[Bioperl-l] (no subject)

Jason Stajich jason at bioperl.org
Fri Jan 5 17:30:31 EST 2007


I'm not sure I understand the question - can't you just test if there  
are no hits?
if( $result->num_hits == 0 ) { # do something
  }

On Jan 5, 2007, at 2:02 PM, Andrew Stewart wrote:

> After running Bio::Tools::StandAloneBlast->blastall on a collection
> of protein sequences, SearchIO then allows me to traverse the list of
> hits returned for those sequences which hits were found for.  Here's
> a question: what if I want to know which query sequences -didn't-
> produce hits?
>
> Now, I realize I could just go back and compare the set of query
> sequences to the set of blast hits to find these 'no-hits', but I'm
> wondering if SearchIO can include the queries for which hits were not
> found.  Anyone know?  Or have any other suggestions?
>
> Thanks,
> Andrew
>
> --
> Andrew Stewart
> Research Assistant, Genomics Team
> Navy Medical Research Center (NMRC)
> Biological Defense Research Directorate (BDRD)
> BDRD Annex
> 12300 Washington Avenue, 2nd Floor
> Rockville, MD 20852
>
> email: stewarta at nmrc.navy.mil
> phone: 301-231-6700 Ext 270
>
>
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