[maker-devel] repeat statistics

[Barry Moore]

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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