[Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing Blast output

[Chris Fields]

My guess is you're running into text parsing problems in
Bio::SearchIO::blast.  Upgrade to the latest developer version (1.5.1) or
bioperl-live (CVS), then see the bug below. 

http://bugzilla.bioperl.org/show_bug.cgi?id=1934

I think the first problem you ran into is solved in bioperl 1.5.1, the last
problem (more recent, not related to the first) has been fixed but hasn't
been committed to bioperl-live yet.  The fixed SearchIO::blast is available
in the link above, but realize it hasn't been committed yet and may change.

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

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Hubert Prielinger
> Sent: Wednesday, February 08, 2006 2:52 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
> parsing Blast output
> 
> Hi,
> If I want to parse a Blast Output (Version 2.2.12) with 
> Bio::SearchIO, I get the following error message:
> 
> MSG: no data for midline Query  1   WWWKWRW  7
> STACK Bio::SearchIO::blast::next_result
> /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
> STACK toplevel
> /home/Hubert/installed/eclipse/workspace/Database_Search/Blast.pl:21
> 
> is that a bug......
> 
> If I want to parse Blast Output (version 2.2.13), I don't get 
> anything.....
> I'm using bioperl 1.4
> 
> before, I have installed bioperl 1.4, it worked fine parsing 
> Blast Output (version 2.2.12), but I don't remember which 
> bioperl version I had installed
> 
> thanks in advance
> 
> Hubert
> 
> 
> 
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