[Bioperl-l] (no subject)

Chris Fields cjfields at uiuc.edu
Fri Jan 5 22:46:20 EST 2007


Looks like there are a few ways to go about doing that, actually.   
According to Search::Result::ResultI POD, no_hits_found() is supposed  
to work like:

if( $result->no_hits_found() ) { # do something

though I can't claim to have tried it myself.

chris

On Jan 5, 2007, at 5:03 PM, Andrew Stewart wrote:

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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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