[Bioperl-l] bioperl script error

[Jason Stajich]

On Jan 4, 2006, at 8:13 PM, Andreo Beck wrote:

> 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?
>
Absolutely.  That is the function causing you problems, as to why it  
is failing, I am guessing it can't figure out how to merge the HSPs.   
Personally I leave this sort of thing to the alignment rather than  
post-processing what BLAST did.  Depending on your question/compute/ 
time you can get a better HSP path by running
* WU-BLAST with the -postsw option which will cleanup these  
overlapping alignments
* FASTA or SSEARCH to get a single alignment path.

>
>
> 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-HS! Ps. 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 -------------
> &! gt;> 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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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12