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:
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.
> On Feb 13, 2007, at 2:43 PM, Thomas J Keller wrote:
>> 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
>> 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?
>> Tom Keller, Ph.D.
>> kellert at ohsu.edu
>> 6339b Basic Science Bldg
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Jason Stajich
> Miller Research Fellow
> University of California, Berkeley
> lab: 510.642.8441
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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Dept of Biochemistry
University of Illinois Urbana-Champaign
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