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

[Chris Fields]

Make sure you ran a full installation of bioperl-1.5.1 or bioperl-live (not
just the modules you want; mixing bioperl versions might work, but you might
run into interoperability problems).  Then replace the Bio::SearchIO::blast
with the one in Bugzilla.  The 'other option' you mentioned might be trying
XML instead of text, which is more stable in the long run.  You will still
need to run a full upgrade to bioperl 1.5.1 for that; make sure you read
this:

http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast

If you're using SearchIO directly instead of Remoteblast, you should be able
to set the '-readmethod' flag to 'blastxml'.

It also wouldn't hurt to know what OS you're using or see some code.  Roger
is out there somewhere (I think) and may also have some input.

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

> -----Original Message-----
> From: Hubert Prielinger [mailto:hubert.prielinger at gmx.at] 
> Sent: Wednesday, February 08, 2006 3:41 PM
> To: Chris Fields; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
> parsing Blast output
> 
> 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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> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>    
> >>
> >
> >
> >  
> >
>