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<a href="Bio-module.html">Package Bio</a> ::
Module kNN
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<h1 class="epydoc">Source Code for <a href="Bio.kNN-module.html">Module Bio.kNN</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/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">This module provides code for doing k-nearest-neighbors classification.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">k Nearest Neighbors is a supervised learning algorithm that classifies</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">a new observation based the classes in its surrounding neighborhood.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">Glossary:</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">distance The distance between two points in the feature space.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">weight The importance given to each point for classification. </tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">kNN Holds information for a nearest neighbors classifier.</tt> </tt>
<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"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">train Train a new kNN classifier.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">calculate Calculate the probabilities of each class, given an observation.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">classify Classify an observation into a class.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> Weighting Functions:</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">equal_weight Every example is given a weight of 1.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-keyword">try</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">from</tt> <tt class="py-name">Numeric</tt> <tt class="py-keyword">import</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">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-0', 'x', 'link-0');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ImportError</tt><tt class="py-op">,</tt> <tt class="py-string">"This module requires Numeric (precursor to NumPy)"</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.listfns=Bio.listfns-module.html"><a title="Bio.listfns" class="py-name" href="#" onclick="return doclink('link-2', 'listfns', 'link-2');">listfns</a></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Method Bio.Nexus.Trees.Tree.distance()=Bio.Nexus.Trees.Tree-class.html#distance,Module Bio.distance=Bio.distance-module.html"><a title="Bio.Nexus.Trees.Tree.distance
Bio.distance" class="py-name" href="#" onclick="return doclink('link-4', 'distance', 'link-4');">distance</a></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="kNN"></a><div id="kNN-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="kNN-toggle" onclick="return toggle('kNN');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.kNN.kNN-class.html">kNN</a><tt class="py-op">:</tt> </tt>
</div><div id="kNN-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="kNN-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information necessary to do nearest neighbors classification.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> classes List of the possible classes.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> xs List of the neighbors.</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> ys List of the classes that the neighbors belong to.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> k Number of neighbors to look at.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="kNN.__init__"></a><div id="kNN.__init__-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="kNN.__init__-toggle" onclick="return toggle('kNN.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.kNN.kNN-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="kNN.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="kNN.__init__-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-docstring">"""kNN()"""</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">classes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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">xs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</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">ys</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div></div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="equal_weight"></a><div id="equal_weight-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="equal_weight-toggle" onclick="return toggle('equal_weight');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.kNN-module.html#equal_weight">equal_weight</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="equal_weight-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="equal_weight-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""equal_weight(x, y) -> 1"""</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-comment"># everything gets 1 vote</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="train"></a><div id="train-def"><a name="L57"></a><tt class="py-lineno"> 57</tt> <a class="py-toggle" href="#" id="train-toggle" onclick="return toggle('train');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.kNN-module.html#train">train</a><tt class="py-op">(</tt><tt class="py-param">xs</tt><tt class="py-op">,</tt> <tt class="py-param">ys</tt><tt class="py-op">,</tt> <tt class="py-param">k</tt><tt class="py-op">,</tt> <tt class="py-param">typecode</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="train-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="train-expanded"><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-docstring">"""train(xs, ys, k) -> kNN</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> Train a k nearest neighbors classifier on a training set. xs is a</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> list of observations and ys is a list of the class assignments.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> Thus, xs and ys should contain the same number of elements. k is</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> the number of neighbors that should be examined when doing the</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> classification.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">knn</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name" targets="Module Bio.kNN=Bio.kNN-module.html,Class Bio.kNN.kNN=Bio.kNN.kNN-class.html"><a title="Bio.kNN
Bio.kNN.kNN" class="py-name" href="#" onclick="return doclink('link-5', 'kNN', 'link-5');">kNN</a></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-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">classes</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.listfns" class="py-name" href="#" onclick="return doclink('link-6', 'listfns', 'link-2');">listfns</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-7', 'items', 'link-7');">items</a></tt><tt class="py-op">(</tt><tt class="py-name">ys</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">xs</tt> <tt class="py-op">=</tt> <tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">xs</tt><tt class="py-op">,</tt> <tt class="py-name">typecode</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">knn</tt><tt class="py-op">.</tt><tt class="py-name">ys</tt> <tt class="py-op">=</tt> <tt class="py-name">ys</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">knn</tt> </tt>
</div><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="calculate"></a><div id="calculate-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="calculate-toggle" onclick="return toggle('calculate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.kNN-module.html#calculate">calculate</a><tt class="py-op">(</tt><tt class="py-param">knn</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">weight_fn</tt><tt class="py-op">=</tt><tt id="link-8" class="py-name" targets="Function Bio.kNN.equal_weight()=Bio.kNN-module.html#equal_weight"><a title="Bio.kNN.equal_weight" class="py-name" href="#" onclick="return doclink('link-8', 'equal_weight', 'link-8');">equal_weight</a></tt><tt class="py-op">,</tt> <tt class="py-param">distance_fn</tt><tt class="py-op">=</tt><tt id="link-9" class="py-name"><a title="Bio.Nexus.Trees.Tree.distance
Bio.distance" class="py-name" href="#" onclick="return doclink('link-9', 'distance', 'link-4');">distance</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Function Bio.distance.euclidean()=Bio.distance-module.html#euclidean"><a title="Bio.distance.euclidean" class="py-name" href="#" onclick="return doclink('link-10', 'euclidean', 'link-10');">euclidean</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="calculate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="calculate-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-docstring">"""calculate(knn, x[, weight_fn][, distance_fn]) -> weight dict</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> Calculate the probability for each class. knn is a kNN object. x</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> is the observed data. weight_fn is an optional function that</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> takes x and a training example, and returns a weight. distance_fn</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> is an optional function that takes two points and returns the</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> distance between them. Returns a dictionary of the class to the</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> weight given to the class.</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-11', 'x', 'link-0');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-12', 'x', 'link-0');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">order</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># list of (distance, index)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-13" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-13', 'i', 'link-13');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">xs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">distance_fn</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-14', 'x', 'link-0');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">xs</tt><tt class="py-op">[</tt><tt id="link-15" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-15', 'i', 'link-13');">i</a></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">order</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-16', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">dist</tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-17', 'i', 'link-13');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">order</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-18', 'sort', 'link-18');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># first 'k' are the ones I want.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">weights</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># class -> number of votes</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</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">knn</tt><tt class="py-op">.</tt><tt class="py-name">classes</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">weights</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-number">0.0</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">dist</tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-19', 'i', 'link-13');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">order</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">k</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">klass</tt> <tt class="py-op">=</tt> <tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">ys</tt><tt class="py-op">[</tt><tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-20', 'i', 'link-13');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-name">klass</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-name">klass</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">weight_fn</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-0');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">knn</tt><tt class="py-op">.</tt><tt class="py-name">xs</tt><tt class="py-op">[</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-22', 'i', 'link-13');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">weights</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="classify"></a><div id="classify-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="classify-toggle" onclick="return toggle('classify');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.kNN-module.html#classify">classify</a><tt class="py-op">(</tt><tt class="py-param">knn</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">weight_fn</tt><tt class="py-op">=</tt><tt id="link-23" class="py-name"><a title="Bio.kNN.equal_weight" class="py-name" href="#" onclick="return doclink('link-23', 'equal_weight', 'link-8');">equal_weight</a></tt><tt class="py-op">,</tt> <tt class="py-param">distance_fn</tt><tt class="py-op">=</tt><tt id="link-24" class="py-name"><a title="Bio.Nexus.Trees.Tree.distance
Bio.distance" class="py-name" href="#" onclick="return doclink('link-24', 'distance', 'link-4');">distance</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.distance.euclidean" class="py-name" href="#" onclick="return doclink('link-25', 'euclidean', 'link-10');">euclidean</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="classify-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="classify-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"""classify(knn, x[, weight_fn][, distance_fn]) -> class</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> Classify an observation into a class. If not specified, weight_fn will</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> give all neighbors equal weight and distance_fn will be the euclidean</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> distance.</tt> </tt>
<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"> """</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">weights</tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name" targets="Function Bio.LogisticRegression.calculate()=Bio.LogisticRegression-module.html#calculate,Function Bio.MaxEntropy.calculate()=Bio.MaxEntropy-module.html#calculate,Function Bio.NaiveBayes.calculate()=Bio.NaiveBayes-module.html#calculate,Function Bio.kNN.calculate()=Bio.kNN-module.html#calculate"><a title="Bio.LogisticRegression.calculate
Bio.MaxEntropy.calculate
Bio.NaiveBayes.calculate
Bio.kNN.calculate" class="py-name" href="#" onclick="return doclink('link-26', 'calculate', 'link-26');">calculate</a></tt><tt class="py-op">(</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">knn</tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-27', 'x', 'link-0');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">weight_fn</tt><tt class="py-op">=</tt><tt class="py-name">weight_fn</tt><tt class="py-op">,</tt> <tt class="py-name">distance_fn</tt><tt class="py-op">=</tt><tt class="py-name">distance_fn</tt><tt class="py-op">)</tt> </tt>
<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 class="py-name">most_class</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">most_weight</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">klass</tt><tt class="py-op">,</tt> <tt class="py-name">weight</tt> <tt class="py-keyword">in</tt> <tt class="py-name">weights</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-28', 'items', 'link-7');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">most_class</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">weight</tt> <tt class="py-op">></tt> <tt class="py-name">most_weight</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">most_class</tt> <tt class="py-op">=</tt> <tt class="py-name">klass</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">most_weight</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">most_class</tt> </tt>
</div><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt><script type="text/javascript">
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