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author | hogart |
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date | Tue, 10 Mar 2015 05:44:28 -0400 |
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children | bda10049b902 |
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itemprop="title">galaxy-tools-unafold</span></a></span></span><span class="separator">/</span><strong class="final-path">unafold.sh</strong> </div> </div> <div class="commit file-history-tease"> <div class="file-history-tease-header"> <img alt="" class="avatar" height="24" src="https://2.gravatar.com/avatar/55ca26a75b8058d263926c67401db626?d=https%3A%2F%2Fassets-cdn.github.com%2Fimages%2Fgravatars%2Fgravatar-user-420.png&r=x&s=140" width="24" /> <span class="author"><span>Sergei Ryazansky</span></span> <time datetime="2015-03-09T14:55:04Z" is="relative-time">Mar 9, 2015</time> <div class="commit-title"> <a href="/DrHogart/galaxy-tools-unafold/commit/f01c0b4c8c79177f45227ce2dbc6222b6a1a371b" class="message" data-pjax="true" title="initial commit">initial commit</a> </div> </div> <div class="participation"> <p class="quickstat"> <a href="#blob_contributors_box" rel="facebox"> <strong>0</strong> contributors </a> </p> </div> <div id="blob_contributors_box" style="display:none"> <h2 class="facebox-header">Users who have contributed to this file</h2> <ul class="facebox-user-list"> </ul> </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=<temperature> (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=<[Na+] in M> (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=<[Mg++] in M> (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=<total strand concentration></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=<maximum basepair distance></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=<name of constraints file> (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=<energy increment percent> (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=<window size> (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=<maximum number of foldings> (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=<base numbering frequency></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=<structure rotation angle></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=<maximum bulge/interior loop size> (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=<filter value></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">"</span>:i:o:t:a:c:s:m:<span class="pl-pds">"</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">$OPTION</span> in</td> </tr> <tr> <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> <td id="LC47" class="blob-code js-file-line"> i) INPUT=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</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">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> </tr> <tr> <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> <td id="LC49" class="blob-code js-file-line"> t) TEMP_DIR=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</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">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> </tr> <tr> <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> <td id="LC51" class="blob-code js-file-line"> c) TM=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</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">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> </tr> <tr> <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> <td id="LC53" class="blob-code js-file-line"> m) MG=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</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">'</span>[:lower:]<span class="pl-pds">'</span></span> <span class="pl-s1"><span class="pl-pds">'</span>[:upper:]<span class="pl-pds">'</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'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">${NA}</span> <span class="pl-k">==</span> <span class="pl-s1"><span class="pl-pds">'</span>DNA<span class="pl-pds">'</span></span> ]]<span class="pl-k">;</span> <span class="pl-k">then</span></td> </tr> <tr> <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> <td id="LC64" class="blob-code js-file-line"> UNAFold.pl -n <span class="pl-vo">${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">${INPUT}</span></td> </tr> <tr> <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> <td id="LC67" class="blob-code js-file-line"><span class="pl-k">fi</span></td> </tr> <tr> <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> <td id="LC68" class="blob-code js-file-line"> </td> </tr> <tr> <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> <td id="LC69" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> </tr> <tr> <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> <td id="LC70" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">"</span>Parametres of UNAFold run:<span class="pl-pds">"</span></span></td> </tr> <tr> <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> <td id="LC71" class="blob-code js-file-line">cat <span class="pl-k">*</span>run</td> </tr> <tr> <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> <td id="LC72" class="blob-code js-file-line"> </td> </tr> <tr> <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> <td id="LC73" class="blob-code js-file-line"><span class="pl-s3">cd</span> ../</td> </tr> <tr> <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> <td id="LC74" class="blob-code js-file-line">zip -r -q unafold.zip unafold</td> </tr> <tr> <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> <td id="LC75" class="blob-code js-file-line">mv unafold.zip <span class="pl-vo">${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> <a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> <div id="jump-to-line" style="display:none"> <form accept-charset="UTF-8" class="js-jump-to-line-form"> <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> <button type="submit" class="button">Go</button> </form> </div> </div> </div><!-- /.repo-container --> <div class="modal-backdrop"></div> </div><!-- /.container --> </div><!-- /.site --> 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