[Bioperl-l] (no subject)

Andrew Stewart stewarta at nmrc.navy.mil
Fri Jan 5 18:03:26 EST 2007


Doh, why didn't I think of that?

Thanks.


On Jan 5, 2007, at 5:30 PM, Jason Stajich wrote:

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



--
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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