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

Chris Fields cjfields at uiuc.edu
Wed Jan 17 12:03:56 EST 2007


On Jan 17, 2007, at 10:54 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> 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?
>
> Sure. In case you didn't notice, the reason it isn't catching the  
> next BLAST report is the lack of alignments. For the few results  
> that do have alignments, that's where it 'works'.

I plan on generating a new BLAST report (from the web, since I don't  
have 2.2.15 installed) with multiple queries and no alignments to see  
what happens (i.e. see if the new multiquery report is similar to  
this one).  If so, there is a 'wrap-up' section of the parser, where  
hit data not in alignments (in the table only) is used to generate  
Hit objects; it's dropping this data likely b/c there is no regex  
signalling the next result event.

chris



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