[Bioperl-l] bioperl script error

[Andreo Beck]

My line 30 has:

$hit->hsp->evalue <= $threshold

But strangely enough, when I ran it the last time it ran successfully.
One point is that, in my line 32 I've added:

     if(($hit->length_aln() >= $sum_of_HSP_len && $hit->length()>= $hit_len ))


Now its clear that this is the line that's creating the problems, more specifically the length_aln function! The calls as you see are length_aln --> tile_hsps --> _adjust_contigs-->matches. Can this have anything to do with overlaps in my data?

 

Jason Stajich <jason.stajich at duke.edu> wrote: 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?

-jason
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  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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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12


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