[Bioperl-l] getting teh NO HITS FOUND with SearchIO

Barry Moore barry.moore at genetics.utah.edu
Mon Nov 29 12:47:34 EST 2004


Which SearchIO script are you using?  You are parsing blast reports with 
SearchIO right?  If so, how are you generating those blast reports - 
local blast, remote blast...?  Running the blast is the point at which 
you should be detecting whether or not you got a hit.  Look at the 
synopsis code for Bio::Tools::Run::RemoteBlast for an example of how to 
do this.


Javier Terol wrote:

> Hi!
> I have been using the SearchIO scripts very happily, but I have 
> noticed that the parsing does not qive any information about the 
> sequences that do not produce any hit.
> How coul I get the NO HITS FOUND sequences? Could I modify the example 
> script to do this?
> Thank you very muc in advance
>    O@@@@@       
>   @@@O@@O@      Javier Terol Alcayde
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Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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