[Bioperl-l] bioperl-hmmer3 question

Thomas Sharpton thomas.sharpton at gmail.com
Mon Nov 22 22:28:52 UTC 2010

Hi Evan,

Glad to hear this software is a promising solution to your needs. I  
just tried running the test script under Bio/t/SearchIO/hmmer3.t and  
everything passed. Can you verify that you are using an up-to-date  
version of bioperl-live? You can grab a snapshot from github if you  
haven't already:


Also, I'm cc'ing this to the bioperl list so that others may benefit  
from our discourse (and chime in - Kai Blin, who created the test  
tools, and others have made substantial contributions and improvements  
to the original code and they might have good suggestions).


On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:

> Hi Thomas,
> Thanks for providing the new bioperl methods for parsing hmmer3  
> reports. Everything seems to be working nicely with the test data  
> and my own reports except for getting the $hsp->query_string and  
> $hsp->hit_string. I noticed that these HSP routines were not working  
> with the test script/data (for me anyway) so I thought I would ask  
> before spending days trying to solve this one.
> Thanks,
> Evan
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602

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