[Bioperl-l] NCBI Blast via HTTP

Chris Fields cjfields at uiuc.edu
Wed Mar 14 15:14:51 EDT 2007


I have a tentative fix for this which I've committed to CVS.  When  
Jason set up the module he checked for the xml header tag as well as  
the status line but had no specific check for text/tabular output.  I  
added a check for the first BLAST line which should break out of the  
loop for all BLAST types (famous last words...) which passes our tests.

chris

On Mar 14, 2007, at 12:25 PM, dwaner at scitegic.com wrote:

>
> Chris,
>
> I have been monitoring the HTTP traffic when submitting blast  
> requests, and the reason that XML format works and TEXT format  
> doesn't is that the XML format still contains the "QBlastInfo...  
> stauts=READY" block, but the TEXT format doesn't.  I'm trying to  
> get NCBI to restore this information to the TEXT result message.    
> Apparently NCBI had a similar problem in February and restored the  
> QBlastInfo comment block on request from someone at Accelrys. I  
> don't know why they changed it back - and they don't seem to know  
> either.  I will let you know if we can get this fixed on NCBI's end.
>
> Regarding XML Blast, is that working in 1.5.1?   We are still  
> relying on TEXT format because it was our understanding that XML  
> parsing was not yet working in the BioPerl version that we are  
> currently using with Pipeline Pilot.
>
> David
>

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





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