<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Correct. And web page is now updated as well.<div><br></div><div>B</div><div><br><div><div>On Apr 29, 2013, at 4:49 PM, Jason Stajich wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div dir="ltr">Barry - I think you mean topaz instead of malachite?<div><br></div><div>svn co svn://<a href="http://topaz.genetics.utah.edu/SOBA/trunk">topaz.genetics.utah.edu/SOBA/trunk</a> SOBA<br></div><div><br></div></div>
<div class="gmail_extra"><br clear="all"><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>
<br><br><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><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Eric,<div><br></div><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><div><br></div><div>
<a href="http://www.sequenceontology.org/resources/sobacl.html" target="_blank">http://www.sequenceontology.org/resources/sobacl.html</a></div><div><br></div><div>Ultimately you'll get it like this:</div><div><br></div>
<div><code>svn co <a>svn://malachite.genetics.utah.edu/SOBA/trunk</a> SOBA </code>
</div><div><br></div><div>Then run:</div><div><br></div><div>SOBA/bin/SOBAcl --help </div><div><br></div><div>For a lot of command line examples have a look in:</div><div><br></div><div>SOBA/t/sobacl_test.sh</div><div><br>
</div><div>B</div><div><div><div class="h5"><br><div><div>On Apr 29, 2013, at 9:58 AM, Ross, Eric wrote:</div><br><blockquote type="cite"><div>Does anyone have a good tool for yanking repeat statistics out of MAKER<br>gff files?<br>
<br>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><br>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><br>Thanks,<br><br>Eric<br><br>--<br>Eric Ross<br>Bioinformatic Specialist I<br>Alejandro Sánchez Alvarado Laboratory<br>Stowers Institute for Medical Research<br>
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<div><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">
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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