bioperl BLAST question

[Sean ohEigeartaigh]

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.

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


     

_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[Chris Fields-5]

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
_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l