 4 19:20:03 EST 2006

What does line 30 in your script say?
>> STACK toplevel /var/spool/slurmd/job01852/script:30

It is trying to merge HSPs to compute a the virtual length of a hit  
from the sub-HSPs.  This happens when you call a function on the HitI  
object like start/end/strand that has to merge the HSPs in order to  
get some sort of overall start/end/length for an alignment.  I don't  
really know what is going on in those Hit functions but they  
shouldn't crash if the HSP path set is unresolveable.  (I bet you are  
thinking the same thing...)  Are you sure you want to be calling  
whatever function it is on line 30?

On Jan 4, 2006, at 6:58 PM, Andreo Beck wrote:

> 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?
> 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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Jason Stajich
Duke University

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