changeset 1:51baa0ab6def draft

Uploaded unafold.sh
author hogart
date Tue, 10 Mar 2015 05:44:28 -0400
parents e186a2d22ea0
children 75a1e3d0842f
files unafold.sh
diffstat 1 files changed, 833 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unafold.sh	Tue Mar 10 05:44:28 2015 -0400
@@ -0,0 +1,833 @@
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+    </div>
+  </div>
+
+<div class="file">
+  <div class="file-header">
+    <div class="file-actions">
+      <div class="button-group">
+        <a href="/DrHogart/galaxy-tools-unafold/raw/master/unafold.sh" class="minibutton " id="raw-url">Raw</a>
+          <a href="/DrHogart/galaxy-tools-unafold/blame/master/unafold.sh" class="minibutton js-update-url-with-hash">Blame</a>
+        <a href="/DrHogart/galaxy-tools-unafold/commits/master/unafold.sh" class="minibutton " rel="nofollow">History</a>
+      </div><!-- /.button-group -->
+
+
+          <a class="octicon-button disabled tooltipped tooltipped-w" href="#"
+             aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a>
+
+        <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#"
+           aria-label="You must be signed in to make or propose changes">
+      </a>
+    </div><!-- /.actions -->
+    <div class="file-info">
+        77 lines (66 sloc)
+        <span class="file-info-divider"></span>
+      1.912 kb
+    </div>
+  </div>
+  
+  <div class="blob-wrapper data type-shell">
+      <table class="highlight tab-size-8 js-file-line-container">
+      <tr>
+        <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
+        <td id="LC1" class="blob-code js-file-line"><span class="pl-c">#!/bin/bash</span></td>
+      </tr>
+      <tr>
+        <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
+        <td id="LC2" class="blob-code js-file-line"><span class="pl-s3">set</span> -e</td>
+      </tr>
+      <tr>
+        <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
+        <td id="LC3" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
+        <td id="LC4" class="blob-code js-file-line"><span class="pl-c">#arguments are  -i input sequence file in fasta </span></td>
+      </tr>
+      <tr>
+        <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
+        <td id="LC5" class="blob-code js-file-line"><span class="pl-c">#               -o output zip arhive  </span></td>
+      </tr>
+      <tr>
+        <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
+        <td id="LC6" class="blob-code js-file-line"><span class="pl-c">#               -t temp directory with results</span></td>
+      </tr>
+      <tr>
+        <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
+        <td id="LC7" class="blob-code js-file-line"><span class="pl-c">#		-a DNA|RNA</span></td>
+      </tr>
+      <tr>
+        <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
+        <td id="LC8" class="blob-code js-file-line"><span class="pl-c">#		-c tempreature (C)</span></td>
+      </tr>
+      <tr>
+        <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
+        <td id="LC9" class="blob-code js-file-line"><span class="pl-c">#		-s [Na+] in M</span></td>
+      </tr>
+      <tr>
+        <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
+        <td id="LC10" class="blob-code js-file-line"><span class="pl-c">#		-m [Mg++] in M</span></td>
+      </tr>
+      <tr>
+        <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
+        <td id="LC11" class="blob-code js-file-line"><span class="pl-c">#		-b maxbp</span></td>
+      </tr>
+      <tr>
+        <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
+        <td id="LC12" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
+        <td id="LC13" class="blob-code js-file-line"><span class="pl-c">#-n, --NA=(RNA | DNA) (defaults to RNA)</span></td>
+      </tr>
+      <tr>
+        <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
+        <td id="LC14" class="blob-code js-file-line"><span class="pl-c">#-t, --temp=&lt;temperature&gt; (defaults to 37)</span></td>
+      </tr>
+      <tr>
+        <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
+        <td id="LC15" class="blob-code js-file-line"><span class="pl-c">#-N, --sodium=&lt;[Na+] in M&gt; (defaults to 1)</span></td>
+      </tr>
+      <tr>
+        <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
+        <td id="LC16" class="blob-code js-file-line"><span class="pl-c">#-M, --magnesium=&lt;[Mg++] in M&gt; (defaults to 0)</span></td>
+      </tr>
+      <tr>
+        <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
+        <td id="LC17" class="blob-code js-file-line"><span class="pl-c">#-p, --polymer</span></td>
+      </tr>
+      <tr>
+        <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
+        <td id="LC18" class="blob-code js-file-line"><span class="pl-c">#-C, --Ct=&lt;total strand concentration&gt;</span></td>
+      </tr>
+      <tr>
+        <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
+        <td id="LC19" class="blob-code js-file-line"><span class="pl-c">#-I, --noisolate</span></td>
+      </tr>
+      <tr>
+        <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
+        <td id="LC20" class="blob-code js-file-line"><span class="pl-c">#-m, --maxbp=&lt;maximum basepair distance&gt;</span></td>
+      </tr>
+      <tr>
+        <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
+        <td id="LC21" class="blob-code js-file-line"><span class="pl-c">#-c, --constraints=&lt;name of constraints file&gt; (defaults to prefix.aux)</span></td>
+      </tr>
+      <tr>
+        <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
+        <td id="LC22" class="blob-code js-file-line"><span class="pl-c">#-P, --percent=&lt;energy increment percent&gt; (defaults to 5)</span></td>
+      </tr>
+      <tr>
+        <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
+        <td id="LC23" class="blob-code js-file-line"><span class="pl-c">#-W, --window=&lt;window size&gt; (default set by sequence length)</span></td>
+      </tr>
+      <tr>
+        <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
+        <td id="LC24" class="blob-code js-file-line"><span class="pl-c">#-X, --max=&lt;maximum number of foldings&gt; (defaults to 100)</span></td>
+      </tr>
+      <tr>
+        <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
+        <td id="LC25" class="blob-code js-file-line"><span class="pl-c">#    --ann=(none | p-num | ss-count) (defaults to none)</span></td>
+      </tr>
+      <tr>
+        <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
+        <td id="LC26" class="blob-code js-file-line"><span class="pl-c">#    --mode=(auto | bases | lines) (defaults to auto)</span></td>
+      </tr>
+      <tr>
+        <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
+        <td id="LC27" class="blob-code js-file-line"><span class="pl-c">#    --label=&lt;base numbering frequency&gt;</span></td>
+      </tr>
+      <tr>
+        <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
+        <td id="LC28" class="blob-code js-file-line"><span class="pl-c">#    --rotate=&lt;structure rotation angle&gt;</span></td>
+      </tr>
+      <tr>
+        <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
+        <td id="LC29" class="blob-code js-file-line"><span class="pl-c">#    --run-type=(text | html) (defaults to text)</span></td>
+      </tr>
+      <tr>
+        <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
+        <td id="LC30" class="blob-code js-file-line"><span class="pl-c">#    --model=(EM | PF) (defaults to EM)</span></td>
+      </tr>
+      <tr>
+        <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
+        <td id="LC31" class="blob-code js-file-line"><span class="pl-c">#    --circular</span></td>
+      </tr>
+      <tr>
+        <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
+        <td id="LC32" class="blob-code js-file-line"><span class="pl-c">#Obscure options:</span></td>
+      </tr>
+      <tr>
+        <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
+        <td id="LC33" class="blob-code js-file-line"><span class="pl-c">#    --allpairs</span></td>
+      </tr>
+      <tr>
+        <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
+        <td id="LC34" class="blob-code js-file-line"><span class="pl-c">#    --maxloop=&lt;maximum bulge/interior loop size&gt; (defaults to 30)</span></td>
+      </tr>
+      <tr>
+        <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
+        <td id="LC35" class="blob-code js-file-line"><span class="pl-c">#    --nodangle</span></td>
+      </tr>
+      <tr>
+        <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
+        <td id="LC36" class="blob-code js-file-line"><span class="pl-c">#    --simple</span></td>
+      </tr>
+      <tr>
+        <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
+        <td id="LC37" class="blob-code js-file-line"><span class="pl-c">#    --prefilter=&lt;filter value&gt;</span></td>
+      </tr>
+      <tr>
+        <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
+        <td id="LC38" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
+        <td id="LC39" class="blob-code js-file-line">NA=RNA</td>
+      </tr>
+      <tr>
+        <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
+        <td id="LC40" class="blob-code js-file-line">TM=37</td>
+      </tr>
+      <tr>
+        <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
+        <td id="LC41" class="blob-code js-file-line">NAT=1</td>
+      </tr>
+      <tr>
+        <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
+        <td id="LC42" class="blob-code js-file-line">MG=0</td>
+      </tr>
+      <tr>
+        <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
+        <td id="LC43" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
+        <td id="LC44" class="blob-code js-file-line"><span class="pl-k">while</span> <span class="pl-s3">getopts</span> <span class="pl-s1"><span class="pl-pds">&quot;</span>:i:o:t:a:c:s:m:<span class="pl-pds">&quot;</span></span> OPTION<span class="pl-k">;</span></td>
+      </tr>
+      <tr>
+        <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
+        <td id="LC45" class="blob-code js-file-line"><span class="pl-k">do</span></td>
+      </tr>
+      <tr>
+        <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
+        <td id="LC46" class="blob-code js-file-line">	<span class="pl-k">case</span> <span class="pl-vo">$OPTION</span> in</td>
+      </tr>
+      <tr>
+        <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
+        <td id="LC47" class="blob-code js-file-line">	i)      INPUT=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
+        <td id="LC48" class="blob-code js-file-line">        o)	ZIP_ARHIVE=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
+        <td id="LC49" class="blob-code js-file-line">        t)	TEMP_DIR=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
+        <td id="LC50" class="blob-code js-file-line">	a)	NA=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
+        <td id="LC51" class="blob-code js-file-line">	c)	TM=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
+        <td id="LC52" class="blob-code js-file-line">	s)	NAT=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
+        <td id="LC53" class="blob-code js-file-line">	m)	MG=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
+      </tr>
+      <tr>
+        <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
+        <td id="LC54" class="blob-code js-file-line">	<span class="pl-k">esac</span></td>
+      </tr>
+      <tr>
+        <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
+        <td id="LC55" class="blob-code js-file-line"><span class="pl-k">done</span></td>
+      </tr>
+      <tr>
+        <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
+        <td id="LC56" class="blob-code js-file-line"> </td>
+      </tr>
+      <tr>
+        <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
+        <td id="LC57" class="blob-code js-file-line">mkdir -p <span class="pl-vo">${TEMP_DIR}</span>/unafold</td>
+      </tr>
+      <tr>
+        <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
+        <td id="LC58" class="blob-code js-file-line"><span class="pl-s3">cd</span> <span class="pl-vo">${TEMP_DIR}</span>/unafold</td>
+      </tr>
+      <tr>
+        <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
+        <td id="LC59" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
+        <td id="LC60" class="blob-code js-file-line">NA=<span class="pl-s1"><span class="pl-pds">$(</span><span class="pl-s3">echo</span> <span class="pl-vo">$NA</span> <span class="pl-k">|</span> tr <span class="pl-s1"><span class="pl-pds">&#39;</span>[:lower:]<span class="pl-pds">&#39;</span></span> <span class="pl-s1"><span class="pl-pds">&#39;</span>[:upper:]<span class="pl-pds">&#39;</span></span><span class="pl-pds">)</span></span></td>
+      </tr>
+      <tr>
+        <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
+        <td id="LC61" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
+        <td id="LC62" class="blob-code js-file-line"><span class="pl-c"># calucalation of RNA don&#39;t need the concentraion of salts</span></td>
+      </tr>
+      <tr>
+        <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
+        <td id="LC63" class="blob-code js-file-line"><span class="pl-k">if</span> [[ <span class="pl-vo">${NA}</span> <span class="pl-k">==</span> <span class="pl-s1"><span class="pl-pds">&#39;</span>DNA<span class="pl-pds">&#39;</span></span> ]]<span class="pl-k">;</span> <span class="pl-k">then</span></td>
+      </tr>
+      <tr>
+        <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
+        <td id="LC64" class="blob-code js-file-line">	UNAFold.pl -n <span class="pl-vo">${NA}</span> -t <span class="pl-vo">${TM}</span> -N <span class="pl-vo">${NAT}</span> -M <span class="pl-vo">${MG}</span> <span class="pl-vo">${INPUT}</span></td>
+      </tr>
+      <tr>
+        <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
+        <td id="LC65" class="blob-code js-file-line"><span class="pl-k">else</span></td>
+      </tr>
+      <tr>
+        <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
+        <td id="LC66" class="blob-code js-file-line">	UNAFold.pl -n <span class="pl-vo">${NA}</span> -t <span class="pl-vo">${TM}</span> <span class="pl-vo">${INPUT}</span></td>
+      </tr>
+      <tr>
+        <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
+        <td id="LC67" class="blob-code js-file-line"><span class="pl-k">fi</span></td>
+      </tr>
+      <tr>
+        <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
+        <td id="LC68" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
+        <td id="LC69" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></td>
+      </tr>
+      <tr>
+        <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
+        <td id="LC70" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">&quot;</span>Parametres of UNAFold run:<span class="pl-pds">&quot;</span></span></td>
+      </tr>
+      <tr>
+        <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
+        <td id="LC71" class="blob-code js-file-line">cat <span class="pl-k">*</span>run</td>
+      </tr>
+      <tr>
+        <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
+        <td id="LC72" class="blob-code js-file-line">
+</td>
+      </tr>
+      <tr>
+        <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
+        <td id="LC73" class="blob-code js-file-line"><span class="pl-s3">cd</span> ../</td>
+      </tr>
+      <tr>
+        <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
+        <td id="LC74" class="blob-code js-file-line">zip -r -q unafold.zip unafold</td>
+      </tr>
+      <tr>
+        <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
+        <td id="LC75" class="blob-code js-file-line">mv unafold.zip <span class="pl-vo">${ZIP_ARHIVE}</span></td>
+      </tr>
+      <tr>
+        <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
+        <td id="LC76" class="blob-code js-file-line">
+</td>
+      </tr>
+</table>
+
+  </div>
+
+</div>
+
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+<div id="jump-to-line" style="display:none">
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+    <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" autofocus>
+    <button type="submit" class="button">Go</button>
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