[Bioperl-l] HowTo:SearchIO

Jason Stajich jason at bioperl.org
Wed Feb 14 11:59:49 EST 2007


As always, reporting the version of BLAST and Bioperl you have  
installed will help someone diagnose if this is a fixed problem or  
not.  If you trawl through the list archives you'll chris and others  
have been playing cat and mouse with the text version output from  
NCBI BLAST which appears to be an ever evolving beast.

So the best advice right now is to get the latest bioperl from CVS   
to insure you have all the patches that might parse this version.  If  
it still fails then the standard response will be to submit the  
report as an attachment to a new bug report on the bugzilla.

thanks,
-jason


On Feb 13, 2007, at 2:43 PM, Thomas J Keller wrote:

> Greetings,
> I've been away from programming and informatics for many months.
> Hoping to get back into it, I thought it would be good to review the
> tutorials.
> I tried the code in the tutorial on the sample blast report in the
> tutorial and it worked fine. So I ran a blastx search and saved the
> results and tried to parse them: It gave the "... parsing" message,
> but no other results get reported.
>
> Any suggestions?
>
> Thanks,
> Tom
>
> Tom Keller, Ph.D.
> kellert at ohsu.edu
> 503-494-2442
> 6339b Basic Science Bldg
> http://www.ohsu.edu/research/core
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org/



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