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fasta2stockholm.pl
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<span class="author-name">Ian Holmes (ihh)</span>
authored <time class="js-relative-date" datetime="2011-09-07T14:59:55-07:00" title="2011-09-07 14:59:55">September 07, 2011</time>
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<div class="highlight"><pre><div class='line' id='LC1'><span class="c1">#!/usr/bin/env perl -w</span></div><div class='line' id='LC2'><br/></div><div class='line' id='LC3'><span class="k">my</span> <span class="nv">$usage</span> <span class="o">=</span> <span class="s">"Usage: $0 <gapped FASTA alignment file(s)>\n"</span><span class="p">;</span></div><div class='line' id='LC4'><br/></div><div class='line' id='LC5'><span class="k">my</span> <span class="nv">@argv</span><span class="p">;</span></div><div class='line' id='LC6'><span class="k">while</span> <span class="p">(</span><span class="nv">@ARGV</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC7'> <span class="k">my</span> <span class="nv">$arg</span> <span class="o">=</span> <span class="nb">shift</span><span class="p">;</span></div><div class='line' id='LC8'> <span class="k">if</span> <span class="p">(</span><span class="nv">$arg</span> <span class="o">=~</span><span class="sr"> /^-/</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC9'> <span class="k">if</span> <span class="p">(</span><span class="nv">$arg</span> <span class="ow">eq</span> <span class="s">"-h"</span><span class="p">)</span> <span class="p">{</span> <span class="k">print</span> <span class="nv">$usage</span><span class="p">;</span> <span class="nb">exit</span> <span class="p">}</span></div><div class='line' id='LC10'> <span class="k">else</span> <span class="p">{</span> <span class="nb">die</span> <span class="nv">$usage</span> <span class="p">}</span></div><div class='line' id='LC11'> <span class="p">}</span> <span class="k">else</span> <span class="p">{</span></div><div class='line' id='LC12'> <span class="nb">push</span> <span class="nv">@argv</span><span class="p">,</span> <span class="nv">$arg</span><span class="p">;</span></div><div class='line' id='LC13'> <span class="p">}</span></div><div class='line' id='LC14'><span class="p">}</span></div><div class='line' id='LC15'><span class="nb">push</span> <span class="nv">@argv</span><span class="p">,</span> <span class="s">"-"</span> <span class="k">unless</span> <span class="nv">@argv</span><span class="p">;</span></div><div class='line' id='LC16'><br/></div><div class='line' id='LC17'><span class="c1"># loop through FASTA files</span></div><div class='line' id='LC18'><span class="k">foreach</span> <span class="k">my</span> <span class="nv">$fasta</span> <span class="p">(</span><span class="nv">@argv</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC19'><span class="c1"># read FASTA file</span></div><div class='line' id='LC20'> <span class="k">my</span> <span class="nv">%seq</span><span class="p">;</span></div><div class='line' id='LC21'> <span class="k">my</span> <span class="nv">@name</span><span class="p">;</span></div><div class='line' id='LC22'> <span class="k">my</span> <span class="nv">$name</span><span class="p">;</span></div><div class='line' id='LC23'> <span class="nb">open</span> <span class="n">FASTA</span><span class="p">,</span> <span class="s">"<$fasta"</span> <span class="ow">or</span> <span class="nb">die</span> <span class="s">"Couldn't open '$fasta': $!"</span><span class="p">;</span></div><div class='line' id='LC24'> <span class="k">while</span> <span class="p">(</span><span class="sr"><FASTA></span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC25'> <span class="k">if</span> <span class="p">(</span><span class="sr">/^\s*>\s*(\S+)/</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC26'> <span class="nv">$name</span> <span class="o">=</span> <span class="nv">$1</span><span class="p">;</span></div><div class='line' id='LC27'> <span class="nb">die</span> <span class="s">"Duplicate name: $name"</span> <span class="k">if</span> <span class="nb">defined</span> <span class="nv">$seq</span><span class="p">{</span><span class="nv">$name</span><span class="p">};</span></div><div class='line' id='LC28'> <span class="nb">push</span> <span class="nv">@name</span><span class="p">,</span> <span class="nv">$name</span><span class="p">;</span></div><div class='line' id='LC29'> <span class="p">}</span> <span class="k">else</span> <span class="p">{</span></div><div class='line' id='LC30'> <span class="k">if</span> <span class="p">(</span><span class="sr">/\S/</span> <span class="o">&&</span> <span class="o">!</span><span class="nb">defined</span> <span class="nv">$name</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC31'> <span class="nb">warn</span> <span class="s">"Ignoring: $_"</span><span class="p">;</span></div><div class='line' id='LC32'> <span class="p">}</span> <span class="k">else</span> <span class="p">{</span></div><div class='line' id='LC33'> <span class="sr">s/\s//g</span><span class="p">;</span></div><div class='line' id='LC34'> <span class="nv">$seq</span><span class="p">{</span><span class="nv">$name</span><span class="p">}</span> <span class="o">.=</span> <span class="nv">$_</span><span class="p">;</span></div><div class='line' id='LC35'> <span class="p">}</span></div><div class='line' id='LC36'> <span class="p">}</span></div><div class='line' id='LC37'> <span class="p">}</span></div><div class='line' id='LC38'> <span class="nb">close</span> <span class="n">FASTA</span><span class="p">;</span></div><div class='line' id='LC39'><br/></div><div class='line' id='LC40'><span class="c1"># check all seqs are same length</span></div><div class='line' id='LC41'> <span class="k">my</span> <span class="nv">$length</span><span class="p">;</span></div><div class='line' id='LC42'> <span class="k">my</span> <span class="nv">$lname</span><span class="p">;</span></div><div class='line' id='LC43'> <span class="k">foreach</span> <span class="k">my</span> <span class="nv">$name</span> <span class="p">(</span><span class="nv">@name</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC44'> <span class="k">my</span> <span class="nv">$l</span> <span class="o">=</span> <span class="nb">length</span> <span class="nv">$seq</span><span class="p">{</span><span class="nv">$name</span><span class="p">};</span></div><div class='line' id='LC45'> <span class="k">if</span> <span class="p">(</span><span class="nb">defined</span> <span class="nv">$length</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC46'> <span class="nb">die</span> <span class="s">"Sequences not all same length ($lname is $length, $name is $l)"</span> <span class="k">unless</span> <span class="nv">$length</span> <span class="o">==</span> <span class="nv">$l</span><span class="p">;</span></div><div class='line' id='LC47'> <span class="p">}</span> <span class="k">else</span> <span class="p">{</span></div><div class='line' id='LC48'> <span class="nv">$length</span> <span class="o">=</span> <span class="nb">length</span> <span class="nv">$seq</span><span class="p">{</span><span class="nv">$name</span><span class="p">};</span></div><div class='line' id='LC49'> <span class="nv">$lname</span> <span class="o">=</span> <span class="nv">$name</span><span class="p">;</span></div><div class='line' id='LC50'> <span class="p">}</span></div><div class='line' id='LC51'> <span class="p">}</span></div><div class='line' id='LC52'><br/></div><div class='line' id='LC53'><span class="c1"># print Stockholm output</span></div><div class='line' id='LC54'> <span class="k">print</span> <span class="s">"# STOCKHOLM 1.0\n"</span><span class="p">;</span></div><div class='line' id='LC55'> <span class="k">foreach</span> <span class="k">my</span> <span class="nv">$name</span> <span class="p">(</span><span class="nv">@name</span><span class="p">)</span> <span class="p">{</span></div><div class='line' id='LC56'> <span class="k">print</span> <span class="nv">$name</span><span class="p">,</span> <span class="s">" "</span><span class="p">,</span> <span class="nv">$seq</span><span class="p">{</span><span class="nv">$name</span><span class="p">},</span> <span class="s">"\n"</span><span class="p">;</span></div><div class='line' id='LC57'> <span class="p">}</span></div><div class='line' id='LC58'> <span class="k">print</span> <span class="s">"//\n"</span><span class="p">;</span></div><div class='line' id='LC59'><span class="p">}</span></div><div class='line' id='LC60'><br/></div><div class='line' id='LC61'><br/></div></pre></div>
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* Item 2a
* Item 2b</pre>
<p>Ordered</p>
<pre>
1. Item 1
2. Item 2
3. Item 3
* Item 3a
* Item 3b</pre>
</div>
<div class="col">
<h3>Miscellaneous</h3>
<p>Images</p>
<pre>
Format: 
</pre>
<p>Links</p>
<pre>
http://github.com - automatic!
[GitHub](http://github.com)</pre>
<p>Blockquotes</p>
<pre>
As Kanye West said:
> We're living the future so
> the present is our past.
</pre>
</div>
</div>
<div class="rule"></div>
<h3>Code Examples in Markdown</h3>
<div class="col">
<p>Syntax highlighting with <a href="http://github.github.com/github-flavored-markdown/" title="GitHub Flavored Markdown" target="_blank">GFM</a></p>
<pre>
```javascript
function fancyAlert(arg) {
if(arg) {
$.facebox({div:'#foo'})
}
}
```</pre>
</div>
<div class="col">
<p>Or, indent your code 4 spaces</p>
<pre>
Here is a Python code example
without syntax highlighting:
def foo:
if not bar:
return true</pre>
</div>
<div class="col">
<p>Inline code for comments</p>
<pre>
I think you should use an
`<addr>` element here instead.</pre>
</div>
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