[maker-devel] repeat statistics

[Barry Moore]

Correct. And web page is now updated as well.

B

On Apr 29, 2013, at 4:49 PM, Jason Stajich wrote:

> Barry - I think you mean topaz instead of malachite?
> 
> svn co svn://topaz.genetics.utah.edu/SOBA/trunk SOBA
> 
> 
> Jason Stajich
> jason at bioperl.org
> jason.stajich at gmail.com
> http://bioperl.org/wiki/User:Jason
> http://twitter.com/hyphaltip
> 
> 
> On Mon, Apr 29, 2013 at 10:59 AM, Barry Moore <barry.moore at genetics.utah.edu> wrote:
> Hi Eric,
> 
> There is a command line version of SOBA.  It does the same things as the web version and much more.  This page has some basic details:
> 
> http://www.sequenceontology.org/resources/sobacl.html
> 
> Ultimately you'll get it like this:
> 
> svn co svn://malachite.genetics.utah.edu/SOBA/trunk SOBA 
> 
> Then run:
> 
> SOBA/bin/SOBAcl --help 
> 
> For a lot of command line examples have a look in:
> 
> SOBA/t/sobacl_test.sh
> 
> B
> 
> On Apr 29, 2013, at 9:58 AM, Ross, Eric wrote:
> 
>> Does anyone have a good tool for yanking repeat statistics out of MAKER
>> gff files?
>> 
>> SOBA can give some basic stats, but it doesn't play well with my giant
>> files and I haven't figured out a way to run it locally.
>> 
>> For that matter does anyone have a script that will calculate SOBA like
>> stats locally?  I'd rather avoid writing one myself if something else is
>> out there.
>> 
>> Thanks,
>> 
>> Eric
>> 
>> --
>> Eric Ross
>> Bioinformatic Specialist I
>> Alejandro Sánchez Alvarado Laboratory
>> Stowers Institute for Medical Research
>> Howard Hughes Medical Institute
>> ejr at stowers.org
>> 
>> 
>> 
>> 
>> _______________________________________________
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> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
> 
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> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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