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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Wed Mar 14 04:02:21 EDT 2007


I believe a lot of work went into the Bio::SearchIO::* modules between 
bioperl 1.4 and the 1.5.2 developer release. It's probably wise to 
update your bioperl installation to the latest version and try this again.

Nath


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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