<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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">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 href="svn://malachite.genetics.utah.edu/SOBA/trunk">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><br><div><div>On Apr 29, 2013, at 9:58 AM, Ross, Eric wrote:</div><br class="Apple-interchange-newline"><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>Howard Hughes Medical Institute<br><a href="mailto:ejr@stowers.org">ejr@stowers.org</a><br><br><br><br><br>_______________________________________________<br>maker-devel mailing list<br>maker-devel@box290.bluehost.com<br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div apple-content-edited="true">
<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; ">University of Utah</div><div style="font-family: Arial; font-size: 12px; ">Salt Lake City, UT 84112</div><div style="font-family: Arial; font-size: 12px; ">--------------------------------------------</div><div style="font-family: Arial; font-size: 12px; ">(801) 585-3543</div><div style="font-family: Arial; font-size: 12px; "><br class="khtml-block-placeholder"></div></div><div><br></div><br class="Apple-interchange-newline">
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