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<a href="Bio-module.html">Package Bio</a> ::
Module distance
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<h1 class="epydoc">Source Code for <a href="Bio.distance-module.html">Module Bio.distance</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">This module provides code for various distance measures.</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">Functions:</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">euclidean Euclidean distance between two points</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">euclidean_py Pure Python implementation of euclidean.</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">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># XXX cosine distance</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">math</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</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="L13"></a><tt class="py-lineno">13</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="L14"></a><tt class="py-lineno">14</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="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 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="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt>
<a name="euclidean"></a><div id="euclidean-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="euclidean-toggle" onclick="return toggle('euclidean');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.distance-module.html#euclidean">euclidean</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="euclidean-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="euclidean-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-docstring">"""euclidean(x, y) -> euclidean distance between x and y"""</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-3', 'x', 'link-0');">x</a></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">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"vectors must be same length"</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-comment">#return sqrt(sum((x-y)**2))</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Optimization by John Corradi (JCorradi@msn.com)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-4" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-4', 'd', 'link-4');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-5', 'x', 'link-0');">x</a></tt><tt class="py-op">-</tt><tt class="py-name">y</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-6" class="py-name" targets="Variable Bio.Affy.CelFile.sqrt=Bio.Affy.CelFile-module.html#sqrt,Variable Bio.LogisticRegression.sqrt=Bio.LogisticRegression-module.html#sqrt,Variable Bio.MarkovModel.sqrt=Bio.MarkovModel-module.html#sqrt,Variable Bio.MaxEntropy.sqrt=Bio.MaxEntropy-module.html#sqrt,Variable Bio.NaiveBayes.sqrt=Bio.NaiveBayes-module.html#sqrt,Variable Bio.PDB.ResidueDepth'.sqrt=Bio.PDB.ResidueDepth%27-module.html#sqrt,Variable Bio.PDB.Vector'.sqrt=Bio.PDB.Vector%27-module.html#sqrt,Variable Bio.SVDSuperimposer.SVDSuperimposer'.sqrt=Bio.SVDSuperimposer.SVDSuperimposer%27-module.html#sqrt,Variable Bio.SVDSuperimposer.sqrt=Bio.SVDSuperimposer-module.html#sqrt,Variable Bio.Statistics.lowess.sqrt=Bio.Statistics.lowess-module.html#sqrt,Variable Bio.distance.sqrt=Bio.distance-module.html#sqrt,Variable Bio.kNN.sqrt=Bio.kNN-module.html#sqrt"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-6', 'sqrt', 'link-6');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">dot</tt><tt class="py-op">(</tt><tt id="link-7" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-7', 'd', 'link-4');">d</a></tt><tt class="py-op">,</tt> <tt id="link-8" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-8', 'd', 'link-4');">d</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> </tt>
<a name="euclidean_py"></a><div id="euclidean_py-def"><a name="L27"></a><tt class="py-lineno">27</tt> <a class="py-toggle" href="#" id="euclidean_py-toggle" onclick="return toggle('euclidean_py');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.distance-module.html#euclidean_py">euclidean_py</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="euclidean_py-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="euclidean_py-expanded"><a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-docstring">"""euclidean_py(x, y) -> euclidean distance between x and y"""</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-comment"># lightly modified from implementation by Thomas Sicheritz-Ponten.</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># This works faster than the Numeric implementation on shorter</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># vectors.</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-9', 'x', 'link-0');">x</a></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">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"vectors must be same length"</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt id="link-10" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Function Bio.utils.sum()=Bio.utils-module.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-10', 'sum', 'link-10');">sum</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-11" 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-11', 'i', 'link-11');">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 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 class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-13', 'sum', 'link-10');">sum</a></tt> <tt class="py-op">+=</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 id="link-15" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-15', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt id="link-16" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-16', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-17', 'sqrt', 'link-6');">sqrt</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-18', 'sum', 'link-10');">sum</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-comment"># Try and load C implementations of functions. If I can't,</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># then just ignore and use the pure python implementations.</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">cdistance</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> </tt><script type="text/javascript">
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