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

Chris Fields cjfields at uiuc.edu
Fri Dec 15 14:21:32 EST 2006


On Dec 15, 2006, at 12:56 PM, Jason Stajich wrote:

> 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

I agree that XML is the only reliable way to go, though I have been  
reading on the BioPython group about some issues with newer (2.2.13  
or greater) BLAST XML output when reports with multiple BLAST  
queries.  Don't know if this affects Bioperl or not.

As for the 'midline' error, there was a similar error a while back  
(fixed for the 1.5.2 release) that had to do with extra lines in the  
alignment section in some BLAST reports.  Unless we have a demo BLAST  
report and sample code we can't do much about it (we need to  
reproduce the error in order to fix it), so the best thing to do it  
file a bug report.

chris

> 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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>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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