[Bioperl-l] HowTo:SearchIO

Chris Fields cjfields at uiuc.edu
Wed Feb 14 12:28:24 EST 2007


I would also strongly encourage switching to using XML-based parsing,  
which is much more stable now.  Here's the link to the NCBI response  
re: BLAST report parsing:

http://bioperl.org/wiki/NCBI_Blast_email

chris (taking a break from shoveling snow...)

On Feb 14, 2007, at 10:59 AM, Jason Stajich wrote:

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





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