[Bioperl-l] bioperl BLAST question

[Chris Fields]

On Jul 6, 2009, at 10:01 AM, Sean ohEigeartaigh wrote:

>
> Hi,
>
> I'm trying to use bioperl to limit the number of BLAST results.  
> However, when I use the following bit of code, it limits to less  
> than the cutoff number, and excludes BLAST results that are halfway  
> up the BLAST results page (without the limit) which it shouldn't  
> exclude.
>
> $blast = Bio::Tools::Run::StandAloneBlast
>    ->new(program => 'tblastn', database =>$blastdb, b =>100, v  
> =>100, F=>$fil, outfile=>$out)
>    ->blastall($seq1);
> }
>
> Using this bit of code, I get 60 results for my query (out of 173  
> with no hit limit and an e-value cutoff of e=10). If I use b =>150,  
> v=>150, I get 85 results, and some BLAST results appear halfway up  
> the results page. In other words, the limit seems to be removing  
> results at random throughout the file, and is also not giving me  
> enough results.

The problem is we can't adequately diagnose the problem with the  
script segment and w/o an example report and description of what you  
expect.  The best way to handle this is to file a bug report so we can  
look things over:

http://www.bioperl.org/wiki/Bugs

> Am I using the b and v parameters (to limit blast results and blast  
> one-line summaries) incorrectly?

> Thanks very much for your help,
> Seán Ó hÉigeartaigh

chris