[Bioperl-l] [Bioperl]problem with E-value

Chris Fields cjfields at uiuc.edu
Wed Jan 17 11:48:03 EST 2007


I pretty sure I know exactly what the problem is and how to fix it  
(if you haven't done it already).  Looks like the parser trashes the  
rest of the BLAST results data since it's not catching the next BLAST  
report header (and not breaking out of the while() loop).  That may  
be what is triggering the e-value error.  I have been parsing new  
BLAST reports recently w/o that one popping up, but it may be a  
difference between the web BLAST report and the executable (wouldn't  
be the first time that has happened.

Did you want me to take a look?

chris

On Jan 17, 2007, at 10:29 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> Is this a supported BLAST report (i.e. listed in  
>> Bio::SearchIO::blast POD)?  If so, could someone please file this  
>> as a bug along with an example report?  Or has this been fixed  
>> already?
>
> No, it hasn't been fixed already. (I made a recent commit that just  
> got rid of the annoying error message.) Waiting to find out how the  
> blast report was created before taking any further action. It  
> claims to be:
>
> BLASTX 2.2.15 [Oct-15-2006]
>
>
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
> Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database  
> search
> programs",  Nucleic Acids Res. 25:3389-3402.
>

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





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