[Bioperl-l] bioperl BLAST question
Chris Fields
cjfields at illinois.edu
Mon Jul 6 16:42:10 UTC 2009
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
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