[Bioperl-l] Bio::SearchIO blastxml for multiple queries
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.
On Mar 13, 2007, at 11:15 PM, Jay Konieczka wrote:
> 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 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
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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