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<a href="core-module.html">Package core</a> ::
Module AnalyseMapping
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<h1 class="epydoc">Source Code for <a href="core.AnalyseMapping-module.html">Module core.AnalyseMapping</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/python3</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">""" This script is used to evalulate the mapping results """</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">HTSeq</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">cPickle</tt> <tt class="py-keyword">as</tt> <tt class="py-name">pickle</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">np</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">subprocess</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable core.AnalyseMapping.alngts=core.AnalyseMapping-module.html#alngts"><a title="core.AnalyseMapping.alngts" class="py-name" href="#" onclick="return doclink('link-0', 'alngts', 'link-0');">alngts</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable core.AnalyseMapping.AlignedReadsdic=core.AnalyseMapping-module.html#AlignedReadsdic"><a title="core.AnalyseMapping.AlignedReadsdic" class="py-name" href="#" onclick="return doclink('link-1', 'AlignedReadsdic', 'link-1');">AlignedReadsdic</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable core.AnalyseMapping.algnedToRef=core.AnalyseMapping-module.html#algnedToRef"><a title="core.AnalyseMapping.algnedToRef" class="py-name" href="#" onclick="return doclink('link-2', 'algnedToRef', 'link-2');">algnedToRef</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable core.AnalyseMapping.algnedToArt=core.AnalyseMapping-module.html#algnedToArt"><a title="core.AnalyseMapping.algnedToArt" class="py-name" href="#" onclick="return doclink('link-3', 'algnedToArt', 'link-3');">algnedToArt</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-string">""" Helper debug functions.... """</tt> </tt>
<a name="savepickle"></a><div id="savepickle-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="savepickle-toggle" onclick="return toggle('savepickle');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#savepickle">savepickle</a><tt class="py-op">(</tt><tt class="py-param">dictionaary</tt><tt class="py-op">,</tt> <tt class="py-param">outputname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="savepickle-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="savepickle-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-name">pickle</tt><tt class="py-op">.</tt><tt class="py-name">dump</tt><tt class="py-op">(</tt><tt class="py-name">dictionaary</tt><tt class="py-op">,</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">outputname</tt> <tt class="py-op">+</tt> <tt class="py-string">".p"</tt><tt class="py-op">,</tt> <tt class="py-string">"wb"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-keyword">print</tt><tt class="py-op">(</tt><tt class="py-string">"Saved .pickle!"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="loadpickle"></a><div id="loadpickle-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="loadpickle-toggle" onclick="return toggle('loadpickle');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#loadpickle">loadpickle</a><tt class="py-op">(</tt><tt class="py-param">inputname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="loadpickle-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="loadpickle-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">dictionary</tt> <tt class="py-op">=</tt> <tt class="py-name">pickle</tt><tt class="py-op">.</tt><tt class="py-name">load</tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">inputname</tt> <tt class="py-op">+</tt> <tt class="py-string">".p"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">print</tt><tt class="py-op">(</tt><tt class="py-string">"Loaded "</tt> <tt class="py-op">+</tt> <tt class="py-name">inputname</tt> <tt class="py-op">+</tt> <tt class="py-string">".pickle!"</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">dictionary</tt><tt class="py-op">)</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="CustomRead"></a><div id="CustomRead-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="CustomRead-toggle" onclick="return toggle('CustomRead');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="core.AnalyseMapping.CustomRead-class.html">CustomRead</a><tt class="py-op">:</tt> </tt>
</div><div id="CustomRead-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="CustomRead-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> Class for exhaustive reading of the sam alignments.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="CustomRead.__init__"></a><div id="CustomRead.__init__-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="CustomRead.__init__-toggle" onclick="return toggle('CustomRead.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.CustomRead-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">readname</tt><tt class="py-op">,</tt> <tt class="py-param">mr</tt><tt class="py-op">,</tt> <tt class="py-param">nm</tt><tt class="py-op">,</tt> <tt class="py-param">subs</tt><tt class="py-op">,</tt> <tt class="py-param">score</tt><tt class="py-op">,</tt> <tt class="py-param">mq</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">,</tt> <tt class="py-param">gaps</tt><tt class="py-op">,</tt> <tt class="py-param">mism</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CustomRead.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="CustomRead.__init__-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-op">=</tt> <tt class="py-name">readname</tt> <tt class="py-comment"># read identifier </tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mr</tt><tt class="py-op">]</tt> <tt class="py-comment"># matched reference</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">subs</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">subs</tt><tt class="py-op">]</tt> <tt class="py-comment"># substitutions in artificial reference genome</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">nm</tt><tt class="py-op">]</tt> <tt class="py-comment"># number of mismatches (according to SAM)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-op">=</tt> <tt class="py-name">score</tt> <tt class="py-comment"># read quality score</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mq</tt><tt class="py-op">]</tt> <tt class="py-comment"># mapping quality</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">start</tt><tt class="py-op">]</tt> <tt class="py-comment"># alignment start</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">end</tt><tt class="py-op">]</tt> <tt class="py-comment"># alignment end</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-comment">#mr,nm,subs,score,mq,start,end</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">gaps</tt><tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mism</tt><tt class="py-op">]</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="CustomRead.toObjself"></a><div id="CustomRead.toObjself-def"><a name="L51"></a><tt class="py-lineno"> 51</tt> <a class="py-toggle" href="#" id="CustomRead.toObjself-toggle" onclick="return toggle('CustomRead.toObjself');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.CustomRead-class.html#toObjself">toObjself</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">read</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">subs</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">subs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="CustomRead.toStr"></a><div id="CustomRead.toStr-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="CustomRead.toStr-toggle" onclick="return toggle('CustomRead.toStr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.CustomRead-class.html#toStr">toStr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">readname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-docstring">"""Converts the object to a string """</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">read</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-comment">#print read</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">readname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">subs</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="CustomRead.toStrNoMem"></a><div id="CustomRead.toStrNoMem-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="CustomRead.toStrNoMem-toggle" onclick="return toggle('CustomRead.toStrNoMem');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.CustomRead-class.html#toStrNoMem">toStrNoMem</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Converts the object to a string """</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">identifier</tt> <tt class="py-op">==</tt> <tt class="py-string">"art"</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">subs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="TPRead"></a><div id="TPRead-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="TPRead-toggle" onclick="return toggle('TPRead');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="core.AnalyseMapping.TPRead-class.html">TPRead</a><tt class="py-op">:</tt> </tt>
</div><div id="TPRead-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="TPRead-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-docstring">""" Class for exhaustive reading of the sam alignments. Only for TP """</tt> </tt>
<a name="TPRead.__init__"></a><div id="TPRead.__init__-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="TPRead.__init__-toggle" onclick="return toggle('TPRead.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.TPRead-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">nm</tt><tt class="py-op">,</tt> <tt class="py-param">score</tt><tt class="py-op">,</tt> <tt class="py-param">mq</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">,</tt> <tt class="py-param">gaps</tt><tt class="py-op">,</tt> <tt class="py-param">mism</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TPRead.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="TPRead.__init__-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">nm</tt><tt class="py-op">]</tt> <tt class="py-comment"># number of mismatches (according to SAM)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-op">=</tt> <tt class="py-name">score</tt> <tt class="py-comment"># read quality score</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mq</tt><tt class="py-op">]</tt> <tt class="py-comment"># mapping quality</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">start</tt><tt class="py-op">]</tt> <tt class="py-comment"># alignment start</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">end</tt><tt class="py-op">]</tt> <tt class="py-comment"># alignment end</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">gaps</tt><tt class="py-op">]</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">mism</tt><tt class="py-op">]</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="TPRead.toObjself"></a><div id="TPRead.toObjself-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="TPRead.toObjself-toggle" onclick="return toggle('TPRead.toObjself');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.TPRead-class.html#toObjself">toObjself</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">read</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="TPRead.toStr"></a><div id="TPRead.toStr-def"><a name="L100"></a><tt class="py-lineno"> 100</tt> <a class="py-toggle" href="#" id="TPRead.toStr-toggle" onclick="return toggle('TPRead.toStr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.TPRead-class.html#toStr">toStr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">readname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L101"></a><tt class="py-lineno"> 101</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L102"></a><tt class="py-lineno"> 102</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">read</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno"> 103</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">readname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno"> 104</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
</div><a name="L105"></a><tt class="py-lineno"> 105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno"> 106</tt> <tt class="py-line"> <tt class="py-string">""" returns 1 if an equal alignment is contained in the array """</tt> </tt>
<a name="TPRead.isContained"></a><div id="TPRead.isContained-def"><a name="L107"></a><tt class="py-lineno"> 107</tt> <a class="py-toggle" href="#" id="TPRead.isContained-toggle" onclick="return toggle('TPRead.isContained');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.TPRead-class.html#isContained">isContained</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">read</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TPRead.isContained-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="TPRead.isContained-expanded"><a name="L108"></a><tt class="py-lineno"> 108</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">position</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno"> 109</tt> <tt class="py-line"> <tt class="py-comment"># Checks if a given Read (more accurate the alignment) is already in the object. this is used to check against FP</tt> </tt>
<a name="L110"></a><tt class="py-lineno"> 110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">position</tt> <tt class="py-op">==</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">start</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno"> 111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno"> 112</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L113"></a><tt class="py-lineno"> 113</tt> <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno"> 114</tt> <tt class="py-line"> </tt>
<a name="ReadID"></a><div id="ReadID-def"><a name="L115"></a><tt class="py-lineno"> 115</tt> <a class="py-toggle" href="#" id="ReadID-toggle" onclick="return toggle('ReadID');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="core.AnalyseMapping.ReadID-class.html">ReadID</a><tt class="py-op">:</tt> </tt>
</div><div id="ReadID-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="ReadID-expanded"><a name="L116"></a><tt class="py-lineno"> 116</tt> <tt class="py-line"> <tt class="py-docstring">""" Class for efficient addressing for np. arrays! """</tt> </tt>
<a name="ReadID.__init__"></a><div id="ReadID.__init__-def"><a name="L117"></a><tt class="py-lineno"> 117</tt> <a class="py-toggle" href="#" id="ReadID.__init__-toggle" onclick="return toggle('ReadID.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping.ReadID-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">internalID</tt><tt class="py-op">,</tt> <tt class="py-param">quality</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReadID.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="ReadID.__init__-expanded"><a name="L118"></a><tt class="py-lineno"> 118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">internalID</tt> <tt class="py-op">=</tt> <tt class="py-name">internalID</tt> </tt>
<a name="L119"></a><tt class="py-lineno"> 119</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">quality</tt> <tt class="py-op">=</tt> <tt class="py-name">quality</tt> </tt>
</div></div><a name="L120"></a><tt class="py-lineno"> 120</tt> <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno"> 121</tt> <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno"> 122</tt> <tt class="py-line"><tt class="py-comment">############################################# CLASSES END###########################################</tt> </tt>
<a name="L123"></a><tt class="py-lineno"> 123</tt> <tt class="py-line"> </tt>
<a name="L124"></a><tt class="py-lineno"> 124</tt> <tt class="py-line"> </tt>
<a name="getTPRead"></a><div id="getTPRead-def"><a name="L125"></a><tt class="py-lineno"> 125</tt> <a class="py-toggle" href="#" id="getTPRead-toggle" onclick="return toggle('getTPRead');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getTPRead">getTPRead</a><tt class="py-op">(</tt><tt class="py-param">alngt</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getTPRead-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getTPRead-expanded"><a name="L126"></a><tt class="py-lineno"> 126</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L127"></a><tt class="py-lineno"> 127</tt> <tt class="py-line"><tt class="py-docstring"> Funtion which transforms an HTSeq alignment to a TPRead class.</tt> </tt>
<a name="L128"></a><tt class="py-lineno"> 128</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L129"></a><tt class="py-lineno"> 129</tt> <tt class="py-line"><tt class="py-docstring"> @type alngt: alignment</tt> </tt>
<a name="L130"></a><tt class="py-lineno"> 130</tt> <tt class="py-line"><tt class="py-docstring"> @param alngt: alignment from the sam file.</tt> </tt>
<a name="L131"></a><tt class="py-lineno"> 131</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L132"></a><tt class="py-lineno"> 132</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: list which indicates differences between reference / artificial</tt> </tt>
<a name="L133"></a><tt class="py-lineno"> 133</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L134"></a><tt class="py-lineno"> 134</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: Contains ranks and qualities for every entry in the fastq file</tt> </tt>
<a name="L135"></a><tt class="py-lineno"> 135</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L136"></a><tt class="py-lineno"> 136</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: TPRead</tt> </tt>
<a name="L137"></a><tt class="py-lineno"> 137</tt> <tt class="py-line"><tt class="py-docstring"> @return: Transformed ReadObject.</tt> </tt>
<a name="L138"></a><tt class="py-lineno"> 138</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L139"></a><tt class="py-lineno"> 139</tt> <tt class="py-line"> <tt class="py-name">cigar</tt> <tt class="py-op">=</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">cigar</tt> </tt>
<a name="L140"></a><tt class="py-lineno"> 140</tt> <tt class="py-line"> <tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cigar</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-string">"I"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-string">"D"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno"> 141</tt> <tt class="py-line"> <tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cigar</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-string">"M"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">optional_field</tt><tt class="py-op">(</tt><tt class="py-string">"MD"</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">s</tt><tt class="py-op">.</tt><tt class="py-name">isdigit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno"> 142</tt> <tt class="py-line"> <tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">optional_field</tt><tt class="py-op">(</tt><tt class="py-string">"NM"</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno"> 143</tt> <tt class="py-line"> </tt>
<a name="L144"></a><tt class="py-lineno"> 144</tt> <tt class="py-line"> <tt class="py-comment">#####->TPRead(nm, score, mq, start, end, gaps, mism, n)</tt> </tt>
<a name="L145"></a><tt class="py-lineno"> 145</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-4" class="py-name" targets="Class core.AnalyseMapping.TPRead=core.AnalyseMapping.TPRead-class.html"><a title="core.AnalyseMapping.TPRead" class="py-name" href="#" onclick="return doclink('link-4', 'TPRead', 'link-4');">TPRead</a></tt><tt class="py-op">(</tt><tt class="py-name">nm</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">[</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">aQual</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">,</tt> <tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mism</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L146"></a><tt class="py-lineno"> 146</tt> <tt class="py-line"> </tt>
<a name="getCustomRead"></a><div id="getCustomRead-def"><a name="L147"></a><tt class="py-lineno"> 147</tt> <a class="py-toggle" href="#" id="getCustomRead-toggle" onclick="return toggle('getCustomRead');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getCustomRead">getCustomRead</a><tt class="py-op">(</tt><tt class="py-param">alngt</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getCustomRead-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getCustomRead-expanded"><a name="L148"></a><tt class="py-lineno"> 148</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L149"></a><tt class="py-lineno"> 149</tt> <tt class="py-line"><tt class="py-docstring"> Funtion which transforms an HTSeq alignment to a CustomRead class.</tt> </tt>
<a name="L150"></a><tt class="py-lineno"> 150</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L151"></a><tt class="py-lineno"> 151</tt> <tt class="py-line"><tt class="py-docstring"> @type alngt: alignment</tt> </tt>
<a name="L152"></a><tt class="py-lineno"> 152</tt> <tt class="py-line"><tt class="py-docstring"> @param alngt: alignment from the sam file.</tt> </tt>
<a name="L153"></a><tt class="py-lineno"> 153</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L154"></a><tt class="py-lineno"> 154</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: list which indicates differences between reference / artificial</tt> </tt>
<a name="L155"></a><tt class="py-lineno"> 155</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L156"></a><tt class="py-lineno"> 156</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: Contains ranks and qualities for every entry in the fastq file</tt> </tt>
<a name="L157"></a><tt class="py-lineno"> 157</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L158"></a><tt class="py-lineno"> 158</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: CustomRead</tt> </tt>
<a name="L159"></a><tt class="py-lineno"> 159</tt> <tt class="py-line"><tt class="py-docstring"> @return: Transformed ReadObject.</tt> </tt>
<a name="L160"></a><tt class="py-lineno"> 160</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L161"></a><tt class="py-lineno"> 161</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L162"></a><tt class="py-lineno"> 162</tt> <tt class="py-line"> <tt class="py-name">cigar</tt> <tt class="py-op">=</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">cigar</tt> </tt>
<a name="L163"></a><tt class="py-lineno"> 163</tt> <tt class="py-line"> <tt class="py-comment"># number of gaps is the sum of "I" (insertions) and "D" deletions.</tt> </tt>
<a name="L164"></a><tt class="py-lineno"> 164</tt> <tt class="py-line"> <tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cigar</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-string">"I"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-string">"D"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno"> 165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno"> 166</tt> <tt class="py-line"> <tt class="py-comment"># mismatches are calculated as cigar XM - MDtag occurrences of numbers</tt> </tt>
<a name="L167"></a><tt class="py-lineno"> 167</tt> <tt class="py-line"> <tt class="py-comment"># which indicate mismatches</tt> </tt>
<a name="L168"></a><tt class="py-lineno"> 168</tt> <tt class="py-line"> <tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cigar</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">.</tt><tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-string">"M"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt id="link-5" class="py-name" targets="Function core.AnalyseMapping.getsum()=core.AnalyseMapping-module.html#getsum"><a title="core.AnalyseMapping.getsum" class="py-name" href="#" onclick="return doclink('link-5', 'getsum', 'link-5');">getsum</a></tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">"(\d+)"</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">optional_field</tt><tt class="py-op">(</tt><tt class="py-string">"MD"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno"> 169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno"> 170</tt> <tt class="py-line"> </tt>
<a name="L171"></a><tt class="py-lineno"> 171</tt> <tt class="py-line"> <tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">optional_field</tt><tt class="py-op">(</tt><tt class="py-string">"NM"</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno"> 172</tt> <tt class="py-line"> </tt>
<a name="L173"></a><tt class="py-lineno"> 173</tt> <tt class="py-line"> <tt class="py-comment">########</tt> </tt>
<a name="L174"></a><tt class="py-lineno"> 174</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">qualstr</tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno"> 175</tt> <tt class="py-line"> </tt>
<a name="L176"></a><tt class="py-lineno"> 176</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-6" class="py-name" targets="Class core.AnalyseMapping.CustomRead=core.AnalyseMapping.CustomRead-class.html"><a title="core.AnalyseMapping.CustomRead" class="py-name" href="#" onclick="return doclink('link-6', 'CustomRead', 'link-6');">CustomRead</a></tt><tt class="py-op">(</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">nm</tt><tt class="py-op">,</tt><tt id="link-7" class="py-name" targets="Function core.AnalyseMapping.getHammingdistance()=core.AnalyseMapping-module.html#getHammingdistance"><a title="core.AnalyseMapping.getHammingdistance" class="py-name" href="#" onclick="return doclink('link-7', 'getHammingdistance', 'link-7');">getHammingdistance</a></tt><tt class="py-op">(</tt><tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">readdic</tt><tt class="py-op">[</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">aQual</tt><tt class="py-op">,</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">,</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">,</tt><tt class="py-name">gaps</tt><tt class="py-op">,</tt><tt class="py-name">mism</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno"> 177</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno"> 178</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="core.AnalyseMapping.CustomRead" class="py-name" href="#" onclick="return doclink('link-8', 'CustomRead', 'link-6');">CustomRead</a></tt><tt class="py-op">(</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">nm</tt><tt class="py-op">,</tt><tt id="link-9" class="py-name"><a title="core.AnalyseMapping.getHammingdistance" class="py-name" href="#" onclick="return doclink('link-9', 'getHammingdistance', 'link-7');">getHammingdistance</a></tt><tt class="py-op">(</tt><tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">qual</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-op">(</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">qual</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">qual</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">aQual</tt><tt class="py-op">,</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">,</tt><tt class="py-name">alngt</tt><tt class="py-op">.</tt><tt class="py-name">iv</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">,</tt><tt class="py-name">gaps</tt><tt class="py-op">,</tt><tt class="py-name">mism</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L179"></a><tt class="py-lineno"> 179</tt> <tt class="py-line"> </tt>
<a name="GetOrderDictionary"></a><div id="GetOrderDictionary-def"><a name="L180"></a><tt class="py-lineno"> 180</tt> <a class="py-toggle" href="#" id="GetOrderDictionary-toggle" onclick="return toggle('GetOrderDictionary');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#GetOrderDictionary">GetOrderDictionary</a><tt class="py-op">(</tt><tt class="py-param">referenceSAM</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GetOrderDictionary-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="GetOrderDictionary-expanded"><a name="L181"></a><tt class="py-lineno"> 181</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L182"></a><tt class="py-lineno"> 182</tt> <tt class="py-line"><tt class="py-docstring"> Function to get a dictionary containing the rank of a read (given a sorted samfile by readname, samtools).</tt> </tt>
<a name="L183"></a><tt class="py-lineno"> 183</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L184"></a><tt class="py-lineno"> 184</tt> <tt class="py-line"><tt class="py-docstring"> @type referenceSAM: string</tt> </tt>
<a name="L185"></a><tt class="py-lineno"> 185</tt> <tt class="py-line"><tt class="py-docstring"> @param referenceSAM: Inputfile name for reference SAM file.</tt> </tt>
<a name="L186"></a><tt class="py-lineno"> 186</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: dictionary</tt> </tt>
<a name="L187"></a><tt class="py-lineno"> 187</tt> <tt class="py-line"><tt class="py-docstring"> @return: Internalnaming according to the sorting of samtools. Key = ReadID, Value = rank</tt> </tt>
<a name="L188"></a><tt class="py-lineno"> 188</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L189"></a><tt class="py-lineno"> 189</tt> <tt class="py-line"> <tt class="py-name">internalDic</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L190"></a><tt class="py-lineno"> 190</tt> <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno"> 191</tt> <tt class="py-line"> <tt class="py-comment"># use ultrafast awk for getting only readnames from aligned fasta file</tt> </tt>
<a name="L192"></a><tt class="py-lineno"> 192</tt> <tt class="py-line"> <tt class="py-name">readnames</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">subprocess</tt><tt class="py-op">.</tt><tt class="py-name">check_output</tt><tt class="py-op">(</tt><tt class="py-string">"""awk < %s -F "\t" '{print $1 }'"""</tt> <tt class="py-op">%</tt> <tt class="py-name">referenceSAM</tt><tt class="py-op">,</tt> <tt class="py-name">shell</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno"> 193</tt> <tt class="py-line"> </tt>
<a name="L194"></a><tt class="py-lineno"> 194</tt> <tt class="py-line"> <tt class="py-comment"># make to list</tt> </tt>
<a name="L195"></a><tt class="py-lineno"> 195</tt> <tt class="py-line"> <tt class="py-name">readnames</tt> <tt class="py-op">=</tt> <tt class="py-name">readnames</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno"> 196</tt> <tt class="py-line"> </tt>
<a name="L197"></a><tt class="py-lineno"> 197</tt> <tt class="py-line"> <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L198"></a><tt class="py-lineno"> 198</tt> <tt class="py-line"> <tt class="py-comment"># skip header files</tt> </tt>
<a name="L199"></a><tt class="py-lineno"> 199</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">readnames</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-op">(</tt><tt class="py-string">"@"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno"> 200</tt> <tt class="py-line"> <tt class="py-name">i</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L201"></a><tt class="py-lineno"> 201</tt> <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno"> 202</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L203"></a><tt class="py-lineno"> 203</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">readnames</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno"> 204</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">readnames</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-name">internalDic</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno"> 205</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L206"></a><tt class="py-lineno"> 206</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno"> 207</tt> <tt class="py-line"> <tt class="py-name">internalDic</tt><tt class="py-op">[</tt><tt class="py-name">readnames</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">index</tt> </tt>
<a name="L208"></a><tt class="py-lineno"> 208</tt> <tt class="py-line"> <tt class="py-comment">#enumeration of the index</tt> </tt>
<a name="L209"></a><tt class="py-lineno"> 209</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L210"></a><tt class="py-lineno"> 210</tt> <tt class="py-line"> </tt>
<a name="L211"></a><tt class="py-lineno"> 211</tt> <tt class="py-line"> </tt>
<a name="L212"></a><tt class="py-lineno"> 212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno"> 213</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">internalDic</tt><tt class="py-op">)</tt> </tt>
</div><a name="L214"></a><tt class="py-lineno"> 214</tt> <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno"> 215</tt> <tt class="py-line"> </tt>
<a name="getNextLine"></a><div id="getNextLine-def"><a name="L216"></a><tt class="py-lineno"> 216</tt> <a class="py-toggle" href="#" id="getNextLine-toggle" onclick="return toggle('getNextLine');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getNextLine">getNextLine</a><tt class="py-op">(</tt><tt class="py-param">textfile</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getNextLine-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getNextLine-expanded"><a name="L217"></a><tt class="py-lineno"> 217</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L218"></a><tt class="py-lineno"> 218</tt> <tt class="py-line"><tt class="py-docstring"> Function which returns the next line from a SAMFile.</tt> </tt>
<a name="L219"></a><tt class="py-lineno"> 219</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L220"></a><tt class="py-lineno"> 220</tt> <tt class="py-line"><tt class="py-docstring"> @type textfile: fileobject stream</tt> </tt>
<a name="L221"></a><tt class="py-lineno"> 221</tt> <tt class="py-line"><tt class="py-docstring"> @param textfile: SAMfile</tt> </tt>
<a name="L222"></a><tt class="py-lineno"> 222</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L223"></a><tt class="py-lineno"> 223</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: AA sequence of the reference genome.</tt> </tt>
<a name="L224"></a><tt class="py-lineno"> 224</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: Dictionary</tt> </tt>
<a name="L225"></a><tt class="py-lineno"> 225</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: Boolean which decides if unbalanced mutations are allowed (only initial mutation is performed)</tt> </tt>
<a name="L226"></a><tt class="py-lineno"> 226</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: Readobj</tt> </tt>
<a name="L227"></a><tt class="py-lineno"> 227</tt> <tt class="py-line"><tt class="py-docstring"> @return: Parsed read from text line.</tt> </tt>
<a name="L228"></a><tt class="py-lineno"> 228</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L229"></a><tt class="py-lineno"> 229</tt> <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno"> 230</tt> <tt class="py-line"> <tt class="py-comment"># dummy is needed because nomem and standart reading return "different" values.</tt> </tt>
<a name="L231"></a><tt class="py-lineno"> 231</tt> <tt class="py-line"> <tt class="py-comment"># dummy, equals readname</tt> </tt>
<a name="L232"></a><tt class="py-lineno"> 232</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">textfile</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno"> 233</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno"> 234</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno"> 235</tt> <tt class="py-line"> <tt class="py-name">CRead</tt><tt class="py-op">,</tt> <tt class="py-name">dummy</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name" targets="Function core.AnalyseMapping.readSAMline()=core.AnalyseMapping-module.html#readSAMline"><a title="core.AnalyseMapping.readSAMline" class="py-name" href="#" onclick="return doclink('link-10', 'readSAMline', 'link-10');">readSAMline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt> <tt class="py-string">"noMem"</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno"> 236</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">CRead</tt><tt class="py-op">)</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno"> 237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno"> 238</tt> <tt class="py-line"> </tt>
<a name="L239"></a><tt class="py-lineno"> 239</tt> <tt class="py-line"> </tt>
<a name="getMisGap"></a><div id="getMisGap-def"><a name="L240"></a><tt class="py-lineno"> 240</tt> <a class="py-toggle" href="#" id="getMisGap-toggle" onclick="return toggle('getMisGap');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getMisGap">getMisGap</a><tt class="py-op">(</tt><tt class="py-param">mdtag</tt><tt class="py-op">,</tt> <tt class="py-param">cigar</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getMisGap-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getMisGap-expanded"><a name="L241"></a><tt class="py-lineno"> 241</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L242"></a><tt class="py-lineno"> 242</tt> <tt class="py-line"><tt class="py-docstring"> Reads the alignment tag given, the text and a tag to search for</tt> </tt>
<a name="L243"></a><tt class="py-lineno"> 243</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L244"></a><tt class="py-lineno"> 244</tt> <tt class="py-line"><tt class="py-docstring"> @type mdtag: string</tt> </tt>
<a name="L245"></a><tt class="py-lineno"> 245</tt> <tt class="py-line"><tt class="py-docstring"> @param mdtag: MDTag from alignment</tt> </tt>
<a name="L246"></a><tt class="py-lineno"> 246</tt> <tt class="py-line"><tt class="py-docstring"> @type cigar: string</tt> </tt>
<a name="L247"></a><tt class="py-lineno"> 247</tt> <tt class="py-line"><tt class="py-docstring"> @param cigar: Cigar from alignment</tt> </tt>
<a name="L248"></a><tt class="py-lineno"> 248</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: gaps,mismatches</tt> </tt>
<a name="L249"></a><tt class="py-lineno"> 249</tt> <tt class="py-line"><tt class="py-docstring"> @return: Parsed gaps and mismatches</tt> </tt>
<a name="L250"></a><tt class="py-lineno"> 250</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L251"></a><tt class="py-lineno"> 251</tt> <tt class="py-line"> <tt class="py-name">deletions</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="core.AnalyseMapping.getsum" class="py-name" href="#" onclick="return doclink('link-11', 'getsum', 'link-5');">getsum</a></tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">"(\d+)D"</tt><tt class="py-op">,</tt> <tt class="py-name">cigar</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno"> 252</tt> <tt class="py-line"> <tt class="py-name">insertions</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="core.AnalyseMapping.getsum" class="py-name" href="#" onclick="return doclink('link-12', 'getsum', 'link-5');">getsum</a></tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">"(\d+)I"</tt><tt class="py-op">,</tt> <tt class="py-name">cigar</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno"> 253</tt> <tt class="py-line"> <tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">insertions</tt> <tt class="py-op">+</tt> <tt class="py-name">deletions</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno"> 254</tt> <tt class="py-line"> </tt>
<a name="L255"></a><tt class="py-lineno"> 255</tt> <tt class="py-line"> <tt class="py-comment"># mismatches are:</tt> </tt>
<a name="L256"></a><tt class="py-lineno"> 256</tt> <tt class="py-line"> <tt class="py-comment"># ALL Matches from CIGAR - RealMatches from MDTag</tt> </tt>
<a name="L257"></a><tt class="py-lineno"> 257</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L258"></a><tt class="py-lineno"> 258</tt> <tt class="py-line"> </tt>
<a name="L259"></a><tt class="py-lineno"> 259</tt> <tt class="py-line"> <tt class="py-name">mismatch</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="core.AnalyseMapping.getsum" class="py-name" href="#" onclick="return doclink('link-13', 'getsum', 'link-5');">getsum</a></tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">"(\d+)M"</tt><tt class="py-op">,</tt> <tt class="py-name">cigar</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt id="link-14" class="py-name"><a title="core.AnalyseMapping.getsum" class="py-name" href="#" onclick="return doclink('link-14', 'getsum', 'link-5');">getsum</a></tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">"(\d+)"</tt><tt class="py-op">,</tt> <tt class="py-name">mdtag</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno"> 260</tt> <tt class="py-line"> </tt>
<a name="L261"></a><tt class="py-lineno"> 261</tt> <tt class="py-line"> </tt>
<a name="L262"></a><tt class="py-lineno"> 262</tt> <tt class="py-line"> <tt class="py-comment">#print ("%s\t%s\t%s\t%s\t%s\t%s" %(mdtag,cigar,deletions,insertions,mismatch,gaps))</tt> </tt>
<a name="L263"></a><tt class="py-lineno"> 263</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mismatch</tt><tt class="py-op">)</tt> </tt>
</div><a name="L264"></a><tt class="py-lineno"> 264</tt> <tt class="py-line"> </tt>
<a name="getAllID"></a><div id="getAllID-def"><a name="L265"></a><tt class="py-lineno"> 265</tt> <a class="py-toggle" href="#" id="getAllID-toggle" onclick="return toggle('getAllID');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getAllID">getAllID</a><tt class="py-op">(</tt><tt class="py-param">textfile</tt><tt class="py-op">,</tt> <tt class="py-param">read</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getAllID-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getAllID-expanded"><a name="L266"></a><tt class="py-lineno"> 266</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L267"></a><tt class="py-lineno"> 267</tt> <tt class="py-line"><tt class="py-docstring"> Reads all alignments for the current read which are in the SAM file (sorted). If a new read ID is scanned the results are returned.</tt> </tt>
<a name="L268"></a><tt class="py-lineno"> 268</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L269"></a><tt class="py-lineno"> 269</tt> <tt class="py-line"><tt class="py-docstring"> @type textfile: fileobject stream</tt> </tt>
<a name="L270"></a><tt class="py-lineno"> 270</tt> <tt class="py-line"><tt class="py-docstring"> @param textfile: SAM file for reading.</tt> </tt>
<a name="L271"></a><tt class="py-lineno"> 271</tt> <tt class="py-line"><tt class="py-docstring"> @type read: read obj</tt> </tt>
<a name="L272"></a><tt class="py-lineno"> 272</tt> <tt class="py-line"><tt class="py-docstring"> @param read: the last read obj which defines the current read id</tt> </tt>
<a name="L273"></a><tt class="py-lineno"> 273</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L274"></a><tt class="py-lineno"> 274</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: Look up for quality values.</tt> </tt>
<a name="L275"></a><tt class="py-lineno"> 275</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: (bool,list,bool)</tt> </tt>
<a name="L276"></a><tt class="py-lineno"> 276</tt> <tt class="py-line"><tt class="py-docstring"> @return: a "triple", where 2 bools are defined as indicator variables and a list with all alignments for one read.</tt> </tt>
<a name="L277"></a><tt class="py-lineno"> 277</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L278"></a><tt class="py-lineno"> 278</tt> <tt class="py-line"> <tt class="py-comment"># end of file?</tt> </tt>
<a name="L279"></a><tt class="py-lineno"> 279</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">read</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno"> 280</tt> <tt class="py-line"> <tt class="py-comment">#parse last read and return</tt> </tt>
<a name="L281"></a><tt class="py-lineno"> 281</tt> <tt class="py-line"> <tt class="py-name">CRead</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Function core.AnalyseMapping.getNextLine()=core.AnalyseMapping-module.html#getNextLine"><a title="core.AnalyseMapping.getNextLine" class="py-name" href="#" onclick="return doclink('link-15', 'getNextLine', 'link-15');">getNextLine</a></tt><tt class="py-op">(</tt><tt class="py-name">textfile</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno"> 282</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name" targets="Function core.AnalyseMapping.getAllID()=core.AnalyseMapping-module.html#getAllID"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-16', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">textfile</tt><tt class="py-op">,</tt> <tt class="py-name">CRead</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno"> 283</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L284"></a><tt class="py-lineno"> 284</tt> <tt class="py-line"> <tt class="py-comment"># start ne list and append read which was read with the last run of getALLID</tt> </tt>
<a name="L285"></a><tt class="py-lineno"> 285</tt> <tt class="py-line"> <tt class="py-name">templist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L286"></a><tt class="py-lineno"> 286</tt> <tt class="py-line"> <tt class="py-name">templist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno"> 287</tt> <tt class="py-line"> <tt class="py-comment"># get all reads with same id as "read" </tt> </tt>
<a name="L288"></a><tt class="py-lineno"> 288</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno"> 289</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">textfile</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno"> 290</tt> <tt class="py-line"> <tt class="py-comment"># no text left infile</tt> </tt>
<a name="L291"></a><tt class="py-lineno"> 291</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno"> 292</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">templist</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno"> 293</tt> <tt class="py-line"> </tt>
<a name="L294"></a><tt class="py-lineno"> 294</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno"> 295</tt> <tt class="py-line"> <tt class="py-name">CRead</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Function core.AnalyseMapping.getCustomRead()=core.AnalyseMapping-module.html#getCustomRead"><a title="core.AnalyseMapping.getCustomRead" class="py-name" href="#" onclick="return doclink('link-17', 'getCustomRead', 'link-17');">getCustomRead</a></tt><tt class="py-op">(</tt><tt class="py-name">HTSeq</tt><tt class="py-op">.</tt><tt class="py-name">SAM_Alignment</tt><tt class="py-op">.</tt><tt class="py-name">from_SAM_line</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L296"></a><tt class="py-lineno"> 296</tt> <tt class="py-line"> <tt class="py-comment">#CRead, dummy = readSAMline(line, "noMem", compareList, readdic)</tt> </tt>
<a name="L297"></a><tt class="py-lineno"> 297</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno"> 298</tt> <tt class="py-line"> <tt class="py-name">CRead</tt><tt class="py-op">,</tt> <tt class="py-name">dummy</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="core.AnalyseMapping.readSAMline" class="py-name" href="#" onclick="return doclink('link-18', 'readSAMline', 'link-10');">readSAMline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt> <tt class="py-string">"noMem"</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno"> 299</tt> <tt class="py-line"> </tt>
<a name="L300"></a><tt class="py-lineno"> 300</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">CRead</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno"> 301</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L302"></a><tt class="py-lineno"> 302</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">templist</tt><tt class="py-op">,</tt> <tt class="py-name">CRead</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno"> 303</tt> <tt class="py-line"> <tt class="py-comment"># same read in current line as was in the last line --> continue reading</tt> </tt>
<a name="L304"></a><tt class="py-lineno"> 304</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">CRead</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-op">==</tt> <tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno"> 305</tt> <tt class="py-line"> <tt class="py-name">templist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">CRead</tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno"> 306</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno"> 307</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">templist</tt><tt class="py-op">,</tt> <tt class="py-name">CRead</tt><tt class="py-op">)</tt> </tt>
</div><a name="L308"></a><tt class="py-lineno"> 308</tt> <tt class="py-line"> </tt>
<a name="L309"></a><tt class="py-lineno"> 309</tt> <tt class="py-line"> </tt>
<a name="CompareAlignments"></a><div id="CompareAlignments-def"><a name="L310"></a><tt class="py-lineno"> 310</tt> <a class="py-toggle" href="#" id="CompareAlignments-toggle" onclick="return toggle('CompareAlignments');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#CompareAlignments">CompareAlignments</a><tt class="py-op">(</tt><tt class="py-param">reflist</tt><tt class="py-op">,</tt> <tt class="py-param">artlist</tt><tt class="py-op">,</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CompareAlignments-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="CompareAlignments-expanded"><a name="L311"></a><tt class="py-lineno"> 311</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L312"></a><tt class="py-lineno"> 312</tt> <tt class="py-line"><tt class="py-docstring"> Compares alignments for the reference and artificial reference for a specific read id.</tt> </tt>
<a name="L313"></a><tt class="py-lineno"> 313</tt> <tt class="py-line"><tt class="py-docstring"> The goal is to identify false positives.</tt> </tt>
<a name="L314"></a><tt class="py-lineno"> 314</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L315"></a><tt class="py-lineno"> 315</tt> <tt class="py-line"><tt class="py-docstring"> @type reflist: read obj list</tt> </tt>
<a name="L316"></a><tt class="py-lineno"> 316</tt> <tt class="py-line"><tt class="py-docstring"> @param reflist: list containing alignments witht the same ID (reference)</tt> </tt>
<a name="L317"></a><tt class="py-lineno"> 317</tt> <tt class="py-line"><tt class="py-docstring"> @type artlist: read obj list</tt> </tt>
<a name="L318"></a><tt class="py-lineno"> 318</tt> <tt class="py-line"><tt class="py-docstring"> @param artlist: list containing alignments witht the same ID (artificial)</tt> </tt>
<a name="L319"></a><tt class="py-lineno"> 319</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: np.array</tt> </tt>
<a name="L320"></a><tt class="py-lineno"> 320</tt> <tt class="py-line"><tt class="py-docstring"> @return: indices of unique alignments</tt> </tt>
<a name="L321"></a><tt class="py-lineno"> 321</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L322"></a><tt class="py-lineno"> 322</tt> <tt class="py-line"> </tt>
<a name="L323"></a><tt class="py-lineno"> 323</tt> <tt class="py-line"> </tt>
<a name="L324"></a><tt class="py-lineno"> 324</tt> <tt class="py-line"> <tt class="py-name">artlen</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">artlist</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno"> 325</tt> <tt class="py-line"> <tt class="py-name">reflen</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">reflist</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno"> 326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno"> 327</tt> <tt class="py-line"> <tt class="py-name">TPcount</tt> <tt class="py-op">=</tt> <tt class="py-name">reflen</tt> </tt>
<a name="L328"></a><tt class="py-lineno"> 328</tt> <tt class="py-line"> <tt class="py-name">FPcount</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L329"></a><tt class="py-lineno"> 329</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">RefRead</tt> <tt class="py-keyword">in</tt> <tt class="py-name">reflist</tt><tt class="py-op">:</tt> </tt>
<a name="L330"></a><tt class="py-lineno"> 330</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">RefRead</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method core.AnalyseMapping.CustomRead.toStrNoMem()=core.AnalyseMapping.CustomRead-class.html#toStrNoMem"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-19', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L331"></a><tt class="py-lineno"> 331</tt> <tt class="py-line"> </tt>
<a name="L332"></a><tt class="py-lineno"> 332</tt> <tt class="py-line"> <tt class="py-comment"># add 1 for every alignment from the artificial that is found on the reference</tt> </tt>
<a name="L333"></a><tt class="py-lineno"> 333</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">artlen</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L334"></a><tt class="py-lineno"> 334</tt> <tt class="py-line"> <tt class="py-comment"># bool which decides if artificial in reference hit</tt> </tt>
<a name="L335"></a><tt class="py-lineno"> 335</tt> <tt class="py-line"> <tt class="py-name">ArtInRef</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L336"></a><tt class="py-lineno"> 336</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">reflen</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L337"></a><tt class="py-lineno"> 337</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">artlist</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">start</tt> <tt class="py-op">==</tt> <tt class="py-name">reflist</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">start</tt> <tt class="py-keyword">and</tt> <tt class="py-name">artlist</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">end</tt> <tt class="py-op">==</tt> <tt class="py-name">reflist</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno"> 338</tt> <tt class="py-line"> <tt class="py-name">ArtInRef</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L339"></a><tt class="py-lineno"> 339</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L340"></a><tt class="py-lineno"> 340</tt> <tt class="py-line"> <tt class="py-comment"># hit on artificial not confirmed on reference --> FP</tt> </tt>
<a name="L341"></a><tt class="py-lineno"> 341</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">ArtInRef</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L342"></a><tt class="py-lineno"> 342</tt> <tt class="py-line"> <tt class="py-name">FPcount</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L343"></a><tt class="py-lineno"> 343</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">artlist</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-20', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"art"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno"> 344</tt> <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno"> 345</tt> <tt class="py-line"> </tt>
<a name="L346"></a><tt class="py-lineno"> 346</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">TPcount</tt><tt class="py-op">,</tt><tt class="py-name">FPcount</tt><tt class="py-op">)</tt> </tt>
</div><a name="L347"></a><tt class="py-lineno"> 347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno"> 348</tt> <tt class="py-line"><tt class="py-string">"""def WriteToFile(file, list, identifier):</tt> </tt>
<a name="L349"></a><tt class="py-lineno"> 349</tt> <tt class="py-line"><tt class="py-string"> </tt> </tt>
<a name="L350"></a><tt class="py-lineno"> 350</tt> <tt class="py-line"><tt class="py-string"> Writes read obj. to a file.</tt> </tt>
<a name="L351"></a><tt class="py-lineno"> 351</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L352"></a><tt class="py-lineno"> 352</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L353"></a><tt class="py-lineno"> 353</tt> <tt class="py-line"><tt class="py-string"> @type file: read obj list</tt> </tt>
<a name="L354"></a><tt class="py-lineno"> 354</tt> <tt class="py-line"><tt class="py-string"> @param file: list containing alignments witht the same ID (reference)</tt> </tt>
<a name="L355"></a><tt class="py-lineno"> 355</tt> <tt class="py-line"><tt class="py-string"> @type list: read obj. list</tt> </tt>
<a name="L356"></a><tt class="py-lineno"> 356</tt> <tt class="py-line"><tt class="py-string"> @param list: list containing alignments witht the same ID (artificial)</tt> </tt>
<a name="L357"></a><tt class="py-lineno"> 357</tt> <tt class="py-line"><tt class="py-string"> @type identifier: string</tt> </tt>
<a name="L358"></a><tt class="py-lineno"> 358</tt> <tt class="py-line"><tt class="py-string"> @param identifier: indicator if the results are from the reference or artificial</tt> </tt>
<a name="L359"></a><tt class="py-lineno"> 359</tt> <tt class="py-line"><tt class="py-string"> </tt> </tt>
<a name="L360"></a><tt class="py-lineno"> 360</tt> <tt class="py-line"><tt class="py-string"> file.write(getBestAlignment(list).toStrNoMem(identifier))"""</tt> </tt>
<a name="L361"></a><tt class="py-lineno"> 361</tt> <tt class="py-line"> </tt>
<a name="SkipHeader"></a><div id="SkipHeader-def"><a name="L362"></a><tt class="py-lineno"> 362</tt> <a class="py-toggle" href="#" id="SkipHeader-toggle" onclick="return toggle('SkipHeader');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#SkipHeader">SkipHeader</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SkipHeader-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="SkipHeader-expanded"><a name="L363"></a><tt class="py-lineno"> 363</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L364"></a><tt class="py-lineno"> 364</tt> <tt class="py-line"><tt class="py-docstring"> Skips the header from a SAM file, but reads the first line of the alignment section.</tt> </tt>
<a name="L365"></a><tt class="py-lineno"> 365</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L366"></a><tt class="py-lineno"> 366</tt> <tt class="py-line"><tt class="py-docstring"> @type file: read obj list</tt> </tt>
<a name="L367"></a><tt class="py-lineno"> 367</tt> <tt class="py-line"><tt class="py-docstring"> @param file: list containing alignments witht the same ID (reference)</tt> </tt>
<a name="L368"></a><tt class="py-lineno"> 368</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L369"></a><tt class="py-lineno"> 369</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: list for accumulation of the same read id</tt> </tt>
<a name="L370"></a><tt class="py-lineno"> 370</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L371"></a><tt class="py-lineno"> 371</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: dictionary containing read ID - read quality mappings.</tt> </tt>
<a name="L372"></a><tt class="py-lineno"> 372</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: read obj.</tt> </tt>
<a name="L373"></a><tt class="py-lineno"> 373</tt> <tt class="py-line"><tt class="py-docstring"> @return: Returns a read obj. from the SAM file.</tt> </tt>
<a name="L374"></a><tt class="py-lineno"> 374</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L375"></a><tt class="py-lineno"> 375</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno"> 376</tt> <tt class="py-line"> <tt class="py-name">temp</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno"> 377</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">temp</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"@"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno"> 378</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L379"></a><tt class="py-lineno"> 379</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L380"></a><tt class="py-lineno"> 380</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="core.AnalyseMapping.readSAMline" class="py-name" href="#" onclick="return doclink('link-21', 'readSAMline', 'link-10');">readSAMline</a></tt><tt class="py-op">(</tt><tt class="py-name">temp</tt><tt class="py-op">,</tt> <tt class="py-string">"noMem"</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno"> 381</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
</div><a name="L382"></a><tt class="py-lineno"> 382</tt> <tt class="py-line"> </tt>
<a name="L383"></a><tt class="py-lineno"> 383</tt> <tt class="py-line"> </tt>
<a name="getRanks"></a><div id="getRanks-def"><a name="L384"></a><tt class="py-lineno"> 384</tt> <a class="py-toggle" href="#" id="getRanks-toggle" onclick="return toggle('getRanks');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getRanks">getRanks</a><tt class="py-op">(</tt><tt class="py-param">RefRead</tt><tt class="py-op">,</tt><tt class="py-param">ArtRead</tt><tt class="py-op">,</tt><tt class="py-param">rankdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getRanks-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getRanks-expanded"><a name="L385"></a><tt class="py-lineno"> 385</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L386"></a><tt class="py-lineno"> 386</tt> <tt class="py-line"><tt class="py-docstring"> Function which returns the ranks of 2 given readIDs (read from reference,read from artificial).</tt> </tt>
<a name="L387"></a><tt class="py-lineno"> 387</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L388"></a><tt class="py-lineno"> 388</tt> <tt class="py-line"><tt class="py-docstring"> @type RefRead: read obj </tt> </tt>
<a name="L389"></a><tt class="py-lineno"> 389</tt> <tt class="py-line"><tt class="py-docstring"> @param RefRead: read obj (reference)</tt> </tt>
<a name="L390"></a><tt class="py-lineno"> 390</tt> <tt class="py-line"><tt class="py-docstring"> @type ArtRead: read obj </tt> </tt>
<a name="L391"></a><tt class="py-lineno"> 391</tt> <tt class="py-line"><tt class="py-docstring"> @param ArtRead: read obj (artificial)</tt> </tt>
<a name="L392"></a><tt class="py-lineno"> 392</tt> <tt class="py-line"><tt class="py-docstring"> @type rankdic: dictionary</tt> </tt>
<a name="L393"></a><tt class="py-lineno"> 393</tt> <tt class="py-line"><tt class="py-docstring"> @param rankdic: dictionary containing ranks of the read IDs (according to the sorted SAM files).</tt> </tt>
<a name="L394"></a><tt class="py-lineno"> 394</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int,int</tt> </tt>
<a name="L395"></a><tt class="py-lineno"> 395</tt> <tt class="py-line"><tt class="py-docstring"> @return: returns the false positives and true positives for a SAM file pair (reference, artificial)</tt> </tt>
<a name="L396"></a><tt class="py-lineno"> 396</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L397"></a><tt class="py-lineno"> 397</tt> <tt class="py-line"> <tt class="py-comment"># get the ranks resulting from the sorted samfile.</tt> </tt>
<a name="L398"></a><tt class="py-lineno"> 398</tt> <tt class="py-line"> <tt class="py-name">RefReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">RefRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L399"></a><tt class="py-lineno"> 399</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rankdic</tt><tt class="py-op">:</tt> </tt>
<a name="L400"></a><tt class="py-lineno"> 400</tt> <tt class="py-line"> <tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L401"></a><tt class="py-lineno"> 401</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno"> 402</tt> <tt class="py-line"> <tt class="py-comment"># if this ReadID is not in the dictionary then it MUST be a FP!</tt> </tt>
<a name="L403"></a><tt class="py-lineno"> 403</tt> <tt class="py-line"> <tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">RefReadRank</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L404"></a><tt class="py-lineno"> 404</tt> <tt class="py-line"> </tt>
<a name="L405"></a><tt class="py-lineno"> 405</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt><tt class="py-op">,</tt><tt class="py-name">ArtReadRank</tt><tt class="py-op">)</tt> </tt>
</div><a name="L406"></a><tt class="py-lineno"> 406</tt> <tt class="py-line"> </tt>
<a name="L407"></a><tt class="py-lineno"> 407</tt> <tt class="py-line"> </tt>
<a name="ReadSAMnoMem"></a><div id="ReadSAMnoMem-def"><a name="L408"></a><tt class="py-lineno"> 408</tt> <a class="py-toggle" href="#" id="ReadSAMnoMem-toggle" onclick="return toggle('ReadSAMnoMem');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#ReadSAMnoMem">ReadSAMnoMem</a><tt class="py-op">(</tt><tt class="py-param">ref</tt><tt class="py-op">,</tt> <tt class="py-param">art</tt><tt class="py-op">,</tt> <tt class="py-param">output</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">,</tt> <tt class="py-param">rankdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReadSAMnoMem-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="ReadSAMnoMem-expanded"><a name="L409"></a><tt class="py-lineno"> 409</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L410"></a><tt class="py-lineno"> 410</tt> <tt class="py-line"><tt class="py-docstring"> Main function for comparing to mappings. This functions takes the complete alignments for artificial and reference genome and goes through them in parallel.</tt> </tt>
<a name="L411"></a><tt class="py-lineno"> 411</tt> <tt class="py-line"><tt class="py-docstring"> Since the mappings are sorted the function alternates the parsing of the samfiles in such a way that no memory is used for comparing these functions.</tt> </tt>
<a name="L412"></a><tt class="py-lineno"> 412</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L413"></a><tt class="py-lineno"> 413</tt> <tt class="py-line"><tt class="py-docstring"> @type ref: string</tt> </tt>
<a name="L414"></a><tt class="py-lineno"> 414</tt> <tt class="py-line"><tt class="py-docstring"> @param ref: path to reference alignments (SAM file)</tt> </tt>
<a name="L415"></a><tt class="py-lineno"> 415</tt> <tt class="py-line"><tt class="py-docstring"> @type art: string</tt> </tt>
<a name="L416"></a><tt class="py-lineno"> 416</tt> <tt class="py-line"><tt class="py-docstring"> @param art: path to artificial alignments (SAM file)</tt> </tt>
<a name="L417"></a><tt class="py-lineno"> 417</tt> <tt class="py-line"><tt class="py-docstring"> @type output: read obj </tt> </tt>
<a name="L418"></a><tt class="py-lineno"> 418</tt> <tt class="py-line"><tt class="py-docstring"> @param output: read obj (artificial)</tt> </tt>
<a name="L419"></a><tt class="py-lineno"> 419</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: read obj </tt> </tt>
<a name="L420"></a><tt class="py-lineno"> 420</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: read obj (artificial)</tt> </tt>
<a name="L421"></a><tt class="py-lineno"> 421</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L422"></a><tt class="py-lineno"> 422</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: dictionary containing read ID - read quality mappings.</tt> </tt>
<a name="L423"></a><tt class="py-lineno"> 423</tt> <tt class="py-line"><tt class="py-docstring"> @type rankdic: dictionary</tt> </tt>
<a name="L424"></a><tt class="py-lineno"> 424</tt> <tt class="py-line"><tt class="py-docstring"> @param rankdic: dictionary containing ranks of the read IDs (according to the sorted SAM files).</tt> </tt>
<a name="L425"></a><tt class="py-lineno"> 425</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: ranks</tt> </tt>
<a name="L426"></a><tt class="py-lineno"> 426</tt> <tt class="py-line"><tt class="py-docstring"> @return: Returns the ranks for the 2 read ids.</tt> </tt>
<a name="L427"></a><tt class="py-lineno"> 427</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L428"></a><tt class="py-lineno"> 428</tt> <tt class="py-line"> </tt>
<a name="L429"></a><tt class="py-lineno"> 429</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">output</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L430"></a><tt class="py-lineno"> 430</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"#ReadID\tMatchedReference\tSubstitutions\tNMtag\tReadQuality\tMappingQuality\tStart\tEnd\tGaps\tMisM\r\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno"> 431</tt> <tt class="py-line"> <tt class="py-name">fileref</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">ref</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
<a name="L432"></a><tt class="py-lineno"> 432</tt> <tt class="py-line"> <tt class="py-name">fileart</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">art</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
<a name="L433"></a><tt class="py-lineno"> 433</tt> <tt class="py-line"> </tt>
<a name="L434"></a><tt class="py-lineno"> 434</tt> <tt class="py-line"> <tt class="py-comment"># SKip Header section of SAM file</tt> </tt>
<a name="L435"></a><tt class="py-lineno"> 435</tt> <tt class="py-line"> <tt class="py-name">CurrentReadRef</tt><tt class="py-op">,</tt> <tt class="py-name">dummy</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name" targets="Function core.AnalyseMapping.SkipHeader()=core.AnalyseMapping-module.html#SkipHeader"><a title="core.AnalyseMapping.SkipHeader" class="py-name" href="#" onclick="return doclink('link-22', 'SkipHeader', 'link-22');">SkipHeader</a></tt><tt class="py-op">(</tt><tt class="py-name">fileref</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno"> 436</tt> <tt class="py-line"> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">dummy</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="core.AnalyseMapping.SkipHeader" class="py-name" href="#" onclick="return doclink('link-23', 'SkipHeader', 'link-22');">SkipHeader</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L437"></a><tt class="py-lineno"> 437</tt> <tt class="py-line"> </tt>
<a name="L438"></a><tt class="py-lineno"> 438</tt> <tt class="py-line"> <tt class="py-comment"># get first readIDs for looping </tt> </tt>
<a name="L439"></a><tt class="py-lineno"> 439</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadArt</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-24', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno"> 440</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadRef</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-25', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileref</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadRef</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L441"></a><tt class="py-lineno"> 441</tt> <tt class="py-line"> <tt class="py-comment"># variables for counting</tt> </tt>
<a name="L442"></a><tt class="py-lineno"> 442</tt> <tt class="py-line"> </tt>
<a name="L443"></a><tt class="py-lineno"> 443</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L444"></a><tt class="py-lineno"> 444</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L445"></a><tt class="py-lineno"> 445</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L446"></a><tt class="py-lineno"> 446</tt> <tt class="py-line"> <tt class="py-name">i</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L447"></a><tt class="py-lineno"> 447</tt> <tt class="py-line"> <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno"> 448</tt> <tt class="py-line"> <tt class="py-comment">#Indicator variables which file is end first</tt> </tt>
<a name="L449"></a><tt class="py-lineno"> 449</tt> <tt class="py-line"> <tt class="py-name">ArtBool</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L450"></a><tt class="py-lineno"> 450</tt> <tt class="py-line"> <tt class="py-name">RefBool</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L451"></a><tt class="py-lineno"> 451</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L452"></a><tt class="py-lineno"> 452</tt> <tt class="py-line"> <tt class="py-name">i</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L453"></a><tt class="py-lineno"> 453</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-op">==</tt> <tt class="py-number">100000</tt><tt class="py-op">:</tt> </tt>
<a name="L454"></a><tt class="py-lineno"> 454</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"\t\t%f"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">start</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L455"></a><tt class="py-lineno"> 455</tt> <tt class="py-line"> </tt>
<a name="L456"></a><tt class="py-lineno"> 456</tt> <tt class="py-line"> <tt class="py-name">RefReadRank</tt><tt class="py-op">,</tt><tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name" targets="Function core.AnalyseMapping.getRanks()=core.AnalyseMapping-module.html#getRanks"><a title="core.AnalyseMapping.getRanks" class="py-name" href="#" onclick="return doclink('link-26', 'getRanks', 'link-26');">getRanks</a></tt><tt class="py-op">(</tt><tt class="py-name">RefRead</tt><tt class="py-op">,</tt><tt class="py-name">ArtRead</tt><tt class="py-op">,</tt><tt class="py-name">rankdic</tt><tt class="py-op">)</tt> </tt>
<a name="L457"></a><tt class="py-lineno"> 457</tt> <tt class="py-line"> </tt>
<a name="L458"></a><tt class="py-lineno"> 458</tt> <tt class="py-line"> <tt class="py-comment">#case 1)</tt> </tt>
<a name="L459"></a><tt class="py-lineno"> 459</tt> <tt class="py-line"> <tt class="py-comment"># Keep reading lines from artificial if the id is < than the one from the reference</tt> </tt>
<a name="L460"></a><tt class="py-lineno"> 460</tt> <tt class="py-line"> <tt class="py-comment"># this means unique hits to the artificial!</tt> </tt>
<a name="L461"></a><tt class="py-lineno"> 461</tt> <tt class="py-line"> <tt class="py-comment">#while (RefRead[0].id > ArtRead[0].id and hasNextLine != 0):</tt> </tt>
<a name="L462"></a><tt class="py-lineno"> 462</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op">></tt> <tt class="py-name">ArtReadRank</tt> <tt class="py-keyword">and</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno"> 463</tt> <tt class="py-line"> <tt class="py-comment"># in case of multiple hits, set all mr variables to 0 and get the best alignment</tt> </tt>
<a name="L464"></a><tt class="py-lineno"> 464</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ArtRead</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L465"></a><tt class="py-lineno"> 465</tt> <tt class="py-line"> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L466"></a><tt class="py-lineno"> 466</tt> <tt class="py-line"> </tt>
<a name="L467"></a><tt class="py-lineno"> 467</tt> <tt class="py-line"> <tt class="py-comment"># write FP to file</tt> </tt>
<a name="L468"></a><tt class="py-lineno"> 468</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno"> 469</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-27', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"art"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno"> 470</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L471"></a><tt class="py-lineno"> 471</tt> <tt class="py-line"> </tt>
<a name="L472"></a><tt class="py-lineno"> 472</tt> <tt class="py-line"> </tt>
<a name="L473"></a><tt class="py-lineno"> 473</tt> <tt class="py-line"> <tt class="py-comment"># use akku for read lines</tt> </tt>
<a name="L474"></a><tt class="py-lineno"> 474</tt> <tt class="py-line"> <tt class="py-name">CurrentReadArt</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadArt</tt> </tt>
<a name="L475"></a><tt class="py-lineno"> 475</tt> <tt class="py-line"> <tt class="py-comment">#get all the reads with the same ID into ArtRead</tt> </tt>
<a name="L476"></a><tt class="py-lineno"> 476</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadArt</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-28', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno"> 477</tt> <tt class="py-line"> </tt>
<a name="L478"></a><tt class="py-lineno"> 478</tt> <tt class="py-line"> <tt class="py-comment">#update rank</tt> </tt>
<a name="L479"></a><tt class="py-lineno"> 479</tt> <tt class="py-line"> <tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">RefReadRank</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rankdic</tt> <tt class="py-keyword">else</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L480"></a><tt class="py-lineno"> 480</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L481"></a><tt class="py-lineno"> 481</tt> <tt class="py-line"> </tt>
<a name="L482"></a><tt class="py-lineno"> 482</tt> <tt class="py-line"> <tt class="py-comment">#case 2)</tt> </tt>
<a name="L483"></a><tt class="py-lineno"> 483</tt> <tt class="py-line"> <tt class="py-comment"># keep reading lines from reference if id is < art.id</tt> </tt>
<a name="L484"></a><tt class="py-lineno"> 484</tt> <tt class="py-line"> <tt class="py-comment"># all these hits are purely TP</tt> </tt>
<a name="L485"></a><tt class="py-lineno"> 485</tt> <tt class="py-line"> <tt class="py-comment">#while (RefRead[0].id < ArtRead[0].id and hasNextLine != 0):</tt> </tt>
<a name="L486"></a><tt class="py-lineno"> 486</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op"><</tt> <tt class="py-name">ArtReadRank</tt> <tt class="py-keyword">and</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L487"></a><tt class="py-lineno"> 487</tt> <tt class="py-line"> </tt>
<a name="L488"></a><tt class="py-lineno"> 488</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">RefRead</tt><tt class="py-op">:</tt> </tt>
<a name="L489"></a><tt class="py-lineno"> 489</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-29', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L490"></a><tt class="py-lineno"> 490</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L491"></a><tt class="py-lineno"> 491</tt> <tt class="py-line"> </tt>
<a name="L492"></a><tt class="py-lineno"> 492</tt> <tt class="py-line"> <tt class="py-name">CurrentReadRef</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadRef</tt> </tt>
<a name="L493"></a><tt class="py-lineno"> 493</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadRef</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-30', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileref</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadRef</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno"> 494</tt> <tt class="py-line"> <tt class="py-name">RefReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">RefRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L495"></a><tt class="py-lineno"> 495</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L496"></a><tt class="py-lineno"> 496</tt> <tt class="py-line"> </tt>
<a name="L497"></a><tt class="py-lineno"> 497</tt> <tt class="py-line"> </tt>
<a name="L498"></a><tt class="py-lineno"> 498</tt> <tt class="py-line"> <tt class="py-comment"># case 3)</tt> </tt>
<a name="L499"></a><tt class="py-lineno"> 499</tt> <tt class="py-line"> <tt class="py-comment">#if (RefRead[0].id == ArtRead[0].id):</tt> </tt>
<a name="L500"></a><tt class="py-lineno"> 500</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op">==</tt> <tt class="py-name">ArtReadRank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L501"></a><tt class="py-lineno"> 501</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L502"></a><tt class="py-lineno"> 502</tt> <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno"> 503</tt> <tt class="py-line"> <tt class="py-comment">#same read.id --> compare all Alignments for one read id (can be multiple alignments)</tt> </tt>
<a name="L504"></a><tt class="py-lineno"> 504</tt> <tt class="py-line"> <tt class="py-comment"># return unique hits to artificial genome</tt> </tt>
<a name="L505"></a><tt class="py-lineno"> 505</tt> <tt class="py-line"> <tt class="py-name">tempTP</tt><tt class="py-op">,</tt><tt class="py-name">tempFP</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name" targets="Function core.AnalyseMapping.CompareAlignments()=core.AnalyseMapping-module.html#CompareAlignments"><a title="core.AnalyseMapping.CompareAlignments" class="py-name" href="#" onclick="return doclink('link-31', 'CompareAlignments', 'link-31');">CompareAlignments</a></tt><tt class="py-op">(</tt><tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt><tt class="py-name">fobj</tt><tt class="py-op">)</tt> </tt>
<a name="L506"></a><tt class="py-lineno"> 506</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt><tt class="py-name">tempTP</tt> </tt>
<a name="L507"></a><tt class="py-lineno"> 507</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt><tt class="py-name">tempFP</tt> </tt>
<a name="L508"></a><tt class="py-lineno"> 508</tt> <tt class="py-line"> <tt class="py-comment"># overwrite akku</tt> </tt>
<a name="L509"></a><tt class="py-lineno"> 509</tt> <tt class="py-line"> <tt class="py-name">CurrentReadRef</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadRef</tt> </tt>
<a name="L510"></a><tt class="py-lineno"> 510</tt> <tt class="py-line"> <tt class="py-name">CurrentReadArt</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadArt</tt> </tt>
<a name="L511"></a><tt class="py-lineno"> 511</tt> <tt class="py-line"> </tt>
<a name="L512"></a><tt class="py-lineno"> 512</tt> <tt class="py-line"> </tt>
<a name="L513"></a><tt class="py-lineno"> 513</tt> <tt class="py-line"> <tt class="py-comment"># get next Read for next ID and check if file has a next line</tt> </tt>
<a name="L514"></a><tt class="py-lineno"> 514</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadRef</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-32', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileref</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadRef</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L515"></a><tt class="py-lineno"> 515</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L516"></a><tt class="py-lineno"> 516</tt> <tt class="py-line"> <tt class="py-comment">#print "REFBREAK"</tt> </tt>
<a name="L517"></a><tt class="py-lineno"> 517</tt> <tt class="py-line"> <tt class="py-name">RefReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">RefRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L518"></a><tt class="py-lineno"> 518</tt> <tt class="py-line"> <tt class="py-name">RefBool</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L519"></a><tt class="py-lineno"> 519</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L520"></a><tt class="py-lineno"> 520</tt> <tt class="py-line"> </tt>
<a name="L521"></a><tt class="py-lineno"> 521</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadArt</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-33', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno"> 522</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L523"></a><tt class="py-lineno"> 523</tt> <tt class="py-line"> <tt class="py-comment">#print "ARTBREAK"</tt> </tt>
<a name="L524"></a><tt class="py-lineno"> 524</tt> <tt class="py-line"> <tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">RefReadRank</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rankdic</tt> <tt class="py-keyword">else</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L525"></a><tt class="py-lineno"> 525</tt> <tt class="py-line"> <tt class="py-name">ArtBool</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L526"></a><tt class="py-lineno"> 526</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L527"></a><tt class="py-lineno"> 527</tt> <tt class="py-line"> </tt>
<a name="L528"></a><tt class="py-lineno"> 528</tt> <tt class="py-line"> <tt class="py-comment"># if the while loop was broken one read has to be read in the not closed file</tt> </tt>
<a name="L529"></a><tt class="py-lineno"> 529</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L530"></a><tt class="py-lineno"> 530</tt> <tt class="py-line"> <tt class="py-comment"># the file which has still some lines is now processed linearly...</tt> </tt>
<a name="L531"></a><tt class="py-lineno"> 531</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">RefBool</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L532"></a><tt class="py-lineno"> 532</tt> <tt class="py-line"> <tt class="py-comment">#print ("REF FILE FINISHED!!!")</tt> </tt>
<a name="L533"></a><tt class="py-lineno"> 533</tt> <tt class="py-line"> <tt class="py-comment"># reference no lines --> read artificial</tt> </tt>
<a name="L534"></a><tt class="py-lineno"> 534</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadArt</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-34', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L535"></a><tt class="py-lineno"> 535</tt> <tt class="py-line"> <tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">RefReadRank</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rankdic</tt> <tt class="py-keyword">else</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L536"></a><tt class="py-lineno"> 536</tt> <tt class="py-line"> </tt>
<a name="L537"></a><tt class="py-lineno"> 537</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op">></tt> <tt class="py-name">ArtReadRank</tt> <tt class="py-keyword">and</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L538"></a><tt class="py-lineno"> 538</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L539"></a><tt class="py-lineno"> 539</tt> <tt class="py-line"> <tt class="py-comment"># in case of multiple hits, set all mr variables to 0 and get the best alignment</tt> </tt>
<a name="L540"></a><tt class="py-lineno"> 540</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ArtRead</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L541"></a><tt class="py-lineno"> 541</tt> <tt class="py-line"> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L542"></a><tt class="py-lineno"> 542</tt> <tt class="py-line"> </tt>
<a name="L543"></a><tt class="py-lineno"> 543</tt> <tt class="py-line"> <tt class="py-comment"># write current FP to file</tt> </tt>
<a name="L544"></a><tt class="py-lineno"> 544</tt> <tt class="py-line"> <tt class="py-comment"># write FP to file</tt> </tt>
<a name="L545"></a><tt class="py-lineno"> 545</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">:</tt> </tt>
<a name="L546"></a><tt class="py-lineno"> 546</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-35', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"art"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L547"></a><tt class="py-lineno"> 547</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L548"></a><tt class="py-lineno"> 548</tt> <tt class="py-line"> <tt class="py-comment"># use akku for read lines</tt> </tt>
<a name="L549"></a><tt class="py-lineno"> 549</tt> <tt class="py-line"> <tt class="py-name">CurrentReadArt</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadArt</tt> </tt>
<a name="L550"></a><tt class="py-lineno"> 550</tt> <tt class="py-line"> <tt class="py-comment">#get all the reads with the same ID into ArtRead</tt> </tt>
<a name="L551"></a><tt class="py-lineno"> 551</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadArt</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-36', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno"> 552</tt> <tt class="py-line"> </tt>
<a name="L553"></a><tt class="py-lineno"> 553</tt> <tt class="py-line"> <tt class="py-comment">#update rank</tt> </tt>
<a name="L554"></a><tt class="py-lineno"> 554</tt> <tt class="py-line"> <tt class="py-name">ArtReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">RefReadRank</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rankdic</tt> <tt class="py-keyword">else</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">ArtRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L555"></a><tt class="py-lineno"> 555</tt> <tt class="py-line"> </tt>
<a name="L556"></a><tt class="py-lineno"> 556</tt> <tt class="py-line"> </tt>
<a name="L557"></a><tt class="py-lineno"> 557</tt> <tt class="py-line"> </tt>
<a name="L558"></a><tt class="py-lineno"> 558</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op">==</tt> <tt class="py-name">ArtReadRank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L559"></a><tt class="py-lineno"> 559</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L560"></a><tt class="py-lineno"> 560</tt> <tt class="py-line"> <tt class="py-comment">#same read.id --> compare all Alignments for one read id (can be multiple alignments)</tt> </tt>
<a name="L561"></a><tt class="py-lineno"> 561</tt> <tt class="py-line"> <tt class="py-comment"># return unique hits to artificial genome</tt> </tt>
<a name="L562"></a><tt class="py-lineno"> 562</tt> <tt class="py-line"> <tt class="py-name">tempTP</tt><tt class="py-op">,</tt><tt class="py-name">tempFP</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="core.AnalyseMapping.CompareAlignments" class="py-name" href="#" onclick="return doclink('link-37', 'CompareAlignments', 'link-31');">CompareAlignments</a></tt><tt class="py-op">(</tt><tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt><tt class="py-name">fobj</tt><tt class="py-op">)</tt> </tt>
<a name="L563"></a><tt class="py-lineno"> 563</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt><tt class="py-name">tempTP</tt> </tt>
<a name="L564"></a><tt class="py-lineno"> 564</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt><tt class="py-name">tempFP</tt> </tt>
<a name="L565"></a><tt class="py-lineno"> 565</tt> <tt class="py-line"> </tt>
<a name="L566"></a><tt class="py-lineno"> 566</tt> <tt class="py-line"> </tt>
<a name="L567"></a><tt class="py-lineno"> 567</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L568"></a><tt class="py-lineno"> 568</tt> <tt class="py-line"> </tt>
<a name="L569"></a><tt class="py-lineno"> 569</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L570"></a><tt class="py-lineno"> 570</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L571"></a><tt class="py-lineno"> 571</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno"> 572</tt> <tt class="py-line"> </tt>
<a name="L573"></a><tt class="py-lineno"> 573</tt> <tt class="py-line"> <tt class="py-name">CurrentReadArt</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadArt</tt> </tt>
<a name="L574"></a><tt class="py-lineno"> 574</tt> <tt class="py-line"> <tt class="py-comment"># read next artificial read!</tt> </tt>
<a name="L575"></a><tt class="py-lineno"> 575</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadArt</tt> <tt class="py-op">=</tt> <tt id="link-38" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-38', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileart</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadArt</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L576"></a><tt class="py-lineno"> 576</tt> <tt class="py-line"> </tt>
<a name="L577"></a><tt class="py-lineno"> 577</tt> <tt class="py-line"> </tt>
<a name="L578"></a><tt class="py-lineno"> 578</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">:</tt> </tt>
<a name="L579"></a><tt class="py-lineno"> 579</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-39', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"art"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L580"></a><tt class="py-lineno"> 580</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L581"></a><tt class="py-lineno"> 581</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L582"></a><tt class="py-lineno"> 582</tt> <tt class="py-line"> </tt>
<a name="L583"></a><tt class="py-lineno"> 583</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L584"></a><tt class="py-lineno"> 584</tt> <tt class="py-line"> <tt class="py-comment"># read again reference file as long as the final read from he artificial file is reached</tt> </tt>
<a name="L585"></a><tt class="py-lineno"> 585</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op"><</tt> <tt class="py-name">ArtReadRank</tt> <tt class="py-keyword">and</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L586"></a><tt class="py-lineno"> 586</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L587"></a><tt class="py-lineno"> 587</tt> <tt class="py-line"> </tt>
<a name="L588"></a><tt class="py-lineno"> 588</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">RefRead</tt><tt class="py-op">:</tt> </tt>
<a name="L589"></a><tt class="py-lineno"> 589</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-40', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L590"></a><tt class="py-lineno"> 590</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L591"></a><tt class="py-lineno"> 591</tt> <tt class="py-line"> <tt class="py-name">CurrentReadRef</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadRef</tt> </tt>
<a name="L592"></a><tt class="py-lineno"> 592</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadRef</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-41', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileref</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadRef</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L593"></a><tt class="py-lineno"> 593</tt> <tt class="py-line"> <tt class="py-name">RefReadRank</tt> <tt class="py-op">=</tt> <tt class="py-name">rankdic</tt><tt class="py-op">[</tt><tt class="py-name">RefRead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> </tt>
<a name="L594"></a><tt class="py-lineno"> 594</tt> <tt class="py-line"> </tt>
<a name="L595"></a><tt class="py-lineno"> 595</tt> <tt class="py-line"> </tt>
<a name="L596"></a><tt class="py-lineno"> 596</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">RefReadRank</tt> <tt class="py-op">==</tt> <tt class="py-name">ArtReadRank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L597"></a><tt class="py-lineno"> 597</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L598"></a><tt class="py-lineno"> 598</tt> <tt class="py-line"> <tt class="py-comment">#same read.id --> compare all Alignments for one read id (can be multiple alignments)</tt> </tt>
<a name="L599"></a><tt class="py-lineno"> 599</tt> <tt class="py-line"> <tt class="py-comment"># return unique hits to artificial genome</tt> </tt>
<a name="L600"></a><tt class="py-lineno"> 600</tt> <tt class="py-line"> <tt class="py-name">tempTP</tt><tt class="py-op">,</tt><tt class="py-name">tempFP</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="core.AnalyseMapping.CompareAlignments" class="py-name" href="#" onclick="return doclink('link-42', 'CompareAlignments', 'link-31');">CompareAlignments</a></tt><tt class="py-op">(</tt><tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">,</tt><tt class="py-name">fobj</tt><tt class="py-op">)</tt> </tt>
<a name="L601"></a><tt class="py-lineno"> 601</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt><tt class="py-name">tempTP</tt> </tt>
<a name="L602"></a><tt class="py-lineno"> 602</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt><tt class="py-name">tempFP</tt> </tt>
<a name="L603"></a><tt class="py-lineno"> 603</tt> <tt class="py-line"> </tt>
<a name="L604"></a><tt class="py-lineno"> 604</tt> <tt class="py-line"> </tt>
<a name="L605"></a><tt class="py-lineno"> 605</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L606"></a><tt class="py-lineno"> 606</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L607"></a><tt class="py-lineno"> 607</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ArtRead</tt><tt class="py-op">:</tt> </tt>
<a name="L608"></a><tt class="py-lineno"> 608</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-43', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"art"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L609"></a><tt class="py-lineno"> 609</tt> <tt class="py-line"> <tt class="py-name">fp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L610"></a><tt class="py-lineno"> 610</tt> <tt class="py-line"> </tt>
<a name="L611"></a><tt class="py-lineno"> 611</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L612"></a><tt class="py-lineno"> 612</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasNextLine</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L613"></a><tt class="py-lineno"> 613</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L614"></a><tt class="py-lineno"> 614</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">RefRead</tt><tt class="py-op">:</tt> </tt>
<a name="L615"></a><tt class="py-lineno"> 615</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-44', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L616"></a><tt class="py-lineno"> 616</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L617"></a><tt class="py-lineno"> 617</tt> <tt class="py-line"> </tt>
<a name="L618"></a><tt class="py-lineno"> 618</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L619"></a><tt class="py-lineno"> 619</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L620"></a><tt class="py-lineno"> 620</tt> <tt class="py-line"> <tt class="py-name">CurrentReadRef</tt> <tt class="py-op">=</tt> <tt class="py-name">NextReadRef</tt> </tt>
<a name="L621"></a><tt class="py-lineno"> 621</tt> <tt class="py-line"> <tt class="py-name">MappedReads</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L622"></a><tt class="py-lineno"> 622</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">RefRead</tt><tt class="py-op">:</tt> </tt>
<a name="L623"></a><tt class="py-lineno"> 623</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="core.AnalyseMapping.CustomRead.toStrNoMem" class="py-name" href="#" onclick="return doclink('link-45', 'toStrNoMem', 'link-19');">toStrNoMem</a></tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L624"></a><tt class="py-lineno"> 624</tt> <tt class="py-line"> <tt class="py-name">tp</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L625"></a><tt class="py-lineno"> 625</tt> <tt class="py-line"> <tt class="py-name">hasNextLine</tt><tt class="py-op">,</tt> <tt class="py-name">RefRead</tt><tt class="py-op">,</tt> <tt class="py-name">NextReadRef</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="core.AnalyseMapping.getAllID" class="py-name" href="#" onclick="return doclink('link-46', 'getAllID', 'link-16');">getAllID</a></tt><tt class="py-op">(</tt><tt class="py-name">fileref</tt><tt class="py-op">,</tt> <tt class="py-name">CurrentReadRef</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L626"></a><tt class="py-lineno"> 626</tt> <tt class="py-line"> </tt>
<a name="L627"></a><tt class="py-lineno"> 627</tt> <tt class="py-line"> <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L628"></a><tt class="py-lineno"> 628</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"\t\t%f\t\t"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">end</tt> <tt class="py-op">-</tt> <tt class="py-name">start</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L629"></a><tt class="py-lineno"> 629</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L630"></a><tt class="py-lineno"> 630</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">tp</tt><tt class="py-op">,</tt> <tt class="py-name">fp</tt><tt class="py-op">,</tt><tt class="py-name">tp</tt><tt class="py-op">+</tt><tt class="py-name">fp</tt><tt class="py-op">,</tt><tt class="py-name">MappedReads</tt><tt class="py-op">)</tt> </tt>
</div><a name="L631"></a><tt class="py-lineno"> 631</tt> <tt class="py-line"><tt class="py-comment">##################END: FUNCTIONS FOR NO-MEMORY ANALYSIS ####################</tt> </tt>
<a name="L632"></a><tt class="py-lineno"> 632</tt> <tt class="py-line"> </tt>
<a name="L633"></a><tt class="py-lineno"> 633</tt> <tt class="py-line"> </tt>
<a name="getNumberOf"></a><div id="getNumberOf-def"><a name="L634"></a><tt class="py-lineno"> 634</tt> <a class="py-toggle" href="#" id="getNumberOf-toggle" onclick="return toggle('getNumberOf');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getNumberOf">getNumberOf</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getNumberOf-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getNumberOf-expanded"><a name="L635"></a><tt class="py-lineno"> 635</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L636"></a><tt class="py-lineno"> 636</tt> <tt class="py-line"><tt class="py-docstring"> Reads the alignment tag, given the text and a tag to search for.</tt> </tt>
<a name="L637"></a><tt class="py-lineno"> 637</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L638"></a><tt class="py-lineno"> 638</tt> <tt class="py-line"><tt class="py-docstring"> @type line: string</tt> </tt>
<a name="L639"></a><tt class="py-lineno"> 639</tt> <tt class="py-line"><tt class="py-docstring"> @param line: SAM line</tt> </tt>
<a name="L640"></a><tt class="py-lineno"> 640</tt> <tt class="py-line"><tt class="py-docstring"> @type tag: string</tt> </tt>
<a name="L641"></a><tt class="py-lineno"> 641</tt> <tt class="py-line"><tt class="py-docstring"> @param tag: SAM tag. i.e: NM,MD</tt> </tt>
<a name="L642"></a><tt class="py-lineno"> 642</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L643"></a><tt class="py-lineno"> 643</tt> <tt class="py-line"><tt class="py-docstring"> @return: number x behind desired tag tag:i:x</tt> </tt>
<a name="L644"></a><tt class="py-lineno"> 644</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L645"></a><tt class="py-lineno"> 645</tt> <tt class="py-line"> </tt>
<a name="L646"></a><tt class="py-lineno"> 646</tt> <tt class="py-line"> <tt class="py-comment"># gives the number of XX back</tt> </tt>
<a name="L647"></a><tt class="py-lineno"> 647</tt> <tt class="py-line"> <tt class="py-comment"># valid tags: X0,XM (number of missmatches</tt> </tt>
<a name="L648"></a><tt class="py-lineno"> 648</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">tag</tt> <tt class="py-op">+</tt> <tt class="py-string">":i:(\d+)"</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L649"></a><tt class="py-lineno"> 649</tt> <tt class="py-line"> <tt class="py-name">besthits</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L650"></a><tt class="py-lineno"> 650</tt> <tt class="py-line"> </tt>
<a name="L651"></a><tt class="py-lineno"> 651</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">besthits</tt><tt class="py-op">)</tt> </tt>
</div><a name="L652"></a><tt class="py-lineno"> 652</tt> <tt class="py-line"> </tt>
<a name="getsum"></a><div id="getsum-def"><a name="L653"></a><tt class="py-lineno"> 653</tt> <a class="py-toggle" href="#" id="getsum-toggle" onclick="return toggle('getsum');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getsum">getsum</a><tt class="py-op">(</tt><tt class="py-param">strlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getsum-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getsum-expanded"><a name="L654"></a><tt class="py-lineno"> 654</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L655"></a><tt class="py-lineno"> 655</tt> <tt class="py-line"><tt class="py-docstring"> Sum of strings (as ints)</tt> </tt>
<a name="L656"></a><tt class="py-lineno"> 656</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L657"></a><tt class="py-lineno"> 657</tt> <tt class="py-line"><tt class="py-docstring"> @type strlist: list(str)</tt> </tt>
<a name="L658"></a><tt class="py-lineno"> 658</tt> <tt class="py-line"><tt class="py-docstring"> @param strlist: SAM line</tt> </tt>
<a name="L659"></a><tt class="py-lineno"> 659</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L660"></a><tt class="py-lineno"> 660</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L661"></a><tt class="py-lineno"> 661</tt> <tt class="py-line"><tt class="py-docstring"> @return: MD tag calculation.</tt> </tt>
<a name="L662"></a><tt class="py-lineno"> 662</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L663"></a><tt class="py-lineno"> 663</tt> <tt class="py-line"> </tt>
<a name="L664"></a><tt class="py-lineno"> 664</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">strlist</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L665"></a><tt class="py-lineno"> 665</tt> <tt class="py-line"> </tt>
<a name="getmean"></a><div id="getmean-def"><a name="L666"></a><tt class="py-lineno"> 666</tt> <a class="py-toggle" href="#" id="getmean-toggle" onclick="return toggle('getmean');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getmean">getmean</a><tt class="py-op">(</tt><tt class="py-param">strlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getmean-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getmean-expanded"><a name="L667"></a><tt class="py-lineno"> 667</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L668"></a><tt class="py-lineno"> 668</tt> <tt class="py-line"><tt class="py-docstring"> Mean of strings.</tt> </tt>
<a name="L669"></a><tt class="py-lineno"> 669</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L670"></a><tt class="py-lineno"> 670</tt> <tt class="py-line"><tt class="py-docstring"> @type strlist: list(str)</tt> </tt>
<a name="L671"></a><tt class="py-lineno"> 671</tt> <tt class="py-line"><tt class="py-docstring"> @param strlist: SAM line</tt> </tt>
<a name="L672"></a><tt class="py-lineno"> 672</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L673"></a><tt class="py-lineno"> 673</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: float</tt> </tt>
<a name="L674"></a><tt class="py-lineno"> 674</tt> <tt class="py-line"><tt class="py-docstring"> @return: mean</tt> </tt>
<a name="L675"></a><tt class="py-lineno"> 675</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L676"></a><tt class="py-lineno"> 676</tt> <tt class="py-line"> <tt class="py-name">sum</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="core.AnalyseMapping.getsum" class="py-name" href="#" onclick="return doclink('link-47', 'getsum', 'link-5');">getsum</a></tt><tt class="py-op">(</tt><tt class="py-name">strlist</tt><tt class="py-op">)</tt> </tt>
<a name="L677"></a><tt class="py-lineno"> 677</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">strlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L678"></a><tt class="py-lineno"> 678</tt> <tt class="py-line"> </tt>
<a name="L679"></a><tt class="py-lineno"> 679</tt> <tt class="py-line"> </tt>
<a name="ComputeRQScore"></a><div id="ComputeRQScore-def"><a name="L680"></a><tt class="py-lineno"> 680</tt> <a class="py-toggle" href="#" id="ComputeRQScore-toggle" onclick="return toggle('ComputeRQScore');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#ComputeRQScore">ComputeRQScore</a><tt class="py-op">(</tt><tt class="py-param">quality</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComputeRQScore-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="ComputeRQScore-expanded"><a name="L681"></a><tt class="py-lineno"> 681</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L682"></a><tt class="py-lineno"> 682</tt> <tt class="py-line"><tt class="py-docstring"> Computes the ReadQualityScore given a quality string</tt> </tt>
<a name="L683"></a><tt class="py-lineno"> 683</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L684"></a><tt class="py-lineno"> 684</tt> <tt class="py-line"><tt class="py-docstring"> @type quality: string</tt> </tt>
<a name="L685"></a><tt class="py-lineno"> 685</tt> <tt class="py-line"><tt class="py-docstring"> @param quality: quality string of a read.</tt> </tt>
<a name="L686"></a><tt class="py-lineno"> 686</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L687"></a><tt class="py-lineno"> 687</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: float</tt> </tt>
<a name="L688"></a><tt class="py-lineno"> 688</tt> <tt class="py-line"><tt class="py-docstring"> @return: ReadQualityScore (RQS)</tt> </tt>
<a name="L689"></a><tt class="py-lineno"> 689</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L690"></a><tt class="py-lineno"> 690</tt> <tt class="py-line"> <tt class="py-comment"># phred --> -33</tt> </tt>
<a name="L691"></a><tt class="py-lineno"> 691</tt> <tt class="py-line"> <tt class="py-name">qualarray</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">33</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quality</tt><tt class="py-op">]</tt> </tt>
<a name="L692"></a><tt class="py-lineno"> 692</tt> <tt class="py-line"> <tt class="py-comment"># solexa --> -64</tt> </tt>
<a name="L693"></a><tt class="py-lineno"> 693</tt> <tt class="py-line"> <tt class="py-name">score</tt> <tt class="py-op">=</tt><tt class="py-op">(</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">qualarray</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">qualarray</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">qualarray</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">qualarray</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L694"></a><tt class="py-lineno"> 694</tt> <tt class="py-line"> </tt>
<a name="L695"></a><tt class="py-lineno"> 695</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">score</tt><tt class="py-op">)</tt> </tt>
</div><a name="L696"></a><tt class="py-lineno"> 696</tt> <tt class="py-line"> </tt>
<a name="L697"></a><tt class="py-lineno"> 697</tt> <tt class="py-line"> </tt>
<a name="getAlignmentLength"></a><div id="getAlignmentLength-def"><a name="L698"></a><tt class="py-lineno"> 698</tt> <a class="py-toggle" href="#" id="getAlignmentLength-toggle" onclick="return toggle('getAlignmentLength');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getAlignmentLength">getAlignmentLength</a><tt class="py-op">(</tt><tt class="py-param">cigar</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getAlignmentLength-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getAlignmentLength-expanded"><a name="L699"></a><tt class="py-lineno"> 699</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L700"></a><tt class="py-lineno"> 700</tt> <tt class="py-line"><tt class="py-docstring"> Computes the alignment length given a cigar string. Needed for Start + End calculation.</tt> </tt>
<a name="L701"></a><tt class="py-lineno"> 701</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L702"></a><tt class="py-lineno"> 702</tt> <tt class="py-line"><tt class="py-docstring"> @type cigar: string</tt> </tt>
<a name="L703"></a><tt class="py-lineno"> 703</tt> <tt class="py-line"><tt class="py-docstring"> @param cigar: Cigar string (SAM)</tt> </tt>
<a name="L704"></a><tt class="py-lineno"> 704</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L705"></a><tt class="py-lineno"> 705</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L706"></a><tt class="py-lineno"> 706</tt> <tt class="py-line"><tt class="py-docstring"> @return: alignmentlength</tt> </tt>
<a name="L707"></a><tt class="py-lineno"> 707</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L708"></a><tt class="py-lineno"> 708</tt> <tt class="py-line"> <tt class="py-comment"># I - insertions do not extend the alignment</tt> </tt>
<a name="L709"></a><tt class="py-lineno"> 709</tt> <tt class="py-line"> <tt class="py-comment"># S - does not extend...</tt> </tt>
<a name="L710"></a><tt class="py-lineno"> 710</tt> <tt class="py-line"> <tt class="py-comment"># P - does not extend...</tt> </tt>
<a name="L711"></a><tt class="py-lineno"> 711</tt> <tt class="py-line"> <tt class="py-comment"># H - does not extend...</tt> </tt>
<a name="L712"></a><tt class="py-lineno"> 712</tt> <tt class="py-line"> <tt class="py-name">match</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">"(\d+)[MDN]"</tt><tt class="py-op">,</tt> <tt class="py-name">cigar</tt><tt class="py-op">)</tt> </tt>
<a name="L713"></a><tt class="py-lineno"> 713</tt> <tt class="py-line"> <tt class="py-name">sumOfMatches</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L714"></a><tt class="py-lineno"> 714</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">match</tt><tt class="py-op">:</tt> </tt>
<a name="L715"></a><tt class="py-lineno"> 715</tt> <tt class="py-line"> <tt class="py-name">sumOfMatches</tt> <tt class="py-op">+=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> </tt>
<a name="L716"></a><tt class="py-lineno"> 716</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">sumOfMatches</tt><tt class="py-op">)</tt> </tt>
</div><a name="L717"></a><tt class="py-lineno"> 717</tt> <tt class="py-line"> </tt>
<a name="L718"></a><tt class="py-lineno"> 718</tt> <tt class="py-line"> </tt>
<a name="isSaneAlignment"></a><div id="isSaneAlignment-def"><a name="L719"></a><tt class="py-lineno"> 719</tt> <a class="py-toggle" href="#" id="isSaneAlignment-toggle" onclick="return toggle('isSaneAlignment');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#isSaneAlignment">isSaneAlignment</a><tt class="py-op">(</tt><tt class="py-param">alignment</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="isSaneAlignment-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="isSaneAlignment-expanded"><a name="L720"></a><tt class="py-lineno"> 720</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L721"></a><tt class="py-lineno"> 721</tt> <tt class="py-line"><tt class="py-docstring"> Checks alignment line for unnecessary informations to skip </tt> </tt>
<a name="L722"></a><tt class="py-lineno"> 722</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L723"></a><tt class="py-lineno"> 723</tt> <tt class="py-line"><tt class="py-docstring"> @type alignment: string</tt> </tt>
<a name="L724"></a><tt class="py-lineno"> 724</tt> <tt class="py-line"><tt class="py-docstring"> @param alignment: Line from SAM</tt> </tt>
<a name="L725"></a><tt class="py-lineno"> 725</tt> <tt class="py-line"><tt class="py-docstring"> @type identifier: string</tt> </tt>
<a name="L726"></a><tt class="py-lineno"> 726</tt> <tt class="py-line"><tt class="py-docstring"> @param identifier: read id</tt> </tt>
<a name="L727"></a><tt class="py-lineno"> 727</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L728"></a><tt class="py-lineno"> 728</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: list of alignments with same read id.</tt> </tt>
<a name="L729"></a><tt class="py-lineno"> 729</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L730"></a><tt class="py-lineno"> 730</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: Dictionary containg a read id; read quality mapping</tt> </tt>
<a name="L731"></a><tt class="py-lineno"> 731</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: readobj, readname</tt> </tt>
<a name="L732"></a><tt class="py-lineno"> 732</tt> <tt class="py-line"><tt class="py-docstring"> @return: Returns the read and it's identifier.</tt> </tt>
<a name="L733"></a><tt class="py-lineno"> 733</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L734"></a><tt class="py-lineno"> 734</tt> <tt class="py-line"> </tt>
<a name="L735"></a><tt class="py-lineno"> 735</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">alignment</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"@"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L736"></a><tt class="py-lineno"> 736</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L737"></a><tt class="py-lineno"> 737</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L738"></a><tt class="py-lineno"> 738</tt> <tt class="py-line"> <tt class="py-name">read</tt><tt class="py-op">,</tt> <tt class="py-name">readname</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="core.AnalyseMapping.readSAMline" class="py-name" href="#" onclick="return doclink('link-48', 'readSAMline', 'link-10');">readSAMline</a></tt><tt class="py-op">(</tt><tt class="py-name">alignment</tt><tt class="py-op">,</tt> <tt class="py-name">identifier</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L739"></a><tt class="py-lineno"> 739</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">read</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L740"></a><tt class="py-lineno"> 740</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L741"></a><tt class="py-lineno"> 741</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L742"></a><tt class="py-lineno"> 742</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">,</tt> <tt class="py-name">readname</tt><tt class="py-op">)</tt> </tt>
</div><a name="L743"></a><tt class="py-lineno"> 743</tt> <tt class="py-line"> </tt>
<a name="L744"></a><tt class="py-lineno"> 744</tt> <tt class="py-line"> </tt>
<a name="CheckForSameAlignments"></a><div id="CheckForSameAlignments-def"><a name="L745"></a><tt class="py-lineno"> 745</tt> <a class="py-toggle" href="#" id="CheckForSameAlignments-toggle" onclick="return toggle('CheckForSameAlignments');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#CheckForSameAlignments">CheckForSameAlignments</a><tt class="py-op">(</tt><tt class="py-param">readref</tt><tt class="py-op">,</tt> <tt class="py-param">readart</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CheckForSameAlignments-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="CheckForSameAlignments-expanded"><a name="L746"></a><tt class="py-lineno"> 746</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L747"></a><tt class="py-lineno"> 747</tt> <tt class="py-line"><tt class="py-docstring"> Function for comparison of artificial alignments and reference alignments. FP are defined such that start and end position must be unique to the artificial reference</tt> </tt>
<a name="L748"></a><tt class="py-lineno"> 748</tt> <tt class="py-line"><tt class="py-docstring"> returns 0 if no same read is found (FP found)</tt> </tt>
<a name="L749"></a><tt class="py-lineno"> 749</tt> <tt class="py-line"><tt class="py-docstring"> returns 1 if an equal alignment is found</tt> </tt>
<a name="L750"></a><tt class="py-lineno"> 750</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L751"></a><tt class="py-lineno"> 751</tt> <tt class="py-line"><tt class="py-docstring"> @type readref: read obj.</tt> </tt>
<a name="L752"></a><tt class="py-lineno"> 752</tt> <tt class="py-line"><tt class="py-docstring"> @param readref: reference</tt> </tt>
<a name="L753"></a><tt class="py-lineno"> 753</tt> <tt class="py-line"><tt class="py-docstring"> @type readart: read obj.</tt> </tt>
<a name="L754"></a><tt class="py-lineno"> 754</tt> <tt class="py-line"><tt class="py-docstring"> @param readart: artificial</tt> </tt>
<a name="L755"></a><tt class="py-lineno"> 755</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: bool</tt> </tt>
<a name="L756"></a><tt class="py-lineno"> 756</tt> <tt class="py-line"><tt class="py-docstring"> @return: Indicator if alignment is the same (start & end equal)</tt> </tt>
<a name="L757"></a><tt class="py-lineno"> 757</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L758"></a><tt class="py-lineno"> 758</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">readref</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L759"></a><tt class="py-lineno"> 759</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">readref</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">readart</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">readref</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">readart</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L760"></a><tt class="py-lineno"> 760</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L761"></a><tt class="py-lineno"> 761</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L762"></a><tt class="py-lineno"> 762</tt> <tt class="py-line"> </tt>
<a name="L763"></a><tt class="py-lineno"> 763</tt> <tt class="py-line"> </tt>
<a name="L764"></a><tt class="py-lineno"> 764</tt> <tt class="py-line"> </tt>
<a name="getHammingdistance"></a><div id="getHammingdistance-def"><a name="L765"></a><tt class="py-lineno"> 765</tt> <a class="py-toggle" href="#" id="getHammingdistance-toggle" onclick="return toggle('getHammingdistance');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#getHammingdistance">getHammingdistance</a><tt class="py-op">(</tt><tt class="py-param">CompareString</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getHammingdistance-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getHammingdistance-expanded"><a name="L766"></a><tt class="py-lineno"> 766</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L767"></a><tt class="py-lineno"> 767</tt> <tt class="py-line"><tt class="py-docstring"> Computes the number of subsitutions in the artificial reference using the CompareString.</tt> </tt>
<a name="L768"></a><tt class="py-lineno"> 768</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L769"></a><tt class="py-lineno"> 769</tt> <tt class="py-line"><tt class="py-docstring"> @type CompareString: string</tt> </tt>
<a name="L770"></a><tt class="py-lineno"> 770</tt> <tt class="py-line"><tt class="py-docstring"> @param CompareString: string of 0 and 1s. 1 = hamming 1 between reference and artificial.</tt> </tt>
<a name="L771"></a><tt class="py-lineno"> 771</tt> <tt class="py-line"><tt class="py-docstring"> @type start: int</tt> </tt>
<a name="L772"></a><tt class="py-lineno"> 772</tt> <tt class="py-line"><tt class="py-docstring"> @param start: start of alignment</tt> </tt>
<a name="L773"></a><tt class="py-lineno"> 773</tt> <tt class="py-line"><tt class="py-docstring"> @type end: int</tt> </tt>
<a name="L774"></a><tt class="py-lineno"> 774</tt> <tt class="py-line"><tt class="py-docstring"> @param end: end ofalignment</tt> </tt>
<a name="L775"></a><tt class="py-lineno"> 775</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L776"></a><tt class="py-lineno"> 776</tt> <tt class="py-line"><tt class="py-docstring"> @return: hamming distance</tt> </tt>
<a name="L777"></a><tt class="py-lineno"> 777</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L778"></a><tt class="py-lineno"> 778</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">CompareString</tt><tt class="py-op">[</tt><tt class="py-name">start</tt><tt class="py-op">:</tt><tt class="py-name">end</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L779"></a><tt class="py-lineno"> 779</tt> <tt class="py-line"> </tt>
<a name="L780"></a><tt class="py-lineno"> 780</tt> <tt class="py-line"> </tt>
<a name="readReadQualities"></a><div id="readReadQualities-def"><a name="L781"></a><tt class="py-lineno"> 781</tt> <a class="py-toggle" href="#" id="readReadQualities-toggle" onclick="return toggle('readReadQualities');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#readReadQualities">readReadQualities</a><tt class="py-op">(</tt><tt class="py-param">fastqfile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="readReadQualities-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="readReadQualities-expanded"><a name="L782"></a><tt class="py-lineno"> 782</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L783"></a><tt class="py-lineno"> 783</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L784"></a><tt class="py-lineno"> 784</tt> <tt class="py-line"><tt class="py-docstring"> Reads a .fastqfile and calculates a defined readscore </tt> </tt>
<a name="L785"></a><tt class="py-lineno"> 785</tt> <tt class="py-line"><tt class="py-docstring"> input: fastq file</tt> </tt>
<a name="L786"></a><tt class="py-lineno"> 786</tt> <tt class="py-line"><tt class="py-docstring"> output: fastq dictionary key = readid; value = qualstr </tt> </tt>
<a name="L787"></a><tt class="py-lineno"> 787</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L788"></a><tt class="py-lineno"> 788</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L789"></a><tt class="py-lineno"> 789</tt> <tt class="py-line"><tt class="py-docstring"> @type fastqfile: string</tt> </tt>
<a name="L790"></a><tt class="py-lineno"> 790</tt> <tt class="py-line"><tt class="py-docstring"> @param fastqfile: path to fastq file</tt> </tt>
<a name="L791"></a><tt class="py-lineno"> 791</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L792"></a><tt class="py-lineno"> 792</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: dictionary</tt> </tt>
<a name="L793"></a><tt class="py-lineno"> 793</tt> <tt class="py-line"><tt class="py-docstring"> @return: dictionary containing read ids and read qualities.</tt> </tt>
<a name="L794"></a><tt class="py-lineno"> 794</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L795"></a><tt class="py-lineno"> 795</tt> <tt class="py-line"> <tt class="py-name">fastq_file</tt> <tt class="py-op">=</tt> <tt class="py-name">HTSeq</tt><tt class="py-op">.</tt><tt class="py-name">FastqReader</tt><tt class="py-op">(</tt><tt class="py-name">fastqfile</tt> <tt class="py-op">,</tt> <tt class="py-string">"phred"</tt><tt class="py-op">)</tt> </tt>
<a name="L796"></a><tt class="py-lineno"> 796</tt> <tt class="py-line"> <tt class="py-name">readdictionary</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L797"></a><tt class="py-lineno"> 797</tt> <tt class="py-line"> </tt>
<a name="L798"></a><tt class="py-lineno"> 798</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">read</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fastq_file</tt><tt class="py-op">:</tt> </tt>
<a name="L799"></a><tt class="py-lineno"> 799</tt> <tt class="py-line"> <tt class="py-name">readdictionary</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name" targets="Function core.AnalyseMapping.ComputeRQScore()=core.AnalyseMapping-module.html#ComputeRQScore"><a title="core.AnalyseMapping.ComputeRQScore" class="py-name" href="#" onclick="return doclink('link-49', 'ComputeRQScore', 'link-49');">ComputeRQScore</a></tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">.</tt><tt class="py-name">qualstr</tt><tt class="py-op">)</tt> </tt>
<a name="L800"></a><tt class="py-lineno"> 800</tt> <tt class="py-line"> <tt class="py-keyword">print</tt><tt class="py-op">(</tt><tt class="py-string">"\tReading Fastq file done!"</tt><tt class="py-op">)</tt> </tt>
<a name="L801"></a><tt class="py-lineno"> 801</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">readdictionary</tt> </tt>
</div><a name="L802"></a><tt class="py-lineno"> 802</tt> <tt class="py-line"> </tt>
<a name="L803"></a><tt class="py-lineno"> 803</tt> <tt class="py-line"> </tt>
<a name="L804"></a><tt class="py-lineno"> 804</tt> <tt class="py-line"> </tt>
<a name="L805"></a><tt class="py-lineno"> 805</tt> <tt class="py-line"> </tt>
<a name="extendReadDic"></a><div id="extendReadDic-def"><a name="L806"></a><tt class="py-lineno"> 806</tt> <a class="py-toggle" href="#" id="extendReadDic-toggle" onclick="return toggle('extendReadDic');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#extendReadDic">extendReadDic</a><tt class="py-op">(</tt><tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="extendReadDic-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="extendReadDic-expanded"><a name="L807"></a><tt class="py-lineno"> 807</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L808"></a><tt class="py-lineno"> 808</tt> <tt class="py-line"><tt class="py-docstring"> Extends a given dictionary with KEY = readid and VALUE = qualstr such that an internal naming is generated which can be used to efficiently create an numpy array</tt> </tt>
<a name="L809"></a><tt class="py-lineno"> 809</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L810"></a><tt class="py-lineno"> 810</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L811"></a><tt class="py-lineno"> 811</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L812"></a><tt class="py-lineno"> 812</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: dictionary containing read ids and read qualities.</tt> </tt>
<a name="L813"></a><tt class="py-lineno"> 813</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L814"></a><tt class="py-lineno"> 814</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: dictionary</tt> </tt>
<a name="L815"></a><tt class="py-lineno"> 815</tt> <tt class="py-line"><tt class="py-docstring"> @return: extended readdic with KEY = ID, VALUE = READID object with READID.internalid and READID.qulstr = qualstr</tt> </tt>
<a name="L816"></a><tt class="py-lineno"> 816</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L817"></a><tt class="py-lineno"> 817</tt> <tt class="py-line"> <tt class="py-name">internalnaming</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L818"></a><tt class="py-lineno"> 818</tt> <tt class="py-line"> <tt class="py-name">reverseReadDic</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">readdic</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-string">'S50'</tt><tt class="py-op">)</tt> </tt>
<a name="L819"></a><tt class="py-lineno"> 819</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">id</tt> <tt class="py-keyword">in</tt> <tt class="py-name">readdic</tt><tt class="py-op">.</tt><tt class="py-name">iterkeys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L820"></a><tt class="py-lineno"> 820</tt> <tt class="py-line"> <tt class="py-comment"># i</tt> </tt>
<a name="L821"></a><tt class="py-lineno"> 821</tt> <tt class="py-line"> <tt class="py-name">readdic</tt><tt class="py-op">[</tt><tt class="py-name">id</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name" targets="Class core.AnalyseMapping.ReadID=core.AnalyseMapping.ReadID-class.html"><a title="core.AnalyseMapping.ReadID" class="py-name" href="#" onclick="return doclink('link-50', 'ReadID', 'link-50');">ReadID</a></tt><tt class="py-op">(</tt><tt class="py-name">internalnaming</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">[</tt><tt class="py-name">id</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L822"></a><tt class="py-lineno"> 822</tt> <tt class="py-line"> <tt class="py-name">reverseReadDic</tt><tt class="py-op">[</tt><tt class="py-name">internalnaming</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">id</tt> </tt>
<a name="L823"></a><tt class="py-lineno"> 823</tt> <tt class="py-line"> <tt class="py-name">internalnaming</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L824"></a><tt class="py-lineno"> 824</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">readdic</tt><tt class="py-op">,</tt> <tt class="py-name">reverseReadDic</tt><tt class="py-op">)</tt> </tt>
</div><a name="L825"></a><tt class="py-lineno"> 825</tt> <tt class="py-line"> </tt>
<a name="L826"></a><tt class="py-lineno"> 826</tt> <tt class="py-line"> </tt>
<a name="L827"></a><tt class="py-lineno"> 827</tt> <tt class="py-line"> </tt>
<a name="returnSequence"></a><div id="returnSequence-def"><a name="L828"></a><tt class="py-lineno"> 828</tt> <a class="py-toggle" href="#" id="returnSequence-toggle" onclick="return toggle('returnSequence');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#returnSequence">returnSequence</a><tt class="py-op">(</tt><tt class="py-param">fasta</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="returnSequence-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="returnSequence-expanded"><a name="L829"></a><tt class="py-lineno"> 829</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L830"></a><tt class="py-lineno"> 830</tt> <tt class="py-line"><tt class="py-docstring"> Returns a sequence string from a fasta file.</tt> </tt>
<a name="L831"></a><tt class="py-lineno"> 831</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L832"></a><tt class="py-lineno"> 832</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L833"></a><tt class="py-lineno"> 833</tt> <tt class="py-line"><tt class="py-docstring"> @type fasta: string</tt> </tt>
<a name="L834"></a><tt class="py-lineno"> 834</tt> <tt class="py-line"><tt class="py-docstring"> @param fasta: path to fasta file.</tt> </tt>
<a name="L835"></a><tt class="py-lineno"> 835</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L836"></a><tt class="py-lineno"> 836</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: string</tt> </tt>
<a name="L837"></a><tt class="py-lineno"> 837</tt> <tt class="py-line"><tt class="py-docstring"> @return: sequence</tt> </tt>
<a name="L838"></a><tt class="py-lineno"> 838</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L839"></a><tt class="py-lineno"> 839</tt> <tt class="py-line"> <tt class="py-name">fastafile</tt> <tt class="py-op">=</tt> <tt class="py-name">HTSeq</tt><tt class="py-op">.</tt><tt class="py-name">FastaReader</tt><tt class="py-op">(</tt><tt class="py-name">fasta</tt><tt class="py-op">)</tt> </tt>
<a name="L840"></a><tt class="py-lineno"> 840</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sequence</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fastafile</tt><tt class="py-op">:</tt> </tt>
<a name="L841"></a><tt class="py-lineno"> 841</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">sequence</tt><tt class="py-op">.</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> </tt>
</div><a name="L842"></a><tt class="py-lineno"> 842</tt> <tt class="py-line"> </tt>
<a name="L843"></a><tt class="py-lineno"> 843</tt> <tt class="py-line"> </tt>
<a name="L844"></a><tt class="py-lineno"> 844</tt> <tt class="py-line"> </tt>
<a name="CreateCompareList"></a><div id="CreateCompareList-def"><a name="L845"></a><tt class="py-lineno"> 845</tt> <a class="py-toggle" href="#" id="CreateCompareList-toggle" onclick="return toggle('CreateCompareList');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#CreateCompareList">CreateCompareList</a><tt class="py-op">(</tt><tt class="py-param">Reference</tt><tt class="py-op">,</tt> <tt class="py-param">ARG</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CreateCompareList-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="CreateCompareList-expanded"><a name="L846"></a><tt class="py-lineno"> 846</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L847"></a><tt class="py-lineno"> 847</tt> <tt class="py-line"><tt class="py-docstring"> Creates a list which is used for comparisons between aligned reads (exact number of mismatches) </tt> </tt>
<a name="L848"></a><tt class="py-lineno"> 848</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L849"></a><tt class="py-lineno"> 849</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L850"></a><tt class="py-lineno"> 850</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L851"></a><tt class="py-lineno"> 851</tt> <tt class="py-line"><tt class="py-docstring"> @type Reference: string</tt> </tt>
<a name="L852"></a><tt class="py-lineno"> 852</tt> <tt class="py-line"><tt class="py-docstring"> @param Reference: reference genome</tt> </tt>
<a name="L853"></a><tt class="py-lineno"> 853</tt> <tt class="py-line"><tt class="py-docstring"> @type ARG: string</tt> </tt>
<a name="L854"></a><tt class="py-lineno"> 854</tt> <tt class="py-line"><tt class="py-docstring"> @param ARG: artificial reference genome.</tt> </tt>
<a name="L855"></a><tt class="py-lineno"> 855</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L856"></a><tt class="py-lineno"> 856</tt> <tt class="py-line"><tt class="py-docstring"> @return: list containt 1s, where there is a difference in the genomes and 0s where the nucleotides are equal.</tt> </tt>
<a name="L857"></a><tt class="py-lineno"> 857</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L858"></a><tt class="py-lineno"> 858</tt> <tt class="py-line"> </tt>
<a name="L859"></a><tt class="py-lineno"> 859</tt> <tt class="py-line"> <tt class="py-name">reference</tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name" targets="Function core.AnalyseMapping.returnSequence()=core.AnalyseMapping-module.html#returnSequence"><a title="core.AnalyseMapping.returnSequence" class="py-name" href="#" onclick="return doclink('link-51', 'returnSequence', 'link-51');">returnSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">Reference</tt><tt class="py-op">)</tt> </tt>
<a name="L860"></a><tt class="py-lineno"> 860</tt> <tt class="py-line"> <tt class="py-name">artificialreference</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="core.AnalyseMapping.returnSequence" class="py-name" href="#" onclick="return doclink('link-52', 'returnSequence', 'link-51');">returnSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">ARG</tt><tt class="py-op">)</tt> </tt>
<a name="L861"></a><tt class="py-lineno"> 861</tt> <tt class="py-line"> <tt class="py-name">complist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L862"></a><tt class="py-lineno"> 862</tt> <tt class="py-line"> </tt>
<a name="L863"></a><tt class="py-lineno"> 863</tt> <tt class="py-line"> </tt>
<a name="L864"></a><tt class="py-lineno"> 864</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">reference</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">artificialreference</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L865"></a><tt class="py-lineno"> 865</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"first 10 letter:\t\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">reference</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">10</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"..."</tt> <tt class="py-op">+</tt> <tt class="py-name">reference</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">10</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L866"></a><tt class="py-lineno"> 866</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"last 10 letter:\t\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">artificialreference</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">10</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"..."</tt> <tt class="py-op">+</tt> <tt class="py-name">artificialreference</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">10</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L867"></a><tt class="py-lineno"> 867</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"Error! Two Sequences have different length! Try to add a line break after the last nucleotide."</tt><tt class="py-op">)</tt> </tt>
<a name="L868"></a><tt class="py-lineno"> 868</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L869"></a><tt class="py-lineno"> 869</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L870"></a><tt class="py-lineno"> 870</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-op">==</tt> <tt class="py-name">artificialreference</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">else</tt> <tt class="py-number">1</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">reference</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L871"></a><tt class="py-lineno"> 871</tt> <tt class="py-line"> </tt>
<a name="L872"></a><tt class="py-lineno"> 872</tt> <tt class="py-line"> </tt>
<a name="L873"></a><tt class="py-lineno"> 873</tt> <tt class="py-line"> </tt>
<a name="readSAMline"></a><div id="readSAMline-def"><a name="L874"></a><tt class="py-lineno"> 874</tt> <a class="py-toggle" href="#" id="readSAMline-toggle" onclick="return toggle('readSAMline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#readSAMline">readSAMline</a><tt class="py-op">(</tt><tt class="py-param">alignment</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="readSAMline-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="readSAMline-expanded"><a name="L875"></a><tt class="py-lineno"> 875</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L876"></a><tt class="py-lineno"> 876</tt> <tt class="py-line"><tt class="py-docstring"> Function for reading SAM alignment text file (one line)</tt> </tt>
<a name="L877"></a><tt class="py-lineno"> 877</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L878"></a><tt class="py-lineno"> 878</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L879"></a><tt class="py-lineno"> 879</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L880"></a><tt class="py-lineno"> 880</tt> <tt class="py-line"><tt class="py-docstring"> @type alignment: string</tt> </tt>
<a name="L881"></a><tt class="py-lineno"> 881</tt> <tt class="py-line"><tt class="py-docstring"> @param alignment: SAM alignment</tt> </tt>
<a name="L882"></a><tt class="py-lineno"> 882</tt> <tt class="py-line"><tt class="py-docstring"> @type identifier: string</tt> </tt>
<a name="L883"></a><tt class="py-lineno"> 883</tt> <tt class="py-line"><tt class="py-docstring"> @param identifier: read id</tt> </tt>
<a name="L884"></a><tt class="py-lineno"> 884</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L885"></a><tt class="py-lineno"> 885</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: list containt 1s, where there is a difference in the genomes and 0s where the nucleotides are equal.</tt> </tt>
<a name="L886"></a><tt class="py-lineno"> 886</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L887"></a><tt class="py-lineno"> 887</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: dictionary containing read ids and read qualities.</tt> </tt>
<a name="L888"></a><tt class="py-lineno"> 888</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: read obj.</tt> </tt>
<a name="L889"></a><tt class="py-lineno"> 889</tt> <tt class="py-line"><tt class="py-docstring"> @return: returns a customRead object</tt> </tt>
<a name="L890"></a><tt class="py-lineno"> 890</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L891"></a><tt class="py-lineno"> 891</tt> <tt class="py-line"> <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L892"></a><tt class="py-lineno"> 892</tt> <tt class="py-line"> </tt>
<a name="L893"></a><tt class="py-lineno"> 893</tt> <tt class="py-line"> <tt class="py-comment"># ignore header</tt> </tt>
<a name="L894"></a><tt class="py-lineno"> 894</tt> <tt class="py-line"> <tt class="py-name">columns</tt> <tt class="py-op">=</tt> <tt class="py-name">alignment</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L895"></a><tt class="py-lineno"> 895</tt> <tt class="py-line"> <tt class="py-name">flag</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L896"></a><tt class="py-lineno"> 896</tt> <tt class="py-line"> </tt>
<a name="L897"></a><tt class="py-lineno"> 897</tt> <tt class="py-line"> <tt class="py-comment"># flag 4 = not mapped to any genome</tt> </tt>
<a name="L898"></a><tt class="py-lineno"> 898</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">flag</tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L899"></a><tt class="py-lineno"> 899</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L900"></a><tt class="py-lineno"> 900</tt> <tt class="py-line"> </tt>
<a name="L901"></a><tt class="py-lineno"> 901</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L902"></a><tt class="py-lineno"> 902</tt> <tt class="py-line"> </tt>
<a name="L903"></a><tt class="py-lineno"> 903</tt> <tt class="py-line"> </tt>
<a name="L904"></a><tt class="py-lineno"> 904</tt> <tt class="py-line"> <tt class="py-name">readname</tt> <tt class="py-op">=</tt> <tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L905"></a><tt class="py-lineno"> 905</tt> <tt class="py-line"> <tt class="py-name">reference</tt> <tt class="py-op">=</tt> <tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L906"></a><tt class="py-lineno"> 906</tt> <tt class="py-line"> <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L907"></a><tt class="py-lineno"> 907</tt> <tt class="py-line"> <tt class="py-name">mappingquality</tt> <tt class="py-op">=</tt> <tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L908"></a><tt class="py-lineno"> 908</tt> <tt class="py-line"> <tt class="py-name">cigar</tt> <tt class="py-op">=</tt> <tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L909"></a><tt class="py-lineno"> 909</tt> <tt class="py-line"> <tt class="py-name">qualstr</tt> <tt class="py-op">=</tt> <tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L910"></a><tt class="py-lineno"> 910</tt> <tt class="py-line"> <tt class="py-name">tags</tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">columns</tt><tt class="py-op">[</tt><tt class="py-number">11</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L911"></a><tt class="py-lineno"> 911</tt> <tt class="py-line"> </tt>
<a name="L912"></a><tt class="py-lineno"> 912</tt> <tt class="py-line"> <tt class="py-name">mdtag</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-string">"MD:Z:([^\s]+)"</tt><tt class="py-op">,</tt> <tt class="py-name">tags</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L913"></a><tt class="py-lineno"> 913</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L914"></a><tt class="py-lineno"> 914</tt> <tt class="py-line"> <tt class="py-name">mdtag</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-string">"MD:Z:([^\s]+)"</tt><tt class="py-op">,</tt> <tt class="py-name">tags</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L915"></a><tt class="py-lineno"> 915</tt> <tt class="py-line"> <tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt id="link-53" class="py-name" targets="Function core.AnalyseMapping.getMisGap()=core.AnalyseMapping-module.html#getMisGap"><a title="core.AnalyseMapping.getMisGap" class="py-name" href="#" onclick="return doclink('link-53', 'getMisGap', 'link-53');">getMisGap</a></tt><tt class="py-op">(</tt><tt class="py-name">mdtag</tt><tt class="py-op">,</tt> <tt class="py-name">cigar</tt><tt class="py-op">)</tt> </tt>
<a name="L916"></a><tt class="py-lineno"> 916</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L917"></a><tt class="py-lineno"> 917</tt> <tt class="py-line"> <tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L918"></a><tt class="py-lineno"> 918</tt> <tt class="py-line"> <tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L919"></a><tt class="py-lineno"> 919</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Error Reading MDtag of %s.Setting gaps = 0,mism = 0"</tt> <tt class="py-op">%</tt> <tt class="py-name">readname</tt> </tt>
<a name="L920"></a><tt class="py-lineno"> 920</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L921"></a><tt class="py-lineno"> 921</tt> <tt class="py-line"> <tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-54" class="py-name" targets="Function core.AnalyseMapping.getNumberOf()=core.AnalyseMapping-module.html#getNumberOf"><a title="core.AnalyseMapping.getNumberOf" class="py-name" href="#" onclick="return doclink('link-54', 'getNumberOf', 'link-54');">getNumberOf</a></tt><tt class="py-op">(</tt><tt class="py-name">tags</tt><tt class="py-op">,</tt> <tt class="py-string">"NM"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L922"></a><tt class="py-lineno"> 922</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L923"></a><tt class="py-lineno"> 923</tt> <tt class="py-line"> <tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L924"></a><tt class="py-lineno"> 924</tt> <tt class="py-line"> </tt>
<a name="L925"></a><tt class="py-lineno"> 925</tt> <tt class="py-line"> <tt class="py-name">leng</tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name" targets="Function core.AnalyseMapping.getAlignmentLength()=core.AnalyseMapping-module.html#getAlignmentLength"><a title="core.AnalyseMapping.getAlignmentLength" class="py-name" href="#" onclick="return doclink('link-55', 'getAlignmentLength', 'link-55');">getAlignmentLength</a></tt><tt class="py-op">(</tt><tt class="py-name">cigar</tt><tt class="py-op">)</tt> </tt>
<a name="L926"></a><tt class="py-lineno"> 926</tt> <tt class="py-line"> </tt>
<a name="L927"></a><tt class="py-lineno"> 927</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">qualstr</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">qualstr</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L928"></a><tt class="py-lineno"> 928</tt> <tt class="py-line"> <tt class="py-name">score</tt> <tt class="py-op">=</tt> <tt class="py-name">readdic</tt><tt class="py-op">[</tt><tt class="py-name">readname</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">quality</tt> </tt>
<a name="L929"></a><tt class="py-lineno"> 929</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L930"></a><tt class="py-lineno"> 930</tt> <tt class="py-line"> <tt class="py-name">score</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="core.AnalyseMapping.ComputeRQScore" class="py-name" href="#" onclick="return doclink('link-56', 'ComputeRQScore', 'link-49');">ComputeRQScore</a></tt><tt class="py-op">(</tt><tt class="py-name">qualstr</tt><tt class="py-op">)</tt> </tt>
<a name="L931"></a><tt class="py-lineno"> 931</tt> <tt class="py-line"> </tt>
<a name="L932"></a><tt class="py-lineno"> 932</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">identifier</tt> <tt class="py-op">==</tt> <tt class="py-string">"art"</tt><tt class="py-op">:</tt> </tt>
<a name="L933"></a><tt class="py-lineno"> 933</tt> <tt class="py-line"> <tt class="py-comment">#tempobj = CustomRead(0,nm, getHammingdistance(compareList, start, start+leng), score, mappingquality,start,start+leng)</tt> </tt>
<a name="L934"></a><tt class="py-lineno"> 934</tt> <tt class="py-line"> <tt class="py-name">tempobj</tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="core.AnalyseMapping.CustomRead" class="py-name" href="#" onclick="return doclink('link-57', 'CustomRead', 'link-6');">CustomRead</a></tt><tt class="py-op">(</tt><tt class="py-name">readname</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nm</tt><tt class="py-op">,</tt> <tt id="link-58" class="py-name"><a title="core.AnalyseMapping.getHammingdistance" class="py-name" href="#" onclick="return doclink('link-58', 'getHammingdistance', 'link-7');">getHammingdistance</a></tt><tt class="py-op">(</tt><tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt> <tt class="py-op">+</tt> <tt class="py-name">leng</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">score</tt><tt class="py-op">,</tt> <tt class="py-name">mappingquality</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt> <tt class="py-op">+</tt> <tt class="py-name">leng</tt><tt class="py-op">,</tt> <tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mism</tt><tt class="py-op">)</tt> </tt>
<a name="L935"></a><tt class="py-lineno"> 935</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">identifier</tt> <tt class="py-op">==</tt> <tt class="py-string">"noMem"</tt><tt class="py-op">:</tt> </tt>
<a name="L936"></a><tt class="py-lineno"> 936</tt> <tt class="py-line"> <tt class="py-name">tempobj</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="core.AnalyseMapping.CustomRead" class="py-name" href="#" onclick="return doclink('link-59', 'CustomRead', 'link-6');">CustomRead</a></tt><tt class="py-op">(</tt><tt class="py-name">readname</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">nm</tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name"><a title="core.AnalyseMapping.getHammingdistance" class="py-name" href="#" onclick="return doclink('link-60', 'getHammingdistance', 'link-7');">getHammingdistance</a></tt><tt class="py-op">(</tt><tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt> <tt class="py-op">+</tt> <tt class="py-name">leng</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">score</tt><tt class="py-op">,</tt> <tt class="py-name">mappingquality</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt> <tt class="py-op">+</tt> <tt class="py-name">leng</tt><tt class="py-op">,</tt> <tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mism</tt><tt class="py-op">)</tt> </tt>
<a name="L937"></a><tt class="py-lineno"> 937</tt> <tt class="py-line"> </tt>
<a name="L938"></a><tt class="py-lineno"> 938</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L939"></a><tt class="py-lineno"> 939</tt> <tt class="py-line"> <tt class="py-comment">##########TPRead(nm, score, mq, start, end, gaps, mism)</tt> </tt>
<a name="L940"></a><tt class="py-lineno"> 940</tt> <tt class="py-line"> <tt class="py-name">tempobj</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="core.AnalyseMapping.TPRead" class="py-name" href="#" onclick="return doclink('link-61', 'TPRead', 'link-4');">TPRead</a></tt><tt class="py-op">(</tt><tt class="py-name">nm</tt><tt class="py-op">,</tt> <tt class="py-name">score</tt><tt class="py-op">,</tt> <tt class="py-name">mappingquality</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">start</tt> <tt class="py-op">+</tt> <tt class="py-name">leng</tt><tt class="py-op">,</tt> <tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mism</tt><tt class="py-op">)</tt> </tt>
<a name="L941"></a><tt class="py-lineno"> 941</tt> <tt class="py-line"> </tt>
<a name="L942"></a><tt class="py-lineno"> 942</tt> <tt class="py-line"> </tt>
<a name="L943"></a><tt class="py-lineno"> 943</tt> <tt class="py-line"> </tt>
<a name="L944"></a><tt class="py-lineno"> 944</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">tempobj</tt><tt class="py-op">,</tt> <tt class="py-name">readname</tt><tt class="py-op">)</tt> </tt>
</div><a name="L945"></a><tt class="py-lineno"> 945</tt> <tt class="py-line"> </tt>
<a name="L946"></a><tt class="py-lineno"> 946</tt> <tt class="py-line"> </tt>
<a name="L947"></a><tt class="py-lineno"> 947</tt> <tt class="py-line"> </tt>
<a name="L948"></a><tt class="py-lineno"> 948</tt> <tt class="py-line"> </tt>
<a name="L949"></a><tt class="py-lineno"> 949</tt> <tt class="py-line"> </tt>
<a name="returnIndex"></a><div id="returnIndex-def"><a name="L950"></a><tt class="py-lineno"> 950</tt> <a class="py-toggle" href="#" id="returnIndex-toggle" onclick="return toggle('returnIndex');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#returnIndex">returnIndex</a><tt class="py-op">(</tt><tt class="py-param">readdic</tt><tt class="py-op">,</tt> <tt class="py-param">readname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="returnIndex-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="returnIndex-expanded"><a name="L951"></a><tt class="py-lineno"> 951</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L952"></a><tt class="py-lineno"> 952</tt> <tt class="py-line"><tt class="py-docstring"> Returns the index of a read. The index is prescribed by the ordering in the sam file.</tt> </tt>
<a name="L953"></a><tt class="py-lineno"> 953</tt> <tt class="py-line"><tt class="py-docstring"> @type readname: string</tt> </tt>
<a name="L954"></a><tt class="py-lineno"> 954</tt> <tt class="py-line"><tt class="py-docstring"> @param readname: read id</tt> </tt>
<a name="L955"></a><tt class="py-lineno"> 955</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L956"></a><tt class="py-lineno"> 956</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: dictionary containing read ids and read qualities.ArtRead</tt> </tt>
<a name="L957"></a><tt class="py-lineno"> 957</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L958"></a><tt class="py-lineno"> 958</tt> <tt class="py-line"><tt class="py-docstring"> @return: index</tt> </tt>
<a name="L959"></a><tt class="py-lineno"> 959</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L960"></a><tt class="py-lineno"> 960</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">readdic</tt><tt class="py-op">[</tt><tt class="py-name">readname</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">internalID</tt><tt class="py-op">)</tt> </tt>
</div><a name="L961"></a><tt class="py-lineno"> 961</tt> <tt class="py-line"> </tt>
<a name="L962"></a><tt class="py-lineno"> 962</tt> <tt class="py-line"> </tt>
<a name="ReadArtificialSAMfileHTSeq"></a><div id="ReadArtificialSAMfileHTSeq-def"><a name="L963"></a><tt class="py-lineno"> 963</tt> <a class="py-toggle" href="#" id="ReadArtificialSAMfileHTSeq-toggle" onclick="return toggle('ReadArtificialSAMfileHTSeq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#ReadArtificialSAMfileHTSeq">ReadArtificialSAMfileHTSeq</a><tt class="py-op">(</tt><tt class="py-param">art</tt><tt class="py-op">,</tt> <tt class="py-param">compareList</tt><tt class="py-op">,</tt> <tt class="py-param">RefArray</tt><tt class="py-op">,</tt> <tt class="py-param">readdic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReadArtificialSAMfileHTSeq-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="ReadArtificialSAMfileHTSeq-expanded"><a name="L964"></a><tt class="py-lineno"> 964</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L965"></a><tt class="py-lineno"> 965</tt> <tt class="py-line"><tt class="py-docstring"> Function for reading the artificial reference genome using HTSeq.This function is mainly used. Only if no quality string is in the SAM line. The custom</tt> </tt>
<a name="L966"></a><tt class="py-lineno"> 966</tt> <tt class="py-line"><tt class="py-docstring"> SAM reading function is used.</tt> </tt>
<a name="L967"></a><tt class="py-lineno"> 967</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L968"></a><tt class="py-lineno"> 968</tt> <tt class="py-line"><tt class="py-docstring"> @type art: string</tt> </tt>
<a name="L969"></a><tt class="py-lineno"> 969</tt> <tt class="py-line"><tt class="py-docstring"> @param art: artificial file.</tt> </tt>
<a name="L970"></a><tt class="py-lineno"> 970</tt> <tt class="py-line"><tt class="py-docstring"> @type RefArray: array</tt> </tt>
<a name="L971"></a><tt class="py-lineno"> 971</tt> <tt class="py-line"><tt class="py-docstring"> @param RefArray: Results from reading the reference SAM file.</tt> </tt>
<a name="L972"></a><tt class="py-lineno"> 972</tt> <tt class="py-line"><tt class="py-docstring"> @type compareList: list</tt> </tt>
<a name="L973"></a><tt class="py-lineno"> 973</tt> <tt class="py-line"><tt class="py-docstring"> @param compareList: list containt 1s, where there is a difference in the genomes and 0s where the nucleotides are equal.</tt> </tt>
<a name="L974"></a><tt class="py-lineno"> 974</tt> <tt class="py-line"><tt class="py-docstring"> @type readdic: dictionary</tt> </tt>
<a name="L975"></a><tt class="py-lineno"> 975</tt> <tt class="py-line"><tt class="py-docstring"> @param readdic: dictionary containing read ids and read qualities.</tt> </tt>
<a name="L976"></a><tt class="py-lineno"> 976</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: array</tt> </tt>
<a name="L977"></a><tt class="py-lineno"> 977</tt> <tt class="py-line"><tt class="py-docstring"> @return: aligned read objects in an array.</tt> </tt>
<a name="L978"></a><tt class="py-lineno"> 978</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L979"></a><tt class="py-lineno"> 979</tt> <tt class="py-line"> <tt class="py-name">start</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L980"></a><tt class="py-lineno"> 980</tt> <tt class="py-line"> <tt class="py-comment">#print ("\tARTIFICIAL:")</tt> </tt>
<a name="L981"></a><tt class="py-lineno"> 981</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">art</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
<a name="L982"></a><tt class="py-lineno"> 982</tt> <tt class="py-line"> <tt class="py-name">artdic</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L983"></a><tt class="py-lineno"> 983</tt> <tt class="py-line"> <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L984"></a><tt class="py-lineno"> 984</tt> <tt class="py-line"> </tt>
<a name="L985"></a><tt class="py-lineno"> 985</tt> <tt class="py-line"> <tt class="py-name">read</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="core.AnalyseMapping.SkipHeader" class="py-name" href="#" onclick="return doclink('link-62', 'SkipHeader', 'link-22');">SkipHeader</a></tt><tt class="py-op">(</tt><tt class="py-name">fobj</tt><tt class="py-op">,</tt><tt class="py-name">compareList</tt><tt class="py-op">,</tt><tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L986"></a><tt class="py-lineno"> 986</tt> <tt class="py-line"> </tt>
<a name="L987"></a><tt class="py-lineno"> 987</tt> <tt class="py-line"> </tt>
<a name="L988"></a><tt class="py-lineno"> 988</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">alignment</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fobj</tt><tt class="py-op">:</tt> </tt>
<a name="L989"></a><tt class="py-lineno"> 989</tt> <tt class="py-line"> <tt class="py-name">k</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L990"></a><tt class="py-lineno"> 990</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">k</tt> <tt class="py-op">%</tt> <tt class="py-number">1000000</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L991"></a><tt class="py-lineno"> 991</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"%d.."</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">/</tt><tt class="py-number">1000000</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L992"></a><tt class="py-lineno"> 992</tt> <tt class="py-line"> <tt class="py-name">read</tt><tt class="py-op">,</tt> <tt class="py-name">readname</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name" targets="Function core.AnalyseMapping.isSaneAlignment()=core.AnalyseMapping-module.html#isSaneAlignment"><a title="core.AnalyseMapping.isSaneAlignment" class="py-name" href="#" onclick="return doclink('link-63', 'isSaneAlignment', 'link-63');">isSaneAlignment</a></tt><tt class="py-op">(</tt><tt class="py-name">alignment</tt><tt class="py-op">,</tt> <tt class="py-string">"art"</tt><tt class="py-op">,</tt> <tt class="py-name">compareList</tt><tt class="py-op">,</tt> <tt class="py-name">readdic</tt><tt class="py-op">)</tt> </tt>
<a name="L993"></a><tt class="py-lineno"> 993</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">read</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L994"></a><tt class="py-lineno"> 994</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L995"></a><tt class="py-lineno"> 995</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L996"></a><tt class="py-lineno"> 996</tt> <tt class="py-line"> <tt class="py-comment"># Check by internal naming if spot in array is taken (!= 0) by a read</tt> </tt>
<a name="L997"></a><tt class="py-lineno"> 997</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name" targets="Function core.AnalyseMapping.returnIndex()=core.AnalyseMapping-module.html#returnIndex"><a title="core.AnalyseMapping.returnIndex" class="py-name" href="#" onclick="return doclink('link-64', 'returnIndex', 'link-64');">returnIndex</a></tt><tt class="py-op">(</tt><tt class="py-name">readdic</tt><tt class="py-op">,</tt> <tt class="py-name">readname</tt><tt class="py-op">)</tt> </tt>
<a name="L998"></a><tt class="py-lineno"> 998</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L999"></a><tt class="py-lineno"> 999</tt> <tt class="py-line"> <tt class="py-comment"># read already in dic? Check if the alignments are the same</tt> </tt>
<a name="L1000"></a><tt class="py-lineno">1000</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Method core.AnalyseMapping.TPRead.isContained()=core.AnalyseMapping.TPRead-class.html#isContained"><a title="core.AnalyseMapping.TPRead.isContained" class="py-name" href="#" onclick="return doclink('link-65', 'isContained', 'link-65');">isContained</a></tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1001"></a><tt class="py-lineno">1001</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">readname</tt> <tt class="py-keyword">in</tt> <tt class="py-name">artdic</tt><tt class="py-op">:</tt> </tt>
<a name="L1002"></a><tt class="py-lineno">1002</tt> <tt class="py-line"> <tt class="py-name">artdic</tt><tt class="py-op">[</tt><tt class="py-name">readname</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method core.AnalyseMapping.CustomRead.toObjself()=core.AnalyseMapping.CustomRead-class.html#toObjself,Method core.AnalyseMapping.TPRead.toObjself()=core.AnalyseMapping.TPRead-class.html#toObjself"><a title="core.AnalyseMapping.CustomRead.toObjself
core.AnalyseMapping.TPRead.toObjself" class="py-name" href="#" onclick="return doclink('link-66', 'toObjself', 'link-66');">toObjself</a></tt><tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">)</tt> </tt>
<a name="L1003"></a><tt class="py-lineno">1003</tt> <tt class="py-line"> </tt>
<a name="L1004"></a><tt class="py-lineno">1004</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1005"></a><tt class="py-lineno">1005</tt> <tt class="py-line"> <tt class="py-name">artdic</tt><tt class="py-op">[</tt><tt class="py-name">readname</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">read</tt> </tt>
<a name="L1006"></a><tt class="py-lineno">1006</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1007"></a><tt class="py-lineno">1007</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L1008"></a><tt class="py-lineno">1008</tt> <tt class="py-line"> </tt>
<a name="L1009"></a><tt class="py-lineno">1009</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1010"></a><tt class="py-lineno">1010</tt> <tt class="py-line"> <tt class="py-comment"># new read? Just add it to the dictionary</tt> </tt>
<a name="L1011"></a><tt class="py-lineno">1011</tt> <tt class="py-line"> <tt class="py-name">artdic</tt><tt class="py-op">[</tt><tt class="py-name">readname</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">read</tt> </tt>
<a name="L1012"></a><tt class="py-lineno">1012</tt> <tt class="py-line"> </tt>
<a name="L1013"></a><tt class="py-lineno">1013</tt> <tt class="py-line"> </tt>
<a name="L1014"></a><tt class="py-lineno">1014</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1015"></a><tt class="py-lineno">1015</tt> <tt class="py-line"> <tt class="py-name">end</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1016"></a><tt class="py-lineno">1016</tt> <tt class="py-line"> <tt class="py-comment">#print("\r\n")</tt> </tt>
<a name="L1017"></a><tt class="py-lineno">1017</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"\t %f "</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">end</tt> <tt class="py-op">-</tt> <tt class="py-name">start</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L1018"></a><tt class="py-lineno">1018</tt> <tt class="py-line"> <tt class="py-comment">#print ("\tdone in %d seconds" % (end-start))</tt> </tt>
<a name="L1019"></a><tt class="py-lineno">1019</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">artdic</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1020"></a><tt class="py-lineno">1020</tt> <tt class="py-line"> </tt>
<a name="L1021"></a><tt class="py-lineno">1021</tt> <tt class="py-line"> </tt>
<a name="L1022"></a><tt class="py-lineno">1022</tt> <tt class="py-line"> </tt>
<a name="writeToTabArt"></a><div id="writeToTabArt-def"><a name="L1023"></a><tt class="py-lineno">1023</tt> <a class="py-toggle" href="#" id="writeToTabArt-toggle" onclick="return toggle('writeToTabArt');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#writeToTabArt">writeToTabArt</a><tt class="py-op">(</tt><tt class="py-param">ReadDic</tt><tt class="py-op">,</tt> <tt class="py-param">outfile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="writeToTabArt-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="writeToTabArt-expanded"><a name="L1024"></a><tt class="py-lineno">1024</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L1025"></a><tt class="py-lineno">1025</tt> <tt class="py-line"><tt class="py-docstring"> Write function for hits ont he reference genome. Only the best alignment (least mismatches)</tt> </tt>
<a name="L1026"></a><tt class="py-lineno">1026</tt> <tt class="py-line"><tt class="py-docstring"> Header :</tt> </tt>
<a name="L1027"></a><tt class="py-lineno">1027</tt> <tt class="py-line"><tt class="py-docstring"> ReadID MatchedReference Substitutions NumberOfMismatches ReadQuality MappingQuality</tt> </tt>
<a name="L1028"></a><tt class="py-lineno">1028</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L1029"></a><tt class="py-lineno">1029</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1030"></a><tt class="py-lineno">1030</tt> <tt class="py-line"><tt class="py-docstring"> @type outfile: string</tt> </tt>
<a name="L1031"></a><tt class="py-lineno">1031</tt> <tt class="py-line"><tt class="py-docstring"> @param outfile: Path to outfile.</tt> </tt>
<a name="L1032"></a><tt class="py-lineno">1032</tt> <tt class="py-line"><tt class="py-docstring"> @type ReadDic: dictionary</tt> </tt>
<a name="L1033"></a><tt class="py-lineno">1033</tt> <tt class="py-line"><tt class="py-docstring"> @param ReadDic: dictionary containing read ids and read qualities.</tt> </tt>
<a name="L1034"></a><tt class="py-lineno">1034</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L1035"></a><tt class="py-lineno">1035</tt> <tt class="py-line"> </tt>
<a name="L1036"></a><tt class="py-lineno">1036</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">,</tt> <tt class="py-string">"a"</tt><tt class="py-op">)</tt> </tt>
<a name="L1037"></a><tt class="py-lineno">1037</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">read</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1038"></a><tt class="py-lineno">1038</tt> <tt class="py-line"> <tt class="py-name">BestReadIndex</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">argmin</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1039"></a><tt class="py-lineno">1039</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">read</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">subs</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ReadDic</tt><tt class="py-op">[</tt><tt class="py-name">read</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1040"></a><tt class="py-lineno">1040</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1041"></a><tt class="py-lineno">1041</tt> <tt class="py-line"> </tt>
<a name="L1042"></a><tt class="py-lineno">1042</tt> <tt class="py-line"> </tt>
<a name="L1043"></a><tt class="py-lineno">1043</tt> <tt class="py-line"> </tt>
<a name="L1044"></a><tt class="py-lineno">1044</tt> <tt class="py-line"> </tt>
<a name="writeToTabRef"></a><div id="writeToTabRef-def"><a name="L1045"></a><tt class="py-lineno">1045</tt> <a class="py-toggle" href="#" id="writeToTabRef-toggle" onclick="return toggle('writeToTabRef');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#writeToTabRef">writeToTabRef</a><tt class="py-op">(</tt><tt class="py-param">RefArray</tt><tt class="py-op">,</tt> <tt class="py-param">outfile</tt><tt class="py-op">,</tt> <tt class="py-param">reverseReadArray</tt><tt class="py-op">,</tt> <tt class="py-param">ReadDic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="writeToTabRef-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="writeToTabRef-expanded"><a name="L1046"></a><tt class="py-lineno">1046</tt> <tt class="py-line"> <tt class="py-docstring">""" </tt> </tt>
<a name="L1047"></a><tt class="py-lineno">1047</tt> <tt class="py-line"><tt class="py-docstring"> Write function for hits ont he reference genome. Only the best alignment (least mismatches)</tt> </tt>
<a name="L1048"></a><tt class="py-lineno">1048</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L1049"></a><tt class="py-lineno">1049</tt> <tt class="py-line"><tt class="py-docstring"> Header :</tt> </tt>
<a name="L1050"></a><tt class="py-lineno">1050</tt> <tt class="py-line"><tt class="py-docstring"> ReadID MatchedReference Substitutions NumberOfMismatches ReadQuality MappingQuality</tt> </tt>
<a name="L1051"></a><tt class="py-lineno">1051</tt> <tt class="py-line"><tt class="py-docstring"> rows in the infile</tt> </tt>
<a name="L1052"></a><tt class="py-lineno">1052</tt> <tt class="py-line"><tt class="py-docstring"> @type RefArray: string</tt> </tt>
<a name="L1053"></a><tt class="py-lineno">1053</tt> <tt class="py-line"><tt class="py-docstring"> @param RefArray: path to inputfile.</tt> </tt>
<a name="L1054"></a><tt class="py-lineno">1054</tt> <tt class="py-line"><tt class="py-docstring"> @type outfile: int</tt> </tt>
<a name="L1055"></a><tt class="py-lineno">1055</tt> <tt class="py-line"><tt class="py-docstring"> @param outfile: rows in the infile</tt> </tt>
<a name="L1056"></a><tt class="py-lineno">1056</tt> <tt class="py-line"><tt class="py-docstring"> @type reverseReadArray: dictionary</tt> </tt>
<a name="L1057"></a><tt class="py-lineno">1057</tt> <tt class="py-line"><tt class="py-docstring"> @param reverseReadArray: Contains reads = values and ranks = keys</tt> </tt>
<a name="L1058"></a><tt class="py-lineno">1058</tt> <tt class="py-line"><tt class="py-docstring"> @type ReadDic: dictionary</tt> </tt>
<a name="L1059"></a><tt class="py-lineno">1059</tt> <tt class="py-line"><tt class="py-docstring"> @param ReadDic: dictionary containing read ids and read qualities.</tt> </tt>
<a name="L1060"></a><tt class="py-lineno">1060</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L1061"></a><tt class="py-lineno">1061</tt> <tt class="py-line"> </tt>
<a name="L1062"></a><tt class="py-lineno">1062</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">,</tt> <tt class="py-string">"a"</tt><tt class="py-op">)</tt> </tt>
<a name="L1063"></a><tt class="py-lineno">1063</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">RefArray</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1064"></a><tt class="py-lineno">1064</tt> <tt class="py-line"> <tt class="py-name">read</tt> <tt class="py-op">=</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L1065"></a><tt class="py-lineno">1065</tt> <tt class="py-line"> <tt class="py-comment"># check if entry == 0</tt> </tt>
<a name="L1066"></a><tt class="py-lineno">1066</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">read</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L1067"></a><tt class="py-lineno">1067</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L1068"></a><tt class="py-lineno">1068</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1069"></a><tt class="py-lineno">1069</tt> <tt class="py-line"> <tt class="py-name">readname</tt> <tt class="py-op">=</tt> <tt class="py-name">reverseReadArray</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L1070"></a><tt class="py-lineno">1070</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="core.AnalyseMapping.returnIndex" class="py-name" href="#" onclick="return doclink('link-67', 'returnIndex', 'link-64');">returnIndex</a></tt><tt class="py-op">(</tt><tt class="py-name">ReadDic</tt><tt class="py-op">,</tt> <tt class="py-name">readname</tt><tt class="py-op">)</tt> </tt>
<a name="L1071"></a><tt class="py-lineno">1071</tt> <tt class="py-line"> <tt class="py-name">BestReadIndex</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">,</tt><tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">argmin</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1072"></a><tt class="py-lineno">1072</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">readname</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">start</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">end</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">RefArray</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-name">BestReadIndex</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1073"></a><tt class="py-lineno">1073</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1074"></a><tt class="py-lineno">1074</tt> <tt class="py-line"> </tt>
<a name="L1075"></a><tt class="py-lineno">1075</tt> <tt class="py-line"> </tt>
<a name="L1076"></a><tt class="py-lineno">1076</tt> <tt class="py-line"> </tt>
<a name="ReadFromTab"></a><div id="ReadFromTab-def"><a name="L1077"></a><tt class="py-lineno">1077</tt> <a class="py-toggle" href="#" id="ReadFromTab-toggle" onclick="return toggle('ReadFromTab');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#ReadFromTab">ReadFromTab</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">arraysize</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReadFromTab-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="ReadFromTab-expanded"><a name="L1078"></a><tt class="py-lineno">1078</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L1079"></a><tt class="py-lineno">1079</tt> <tt class="py-line"><tt class="py-docstring"> Reads the results from writeToTab in for plotting and analysis</tt> </tt>
<a name="L1080"></a><tt class="py-lineno">1080</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L1081"></a><tt class="py-lineno">1081</tt> <tt class="py-line"><tt class="py-docstring"> Header :</tt> </tt>
<a name="L1082"></a><tt class="py-lineno">1082</tt> <tt class="py-line"><tt class="py-docstring"> ReadID MatchedReference Substitutions NumberOfMismatches ReadQuality MappingQuality</tt> </tt>
<a name="L1083"></a><tt class="py-lineno">1083</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L1084"></a><tt class="py-lineno">1084</tt> <tt class="py-line"><tt class="py-docstring"> @type infile: string</tt> </tt>
<a name="L1085"></a><tt class="py-lineno">1085</tt> <tt class="py-line"><tt class="py-docstring"> @param infile: path to inputfile.</tt> </tt>
<a name="L1086"></a><tt class="py-lineno">1086</tt> <tt class="py-line"><tt class="py-docstring"> @type arraysize: int</tt> </tt>
<a name="L1087"></a><tt class="py-lineno">1087</tt> <tt class="py-line"><tt class="py-docstring"> @param arraysize: rows in the infile</tt> </tt>
<a name="L1088"></a><tt class="py-lineno">1088</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1089"></a><tt class="py-lineno">1089</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: np.array(obj)</tt> </tt>
<a name="L1090"></a><tt class="py-lineno">1090</tt> <tt class="py-line"><tt class="py-docstring"> @return: array for unique classified reads.</tt> </tt>
<a name="L1091"></a><tt class="py-lineno">1091</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L1092"></a><tt class="py-lineno">1092</tt> <tt class="py-line"> </tt>
<a name="L1093"></a><tt class="py-lineno">1093</tt> <tt class="py-line"> </tt>
<a name="L1094"></a><tt class="py-lineno">1094</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
<a name="L1095"></a><tt class="py-lineno">1095</tt> <tt class="py-line"> <tt class="py-name">dataArray</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">arraysize</tt><tt class="py-op">,</tt> <tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-name">object</tt><tt class="py-op">)</tt> </tt>
<a name="L1096"></a><tt class="py-lineno">1096</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">fobj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1097"></a><tt class="py-lineno">1097</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"#"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1098"></a><tt class="py-lineno">1098</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L1099"></a><tt class="py-lineno">1099</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1100"></a><tt class="py-lineno">1100</tt> <tt class="py-line"> <tt class="py-name">zeile</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L1101"></a><tt class="py-lineno">1101</tt> <tt class="py-line"> <tt class="py-name">id</tt> <tt class="py-op">=</tt> <tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L1102"></a><tt class="py-lineno">1102</tt> <tt class="py-line"> <tt class="py-name">mr</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1103"></a><tt class="py-lineno">1103</tt> <tt class="py-line"> <tt class="py-name">subs</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1104"></a><tt class="py-lineno">1104</tt> <tt class="py-line"> <tt class="py-name">nm</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1105"></a><tt class="py-lineno">1105</tt> <tt class="py-line"> <tt class="py-name">rq</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1106"></a><tt class="py-lineno">1106</tt> <tt class="py-line"> <tt class="py-name">mq</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1107"></a><tt class="py-lineno">1107</tt> <tt class="py-line"> <tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1108"></a><tt class="py-lineno">1108</tt> <tt class="py-line"> <tt class="py-name">mism</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1109"></a><tt class="py-lineno">1109</tt> <tt class="py-line"> <tt class="py-comment">#n = int(zeile[10].strip())</tt> </tt>
<a name="L1110"></a><tt class="py-lineno">1110</tt> <tt class="py-line"> <tt class="py-comment"># id is not needed for the analysis </tt> </tt>
<a name="L1111"></a><tt class="py-lineno">1111</tt> <tt class="py-line"> <tt class="py-name">dataArray</tt><tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="core.AnalyseMapping.CustomRead" class="py-name" href="#" onclick="return doclink('link-68', 'CustomRead', 'link-6');">CustomRead</a></tt><tt class="py-op">(</tt><tt class="py-name">id</tt><tt class="py-op">,</tt> <tt class="py-name">mr</tt><tt class="py-op">,</tt> <tt class="py-name">nm</tt><tt class="py-op">,</tt> <tt class="py-name">subs</tt><tt class="py-op">,</tt> <tt class="py-name">rq</tt><tt class="py-op">,</tt> <tt class="py-name">mq</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">mism</tt><tt class="py-op">)</tt> </tt>
<a name="L1112"></a><tt class="py-lineno">1112</tt> <tt class="py-line"> </tt>
<a name="L1113"></a><tt class="py-lineno">1113</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1114"></a><tt class="py-lineno">1114</tt> <tt class="py-line"> </tt>
<a name="L1115"></a><tt class="py-lineno">1115</tt> <tt class="py-line"> </tt>
<a name="L1116"></a><tt class="py-lineno">1116</tt> <tt class="py-line"> </tt>
<a name="readInput"></a><div id="readInput-def"><a name="L1117"></a><tt class="py-lineno">1117</tt> <a class="py-toggle" href="#" id="readInput-toggle" onclick="return toggle('readInput');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#readInput">readInput</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="readInput-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="readInput-expanded"><a name="L1118"></a><tt class="py-lineno">1118</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L1119"></a><tt class="py-lineno">1119</tt> <tt class="py-line"><tt class="py-docstring"> Function for reading in the controldictionary from the inputfile.</tt> </tt>
<a name="L1120"></a><tt class="py-lineno">1120</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1121"></a><tt class="py-lineno">1121</tt> <tt class="py-line"><tt class="py-docstring"> @type file: string </tt> </tt>
<a name="L1122"></a><tt class="py-lineno">1122</tt> <tt class="py-line"><tt class="py-docstring"> @param file: Path to the input file.</tt> </tt>
<a name="L1123"></a><tt class="py-lineno">1123</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L1124"></a><tt class="py-lineno">1124</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: files</tt> </tt>
<a name="L1125"></a><tt class="py-lineno">1125</tt> <tt class="py-line"><tt class="py-docstring"> @return: Controldictionary which is used to regulate the programs workflow.</tt> </tt>
<a name="L1126"></a><tt class="py-lineno">1126</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L1127"></a><tt class="py-lineno">1127</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L1128"></a><tt class="py-lineno">1128</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
<a name="L1129"></a><tt class="py-lineno">1129</tt> <tt class="py-line"> <tt class="py-name">files</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1130"></a><tt class="py-lineno">1130</tt> <tt class="py-line"> <tt class="py-name">files</tt><tt class="py-op">[</tt><tt class="py-string">"mapper"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1131"></a><tt class="py-lineno">1131</tt> <tt class="py-line"> <tt class="py-name">files</tt><tt class="py-op">[</tt><tt class="py-string">"fasta"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1132"></a><tt class="py-lineno">1132</tt> <tt class="py-line"> <tt class="py-name">tempref</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1133"></a><tt class="py-lineno">1133</tt> <tt class="py-line"> <tt class="py-name">temparg</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1134"></a><tt class="py-lineno">1134</tt> <tt class="py-line"> <tt class="py-name">reffasta</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L1135"></a><tt class="py-lineno">1135</tt> <tt class="py-line"> <tt class="py-name">artfasta</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1136"></a><tt class="py-lineno">1136</tt> <tt class="py-line"> </tt>
<a name="L1137"></a><tt class="py-lineno">1137</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fobj</tt><tt class="py-op">:</tt> </tt>
<a name="L1138"></a><tt class="py-lineno">1138</tt> <tt class="py-line"> <tt class="py-comment"># reference</tt> </tt>
<a name="L1139"></a><tt class="py-lineno">1139</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"$"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1140"></a><tt class="py-lineno">1140</tt> <tt class="py-line"> <tt class="py-name">files</tt><tt class="py-op">[</tt><tt class="py-string">"fasta"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"reffasta"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name" targets="Function core.AnalyseMapping.GetCompletePath()=core.AnalyseMapping-module.html#GetCompletePath"><a title="core.AnalyseMapping.GetCompletePath" class="py-name" href="#" onclick="return doclink('link-69', 'GetCompletePath', 'link-69');">GetCompletePath</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1141"></a><tt class="py-lineno">1141</tt> <tt class="py-line"> <tt class="py-comment"># artificial</tt> </tt>
<a name="L1142"></a><tt class="py-lineno">1142</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"#"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1143"></a><tt class="py-lineno">1143</tt> <tt class="py-line"> <tt class="py-name">artfasta</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="core.AnalyseMapping.GetCompletePath" class="py-name" href="#" onclick="return doclink('link-70', 'GetCompletePath', 'link-69');">GetCompletePath</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1144"></a><tt class="py-lineno">1144</tt> <tt class="py-line"> <tt class="py-comment"># fastq file</tt> </tt>
<a name="L1145"></a><tt class="py-lineno">1145</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"&"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1146"></a><tt class="py-lineno">1146</tt> <tt class="py-line"> <tt class="py-name">files</tt><tt class="py-op">[</tt><tt class="py-string">"fastqfile"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="core.AnalyseMapping.GetCompletePath" class="py-name" href="#" onclick="return doclink('link-71', 'GetCompletePath', 'link-69');">GetCompletePath</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1147"></a><tt class="py-lineno">1147</tt> <tt class="py-line"> <tt class="py-comment"># start sequence for mapper section</tt> </tt>
<a name="L1148"></a><tt class="py-lineno">1148</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"@"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1149"></a><tt class="py-lineno">1149</tt> <tt class="py-line"> <tt class="py-name">zeile</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L1150"></a><tt class="py-lineno">1150</tt> <tt class="py-line"> <tt class="py-name">mapper</tt> <tt class="py-op">=</tt> <tt class="py-name">zeile</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1151"></a><tt class="py-lineno">1151</tt> <tt class="py-line"> <tt class="py-name">files</tt><tt class="py-op">[</tt><tt class="py-string">"fasta"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"artfasta"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">artfasta</tt> </tt>
<a name="L1152"></a><tt class="py-lineno">1152</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1153"></a><tt class="py-lineno">1153</tt> <tt class="py-line"> <tt class="py-name">tempref</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="core.AnalyseMapping.GetCompletePath" class="py-name" href="#" onclick="return doclink('link-72', 'GetCompletePath', 'link-69');">GetCompletePath</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1154"></a><tt class="py-lineno">1154</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"art"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1155"></a><tt class="py-lineno">1155</tt> <tt class="py-line"> <tt class="py-name">temparg</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="core.AnalyseMapping.GetCompletePath" class="py-name" href="#" onclick="return doclink('link-73', 'GetCompletePath', 'link-69');">GetCompletePath</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1156"></a><tt class="py-lineno">1156</tt> <tt class="py-line"> <tt class="py-comment"># end of mapper section</tt> </tt>
<a name="L1157"></a><tt class="py-lineno">1157</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"+"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1158"></a><tt class="py-lineno">1158</tt> <tt class="py-line"> <tt class="py-name">files</tt><tt class="py-op">[</tt><tt class="py-string">"mapper"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">mapper</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">tempref</tt><tt class="py-op">,</tt> <tt class="py-name">temparg</tt><tt class="py-op">]</tt> </tt>
<a name="L1159"></a><tt class="py-lineno">1159</tt> <tt class="py-line"> <tt class="py-name">tempref</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1160"></a><tt class="py-lineno">1160</tt> <tt class="py-line"> <tt class="py-name">temparg</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1161"></a><tt class="py-lineno">1161</tt> <tt class="py-line"> </tt>
<a name="L1162"></a><tt class="py-lineno">1162</tt> <tt class="py-line"> </tt>
<a name="L1163"></a><tt class="py-lineno">1163</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1164"></a><tt class="py-lineno">1164</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">files</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1165"></a><tt class="py-lineno">1165</tt> <tt class="py-line"> </tt>
<a name="GetCompletePath"></a><div id="GetCompletePath-def"><a name="L1166"></a><tt class="py-lineno">1166</tt> <a class="py-toggle" href="#" id="GetCompletePath-toggle" onclick="return toggle('GetCompletePath');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#GetCompletePath">GetCompletePath</a><tt class="py-op">(</tt><tt class="py-param">path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GetCompletePath-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="GetCompletePath-expanded"><a name="L1167"></a><tt class="py-lineno">1167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"~"</tt><tt class="py-op">,</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">expanduser</tt><tt class="py-op">(</tt><tt class="py-string">"~"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1168"></a><tt class="py-lineno">1168</tt> <tt class="py-line"> </tt>
<a name="initOutFiles"></a><div id="initOutFiles-def"><a name="L1169"></a><tt class="py-lineno">1169</tt> <a class="py-toggle" href="#" id="initOutFiles-toggle" onclick="return toggle('initOutFiles');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.AnalyseMapping-module.html#initOutFiles">initOutFiles</a><tt class="py-op">(</tt><tt class="py-param">controlDic</tt><tt class="py-op">,</tt> <tt class="py-param">mapper</tt><tt class="py-op">,</tt> <tt class="py-param">outpath</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="initOutFiles-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="initOutFiles-expanded"><a name="L1170"></a><tt class="py-lineno">1170</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L1171"></a><tt class="py-lineno">1171</tt> <tt class="py-line"><tt class="py-docstring"> Since we append in the program, we need to make sure no old files remain... </tt> </tt>
<a name="L1172"></a><tt class="py-lineno">1172</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1173"></a><tt class="py-lineno">1173</tt> <tt class="py-line"><tt class="py-docstring"> @type controlDic: dictionary </tt> </tt>
<a name="L1174"></a><tt class="py-lineno">1174</tt> <tt class="py-line"><tt class="py-docstring"> @param controlDic: dictionary containing future filenames.</tt> </tt>
<a name="L1175"></a><tt class="py-lineno">1175</tt> <tt class="py-line"><tt class="py-docstring"> @type mapper: string </tt> </tt>
<a name="L1176"></a><tt class="py-lineno">1176</tt> <tt class="py-line"><tt class="py-docstring"> @param mapper: current identifier mapper for which the results are written</tt> </tt>
<a name="L1177"></a><tt class="py-lineno">1177</tt> <tt class="py-line"><tt class="py-docstring"> @type outpath: string</tt> </tt>
<a name="L1178"></a><tt class="py-lineno">1178</tt> <tt class="py-line"><tt class="py-docstring"> @param outpath: existing path, where the outfiles will be written.</tt> </tt>
<a name="L1179"></a><tt class="py-lineno">1179</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L1180"></a><tt class="py-lineno">1180</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">artificial</tt> <tt class="py-keyword">in</tt> <tt class="py-name">controlDic</tt><tt class="py-op">[</tt><tt class="py-string">"mapper"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">mapper</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1181"></a><tt class="py-lineno">1181</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">artificial</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1182"></a><tt class="py-lineno">1182</tt> <tt class="py-line"> <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt class="py-name">mapper</tt> <tt class="py-op">+</tt> <tt class="py-string">"_"</tt> <tt class="py-op">+</tt> <tt class="py-name">artificial</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">".esam"</tt> </tt>
<a name="L1183"></a><tt class="py-lineno">1183</tt> <tt class="py-line"> <tt class="py-comment">#easy Sam output </tt> </tt>
<a name="L1184"></a><tt class="py-lineno">1184</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">outpath</tt> <tt class="py-op">+</tt> <tt class="py-name">outfile</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L1185"></a><tt class="py-lineno">1185</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"#ReadID\tMatchedReference\tSubstitutions\tNumberOfMismatches\tReadQuality\tMappingQuality\tStart\tEnd\tGaps\tMisM\r\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L1186"></a><tt class="py-lineno">1186</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1187"></a><tt class="py-lineno">1187</tt> <tt class="py-line"> </tt><script type="text/javascript">
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