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<div>Should this be accessible anonymously?</div>
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<div>I'm unable to connect.</div>
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<div>Eric</div>
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<div>--</div>
<div>Eric Ross</div>
<div>Bioinformatic Specialist I</div>
<div>Alejandro Sánchez Alvarado Laboratory</div>
<div>Stowers Institute for Medical Research</div>
<div>Howard Hughes Medical Institute</div>
<div>ejr@stowers.org</div>
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<span style="font-weight:bold">From: </span>Jason Stajich <<a href="mailto:jason.stajich@gmail.com">jason.stajich@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Monday, April 29, 2013 5:49 PM<br>
<span style="font-weight:bold">To: </span>Barry Moore <<a href="mailto:barry.moore@genetics.utah.edu">barry.moore@genetics.utah.edu</a>><br>
<span style="font-weight:bold">Cc: </span>Eric Ross <<a href="mailto:ejr@stowers.org">ejr@stowers.org</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] repeat statistics<br>
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<div dir="ltr">Barry - I think you mean topaz instead of malachite?
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<div>svn co svn://<a href="http://topaz.genetics.utah.edu/SOBA/trunk">topaz.genetics.utah.edu/SOBA/trunk</a> SOBA<br>
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<div>Jason Stajich<br>
<a href="mailto:jason@bioperl.org">jason@bioperl.org</a><br>
<a href="mailto:jason.stajich@gmail.com">jason.stajich@gmail.com</a><br>
<a href="http://bioperl.org/wiki/User:Jason">http://bioperl.org/wiki/User:Jason</a><br>
<a href="http://twitter.com/hyphaltip">http://twitter.com/hyphaltip</a></div>
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<div class="gmail_quote">On Mon, Apr 29, 2013 at 10:59 AM, Barry Moore <span dir="ltr">
<<a href="mailto:barry.moore@genetics.utah.edu" target="_blank">barry.moore@genetics.utah.edu</a>></span> wrote:<br>
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<div style="word-wrap:break-word">Hi Eric,
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<div>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:</div>
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<div><a href="http://www.sequenceontology.org/resources/sobacl.html" target="_blank">http://www.sequenceontology.org/resources/sobacl.html</a></div>
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<div>Ultimately you'll get it like this:</div>
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<div><code>svn co <a>svn://malachite.genetics.utah.edu/SOBA/trunk</a> SOBA </code></div>
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<div>Then run:</div>
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<div>SOBA/bin/SOBAcl --help </div>
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<div>For a lot of command line examples have a look in:</div>
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<div>SOBA/t/sobacl_test.sh</div>
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<div>On Apr 29, 2013, at 9:58 AM, Ross, Eric wrote:</div>
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<div>Does anyone have a good tool for yanking repeat statistics out of MAKER<br>
gff files?<br>
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SOBA can give some basic stats, but it doesn't play well with my giant<br>
files and I haven't figured out a way to run it locally.<br>
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For that matter does anyone have a script that will calculate SOBA like<br>
stats locally? I'd rather avoid writing one myself if something else is<br>
out there.<br>
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Thanks,<br>
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Eric<br>
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Eric Ross<br>
Bioinformatic Specialist I<br>
Alejandro Sánchez Alvarado Laboratory<br>
Stowers Institute for Medical Research<br>
Howard Hughes Medical Institute<br>
<a href="mailto:ejr@stowers.org" target="_blank">ejr@stowers.org</a><br>
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<div style="font-family:Arial;font-size:12px">Barry Moore</div>
<div style="font-family:Arial;font-size:12px">Research Scientist</div>
<div style="font-family:Arial;font-size:12px">Dept. of Human Genetics</div>
<div style="font-family:Arial;font-size:12px">University of Utah</div>
<div style="font-family:Arial;font-size:12px">Salt Lake City, UT 84112</div>
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<div style="font-family:Arial;font-size:12px"><a href="tel:%28801%29%20585-3543" value="+18015853543" target="_blank">(801) 585-3543</a></div>
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