[Bioperl-l] Bio::SearchIO blastxml for multiple queries

Chris Fields cjfields at uiuc.edu
Wed Mar 14 09:05:20 EDT 2007


This has been fixed in CVS.  You will need to update to 1.5.2 since  
you're running bioperl 1.4, but I would recommend just installing  
from CVS if that's possible.

I will probably do some tweaking to the blastxml parser to better  
deal with multiple reports.  At the moment it parses the full XML  
output and caches the Result objects, so if you have a huge XML file  
it will likely choke your system.

chris

On Mar 13, 2007, at 11:15 PM, Jay Konieczka wrote:

> Hi,
>
> My blastxml output, which is supposed to contain multiple queries,
> each having multiple hits, is improperly parsed by Bio::SearchIO -
> only the first query is recognized.  I realize there has been plenty
> of talk about this issue since it arose, but I've been having trouble
> finding instructions for a patch.  Is there an easy fix for this?
> I'm running blastall version 2.2.15 (using blastn) and attempting to
> parse the output with bioperl 1.4.
>
> Thanks for any help,
>
> Jay
>
> --
> Jay H. Konieczka
> Ph.D. Student, Antin Lab
> Molecular & Cellular Biology
> University of Arizona
>
> Phone:  1.520.591.3446
>
> 1656 E. Mabel, MRB 317
> Tucson, AZ 85724 USA
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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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