[Bioperl-l] Bio::SearchIO::blast::next_result exception thrown

Jason Stajich jason at bioperl.org
Fri Dec 15 13:56:13 EST 2006


It means it is expecting alignment block of data and there is none  
(or there is none in the context it is expecting it) - so something  
is wrong with the report as it gets tripped up.

I'm not sure reading the code is going to help you - what someone  
will have to do is figure out what is different about this report  
than reports that do work for the parser.
You'll do better if you just provide an example report that is  
failing as a bug report.

Providing the version of BLAST you are using and version of bioperl  
will help.  I seem to remember NCBI changing the BLAST text format so  
that will break the parser if it is a significant change.

As has been mentioned in the past, this playing cat and mouse with  
format changes means things will periodically break. If you need rock- 
solid always going to work, I guess the XML is better route to go.

-jason
On Dec 14, 2006, at 6:30 PM, Andrew Stewart wrote:

> I'm getting the following exception...
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no data for midline     Posted date:  Dec 14, 2006  2:52 PM
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /sw/lib/perl5/5.8.6/Bio/Root/Root.pm:328
> STACK: Bio::SearchIO::blast::next_result /sw/lib/perl5/5.8.6/Bio/
> SearchIO/blast.pm:1172
> STACK: main::process_reports ./new_blast_script.pl:254
> STACK: ./new_blast_script.pl:132
> -----------------------------------------------------------
>
>
> next_result is a pretty dense chunk of code to decipher.  I was
> wondering if anyone more familiar with that code might know what the
> "no data for midline $_" exception is referring to?
>
>
> --
> Andrew Stewart
> Research Assistant, Genomics Team
> Navy Medical Research Center (NMRC)
> Biological Defense Research Directorate (BDRD)
> BDRD Annex
> 12300 Washington Avenue, 2nd Floor
> Rockville, MD 20852
>
> email: stewarta at nmrc.navy.mil
> phone: 301-231-6700 Ext 270
>
>
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