[Bioperl-l] bioperl-hmmer3 question

[Evan Staton]

Hi Thomas,

Everything works with the latest release of bioperl-live. My bioperl was
1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
did not realize it had been incorporated into the latest distribution). All
the tests passed and all the routines worked before except for the
$hsp->query_string and $hsp->hit_string, but that is resolved now.

Thanks for the quick response, it saved me a lot of time.

Evan

On Mon, Nov 22, 2010 at 5:28 PM, Thomas Sharpton
<thomas.sharpton at gmail.com>wrote:

> 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:
>
> https://github.com/bioperl/bioperl-live
>
> 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).
>
> T
>
>
>
> 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
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
S. Evan Staton
PhD Student - Burke Lab
University of Georgia
Department of Genetics
3507 Miller Plant Sciences
Athens, GA 30602