<div dir="ltr"><div>Hello all,</div><div><font class="Apple-style-span" face="&#39;Times New Roman&#39;, Times, serif"><span class="Apple-style-span" style="font-size: medium;"><font class="Apple-style-span" face="arial"><span class="Apple-style-span" style="font-size: small;"><div>

<br></div><div>For some work I am doing on RNA, I want to use R to do string parsing that (I think) is like a simplistic HTML parsing.</div><div><br></div><div><br></div><div>For example, let&#39;s say we have the following two variables:</div>

<div><br></div><div>    Seq &lt;- &quot;GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGGGCA&quot;</div><div>    Str &lt;- &quot;&gt;&gt;&gt;&gt;&gt;&gt;&gt;..&gt;&gt;&gt;&gt;........&lt;&lt;&lt;&lt;.&gt;&gt;&gt;&gt;&gt;.......&lt;&lt;&lt;&lt;&lt;.....&gt;&gt;&gt;&gt;&gt;.......&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;.&quot;</div>

<div><br></div><div>Say that I want to parse &quot;Seq&quot; According to &quot;Str&quot;, by using the legend here </div><div><br></div><div><span class="Apple-style-span" style="font-family: Arial, &#39;Liberation Sans&#39;, &#39;DejaVu Sans&#39;, sans-serif; font-size: 14px; line-height: 18px; "><pre class="prettyprint" style="margin-top: 0px; margin-right: 0px; margin-bottom: 10px; margin-left: 0px; padding-top: 5px; padding-right: 5px; padding-bottom: 5px; padding-left: 5px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: rgb(238, 238, 238); font-family: Consolas, Monaco, &#39;Lucida Console&#39;, &#39;Liberation Mono&#39;, &#39;DejaVu Sans Mono&#39;, &#39;Bitstream Vera Sans Mono&#39;, &#39;Courier New&#39;; overflow-x: auto; overflow-y: auto; width: auto; max-height: 600px; background-position: initial initial; background-repeat: initial initial; ">

<code style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: rgb(238, 238, 238); font-family: Consolas, Monaco, &#39;Lucida Console&#39;, &#39;Liberation Mono&#39;, &#39;DejaVu Sans Mono&#39;, &#39;Bitstream Vera Sans Mono&#39;, &#39;Courier New&#39;; background-position: initial initial; background-repeat: initial initial; "><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">Seq</span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">:</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGGGCA</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

</span><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">Str</span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">:</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">&gt;&gt;&gt;&gt;&gt;&gt;&gt;..&gt;&gt;&gt;&gt;........&lt;&lt;&lt;&lt;.&gt;&gt;&gt;&gt;&gt;.......&lt;&lt;&lt;&lt;&lt;.....&gt;&gt;&gt;&gt;&gt;.......&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;.</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

     </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">     </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">  </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">              </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">               </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">     </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">               </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">||</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">     </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

     </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">+-----+</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">  </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">+--------------+</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">+---------------+</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">     </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">+---------------++-----+</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

        </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">        </span><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">Stem</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="lit" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: maroon; background-position: initial initial; background-repeat: initial initial; ">1</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">            </span><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">Stem</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="lit" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: maroon; background-position: initial initial; background-repeat: initial initial; ">2</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">                 </span><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">Stem</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="lit" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: maroon; background-position: initial initial; background-repeat: initial initial; ">3</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">         </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

        </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">                                                                </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">|</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

        </span><span class="pun" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; ">+----------------------------------------------------------------+</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "><br>

                                </span><span class="typ" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: rgb(43, 145, 175); background-position: initial initial; background-repeat: initial initial; ">Stem</span><span class="pln" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: black; background-position: initial initial; background-repeat: initial initial; "> </span><span class="lit" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; font-size: 14px; vertical-align: baseline; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: transparent; color: maroon; background-position: initial initial; background-repeat: initial initial; ">0</span></code></pre>

</span></div><div>Assume that we always have 4 stems (0 to 3), but that the length of letters before and after each of them can very.</div><div><br></div><div>The output should be something like the following list structure:</div>

<div><br></div><div><br></div><div>    list(</div><div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;Stem 0 opening&quot; = &quot;GCCTCGA&quot;,</div><div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;before Stem 1&quot; = &quot;TA&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;Stem 1&quot; = list(opening = &quot;GCTC&quot;,</div><div>    <span class="Apple-tab-span" style="white-space:pre">                                </span>inside = &quot;AGTTGGGA&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">                                </span>closing = &quot;GAGC&quot;</div><div>    <span class="Apple-tab-span" style="white-space:pre">                        </span>),</div><div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;between Stem 1 and 2&quot; = &quot;G&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;Stem 2&quot; = list(opening = &quot;TACGA&quot;,</div><div>    <span class="Apple-tab-span" style="white-space:pre">                                </span>inside = &quot;CTGAAGA&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">                                </span>closing = &quot;TCGTA&quot;</div><div>    <span class="Apple-tab-span" style="white-space:pre">                        </span>),</div><div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;between Stem 2 and 3&quot; = &quot;AGGtC&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;Stem 3&quot; = list(opening = &quot;ACCAG&quot;,</div><div>    <span class="Apple-tab-span" style="white-space:pre">                                </span>inside = &quot;TTCGATC&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">                                </span>closing = &quot;CTGGT&quot;</div><div>    <span class="Apple-tab-span" style="white-space:pre">                        </span>),</div><div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;After Stem 3&quot; = &quot;&quot;,</div>

<div>    <span class="Apple-tab-span" style="white-space:pre">        </span>&quot;Stem 0 closing&quot; = &quot;TCGGGGC&quot;</div><div>    )</div><div><br></div><div><br></div><div>I don&#39;t have any experience with programming a parser, and would like advices as to what strategy to use when programming something like this (and any recommended R commands to use).</div>

<div><br></div><div><br></div><div>What I was thinking of is to first get rid of the &quot;Stem 0&quot;, then go through the inner string with a recursive function (let&#39;s call it &quot;seperate.stem&quot;) that each time will split the string into:</div>

<div>1. before stem</div><div>2. opening stem</div><div>3. inside stem</div><div>4. closing stem</div><div>5. after stem</div><div><br></div><div>Where the &quot;after stem&quot; will then be recursively entered into the same function (&quot;seperate.stem&quot;)</div>

<div><br></div><div>The thing is that I am not sure how to try and do this coding without using a loop.</div><div><br></div><div>Any advices will be most welcomed.</div></span></font></span></font></div><br clear="all"><br>

----------------Contact Details:-------------------------------------------------------<br>Contact me: <a href="mailto:Tal.Galili@gmail.com">Tal.Galili@gmail.com</a> |  972-52-7275845<br>Read me: <a href="http://www.talgalili.com">www.talgalili.com</a> (Hebrew) | <a href="http://www.biostatistics.co.il">www.biostatistics.co.il</a> (Hebrew) | <a href="http://www.r-statistics.com">www.r-statistics.com</a> (English)<br>

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