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<a href="core-module.html">Package core</a> ::
Module ReadAndWrite
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<h1 class="epydoc">Source Code for <a href="core.ReadAndWrite-module.html">Module core.ReadAndWrite</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">'''
</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">Created 2012
</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">Contains various help functions which read or produce an input/ output
</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">@author: Sven Giese
</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">'''</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">os</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">HTSeq</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="readdna"></a><div id="readdna-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="readdna-toggle" onclick="return toggle('readdna');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.ReadAndWrite-module.html#readdna">readdna</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="readdna-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="readdna-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> Reads in the dna sequence of the given fasta
</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> @type filename: string
</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> @param filename: Fasta-file used as input.
</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: HTSeq Sequence object
</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> @return: Reference Fasta.
</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">chr</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">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">fasta</tt> <tt class="py-keyword">in</tt> <tt class="py-name">chr</tt><tt class="py-op">:</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-name">referenz</tt> <tt class="py-op">=</tt> <tt class="py-name">HTSeq</tt><tt class="py-op">.</tt><tt class="py-name">Sequence</tt><tt class="py-op">(</tt><tt class="py-name">fasta</tt><tt class="py-op">.</tt><tt class="py-name">seq</tt><tt class="py-op">,</tt><tt class="py-name">fasta</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">referenz</tt><tt class="py-op">)</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line">
</tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line">
</tt>
<a name="writefile"></a><div id="writefile-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="writefile-toggle" onclick="return toggle('writefile');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.ReadAndWrite-module.html#writefile">writefile</a><tt class="py-op">(</tt><tt class="py-param">sequenceObject</tt><tt class="py-op">,</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="writefile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="writefile-expanded"><a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> Writes a given sequence object to a fasta file.
</tt> </tt>
<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"> @type sequenceObject: HTSeq Sequence object
</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> @param sequenceObject: Reference sequence as fasta.
</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="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">outfasta</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">sequenceObject</tt><tt class="py-op">.</tt><tt class="py-name">write_to_fasta_file</tt><tt class="py-op">(</tt><tt class="py-name">outfasta</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">outfasta</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="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line">
</tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line">
</tt>
<a name="writeoverview"></a><div id="writeoverview-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="writeoverview-toggle" onclick="return toggle('writeoverview');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.ReadAndWrite-module.html#writeoverview">writeoverview</a><tt class="py-op">(</tt><tt class="py-param">Ndic_G</tt><tt class="py-op">,</tt><tt class="py-param">aadic_G</tt><tt class="py-op">,</tt><tt class="py-param">Ndic_AR</tt><tt class="py-op">,</tt><tt class="py-param">aadic_AR</tt><tt class="py-op">,</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="writeoverview-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="writeoverview-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> Creates the "delta" file for the comparison of the two chromosoms. This file contains the differences in nucleotide distribution between reference and artificial.
</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> input: nucleotid dictionary genom, aa dictionary genome, nucleotid dictionary artificial chromosom, aa dictionary, filename
</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> @type Ndic_G: dictionary
</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> @param Ndic_G: Nucleotid dictionary genom.
</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> @type aadic_G: dictionary
</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> @param aadic_G: AA dictionary genome.
</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> @type Ndic_AR: dictionary
</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> @param Ndic_AR: Nucleotid dictionary artificial.
</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> @type aadic_AR: dictionary
</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> @param aadic_AR: AA dictionary artificial
</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> @type filename: string
</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> @param filename: Output filename.
</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</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">filename</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</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">"NUC /AA \t Genom \t Artificial Reference \t Delta \n"</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line">
</tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">sum1</tt> <tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">sum2</tt><tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</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">Ndic_G</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="L65"></a><tt class="py-lineno"> 65</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">item</tt> <tt class="py-op">+</tt><tt class="py-string">"\t"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">Ndic_G</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\t"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">Ndic_AR</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\t"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">Ndic_G</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">Ndic_AR</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">sum1</tt> <tt class="py-op">+=</tt><tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">Ndic_G</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">Ndic_AR</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</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">str</tt><tt class="py-op">(</tt><tt class="py-name">sum1</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line">
</tt>
<a name="L69"></a><tt class="py-lineno"> 69</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">aadic_G</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="L70"></a><tt class="py-lineno"> 70</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">item</tt> <tt class="py-op">+</tt><tt class="py-string">"\t"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">aadic_G</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\t"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">aadic_AR</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\t"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">aadic_G</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">aadic_AR</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">sum2</tt> <tt class="py-op">+=</tt><tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">aadic_G</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">aadic_AR</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</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">str</tt><tt class="py-op">(</tt><tt class="py-name">sum2</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line">
</tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line">
</tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line">
</tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line">
</tt>
<a name="nucleotide_dist_seq"></a><div id="nucleotide_dist_seq-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="nucleotide_dist_seq-toggle" onclick="return toggle('nucleotide_dist_seq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.ReadAndWrite-module.html#nucleotide_dist_seq">nucleotide_dist_seq</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt><tt class="py-param">txt_file</tt><tt class="py-op">,</tt><tt class="py-param">shallwrite</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="nucleotide_dist_seq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="nucleotide_dist_seq-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> Writes the nucleotide distribution in a file and returns the dictionary. adjust s for % results.
</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> @type seq: string
</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> @param seq: Nucleotide sequence.
</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> @type txt_file: string
</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> @param txt_file: Output compare file.
</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> @type shallwrite: Bool
</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> @param shallwrite: Decides if percentages values are written to the output.
</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">Nndic</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">"A"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"C"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"G"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"T"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"N"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">}</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line">
</tt>
<a name="L89"></a><tt class="py-lineno"> 89</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">range</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">seq</tt><tt class="py-op">)</tt><tt class="py-op">)</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">Nndic</tt><tt class="py-op">[</tt><tt class="py-name">seq</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-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line">
</tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">shallwrite</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="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">output_file</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">txt_file</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</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">Nndic</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="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">Nndic</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">Nndic</tt><tt class="py-op">[</tt><tt class="py-name">item</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">s</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">output_file</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">item</tt> <tt class="py-op">+</tt> <tt class="py-string">"\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">Nndic</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line">
</tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">output_file</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="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</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">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">Nndic</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="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">Nndic</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">Nndic</tt><tt class="py-op">[</tt><tt class="py-name">item</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">s</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">Nndic</tt><tt class="py-op">)</tt> <tt class="py-comment">#N can be used for checking: should be the same number in real</tt> </tt>
</div><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-comment"># and artificial chromosome</tt>
</tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line">
</tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line">
</tt>
<a name="aa_dist_seq"></a><div id="aa_dist_seq-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="aa_dist_seq-toggle" onclick="return toggle('aa_dist_seq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.ReadAndWrite-module.html#aa_dist_seq">aa_dist_seq</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt><tt class="py-param">txt_file</tt><tt class="py-op">,</tt><tt class="py-param">shallwrite</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="aa_dist_seq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="aa_dist_seq-expanded"><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> Writes the AA distribution in a file and returns the dictionary. adjust s for % results.
</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> @type seq: string
</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> @param seq: Nucleotide sequence.
</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> @type txt_file: string
</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> @param txt_file: Output compare file.
</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> @type shallwrite: Bool
</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> @param shallwrite: Write output in percentages..
</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">aadic</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"A"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"R"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"N"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"D"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"C"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"E"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"Q"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"G"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"H"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"I"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"L"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"K"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"M"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"F"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"P"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"S"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"T"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"W"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"Y"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"V"</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 class="py-number">0</tt><tt class="py-op">}</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</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">range</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">seq</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<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 class="py-string">'''escape 'n' Sequences '''</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-name">aadic</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">aadic</tt><tt class="py-op">[</tt><tt class="py-name">seq</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-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line">
</tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line">
</tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">shallwrite</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="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">output_file</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">txt_file</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</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">aadic</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="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">aadic</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">aadic</tt><tt class="py-op">[</tt><tt class="py-name">item</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">n</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">output_file</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">item</tt> <tt class="py-op">+</tt> <tt class="py-string">"\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">aadic</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line">
</tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">output_file</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="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</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">aadic</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="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">aadic</tt><tt class="py-op">[</tt><tt class="py-name">item</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">aadic</tt><tt class="py-op">[</tt><tt class="py-name">item</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">n</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line">
</tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">aadic</tt><tt class="py-op">)</tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line">
</tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-string">'''
</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-string">input: DNA Sequence, outputfilename and 1/0 for writing/not writing outputfile '''</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line">
</tt>
<a name="nucleotide_dist_file"></a><div id="nucleotide_dist_file-def"><a name="L146"></a><tt class="py-lineno">146</tt> <a class="py-toggle" href="#" id="nucleotide_dist_file-toggle" onclick="return toggle('nucleotide_dist_file');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.ReadAndWrite-module.html#nucleotide_dist_file">nucleotide_dist_file</a><tt class="py-op">(</tt><tt class="py-param">file_fasta</tt><tt class="py-op">,</tt><tt class="py-param">txt_file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="nucleotide_dist_file-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="nucleotide_dist_file-expanded"><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> Writes the DNA distribution in a file and returns the dictionary. adjust n for % results
</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> @type file_fasta: string
</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> @param file_fasta: DNA Sequence
</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> @type txt_file: string
</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> @param txt_file: Filename for output.
</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">input_file</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">file_fasta</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">output_file</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">txt_file</tt><tt class="py-op">,</tt><tt class="py-string">'a'</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">seq</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</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">input_file</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</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-number">0</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-string">'>'</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">seq</tt><tt class="py-op">+=</tt><tt class="py-name">line</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">output_file</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-0" class="py-name" targets="Function core.ReadAndWrite.nucleotide_dist_seq()=core.ReadAndWrite-module.html#nucleotide_dist_seq"><a title="core.ReadAndWrite.nucleotide_dist_seq" class="py-name" href="#" onclick="return doclink('link-0', 'nucleotide_dist_seq', 'link-0');">nucleotide_dist_seq</a></tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">output_file</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">output_file</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="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">input_file</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="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line">
</tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line">
</tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-string">'''gets the number of missmatches between 2 sequences
</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-string">input: orig sequence, decoy sequence '''</tt> </tt>
<a name="gethammingdistance"></a><div id="gethammingdistance-def"><a name="L170"></a><tt class="py-lineno">170</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.ReadAndWrite-module.html#gethammingdistance">gethammingdistance</a><tt class="py-op">(</tt><tt class="py-param">original</tt><tt class="py-op">,</tt><tt class="py-param">artificial</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="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the hamming distances between two sequences.
</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> @type original: list
</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> @param original: Nucleotide sequence from the reference.
</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> @type artificial: list
</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> @param artificial: Nucleotide sequence from the artificial reference.
</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">hamming</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">not_hamming</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</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">range</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">original</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">original</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">artificial</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-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">hamming</tt> <tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line">
</tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">not_hamming</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"#hamming distance REF-ART\t"</tt><tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">hamming</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"avg. distance:\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">original</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">hamming</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">print</tt><tt class="py-op">(</tt><tt class="py-string">"###########################\r\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt><script type="text/javascript">
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