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for this subset of sequences as follows:
</p>



<pre class="example">for i in $(cat ids.txt); do fasgrep $i sequences.fas; done &gt; subset.fas
</pre>


<p>
Now we have a subest of sequences located in <i>subset.fas</i> that correspond
to the identifiers listed in <i>ids.txt</i>. 
</p>

</div>

<div id="outline-container-2-5-1" class="outline-4">
<h4 id="sec-2-5-1"><span class="section-number-4">2.5.1</span> Note on searching for identifiers</h4>
<div class="outline-text-4" id="text-2-5-1">

<p>Fasgrep works with perl regular expression syntax.It is often beneficial 
to code the identifiers in <i>ids.txt</i> with some sort of a line or a word 
anchor. For example, if you are looking for a complete identifier like
 <code>sequence_1</code>
but have sequences in your file named <code>sequence_11</code> and <code>sequence_12</code>, 
</p>



<pre class="example">fasgrep "sequence_1" sequences.fas
</pre>


<p>
will return all three sequences. If
you'd like to just look for <code>sequence_1</code>, adding a line anchor, such as:
</p>



<pre class="example">fasgrep "sequence_1$" sequences.fas
</pre>


<p>
will return <code>sequence_1</code> and skip <code>sequence_11</code> and <code>sequence_12</code>. This
only works if <code>sequence_1</code> is at the end of your identifier. If you are
looking for <code>sequence_1</code> within a larger identifier, you may need to 
take extra precautions to not retrieve other names that are more
specific to the structure of your identifiers.
</p></div>
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<p class="date">Date: 2015-01-07T13:40-0800</p>
<p class="author">Author: Katherine C.H. Amrine \&amp; David H. Ardell</p>
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