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

[Hubert Prielinger]

hi chris,
thanks, I have upgraded to version 1.5.1 but it isn't still working, do 
you have any ohter idea, the problem I have is that I have to parse a 
lot of textfiles....
or shall I look for another option to parse those files...

regards
Hubert



Chris Fields wrote:

>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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