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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SubsMat-module.html">Package SubsMat</a> ::
Module FreqTable
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<h1 class="epydoc">Source Code for <a href="Bio.SubsMat.FreqTable-module.html">Module Bio.SubsMat.FreqTable</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.SubsMat.FreqTable.COUNT=Bio.SubsMat.FreqTable-module.html#COUNT"><a title="Bio.SubsMat.FreqTable.COUNT" class="py-name" href="#" onclick="return doclink('link-2', 'COUNT', 'link-2');">COUNT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.SubsMat.FreqTable.FREQ=Bio.SubsMat.FreqTable-module.html#FREQ"><a title="Bio.SubsMat.FreqTable.FREQ" class="py-name" href="#" onclick="return doclink('link-3', 'FREQ', 'link-3');">FREQ</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment">##################################################################</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># A class to handle frequency tables</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># Copyright Iddo Friedberg idoerg@cc.huji.ac.il</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># Biopython (http://biopython.org) license applies</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># Methods to read a letter frequency or a letter count file:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># Example files for a DNA alphabet:</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-comment"># A count file (whitespace seperated):</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-comment"># A 50</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-comment"># C 37</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-comment"># G 23</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-comment"># T 58</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-comment"># The same info as a frequency file:</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-comment"># A 0.2976</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-comment"># C 0.2202</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment"># G 0.1369</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment"># T 0.3452</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"># </tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-comment"># Functions:</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-comment"># read_count(f): read a count file from stream f. Then convert to</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-comment"># frequencies</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-comment"># read_freq(f): read a frequency data file from stream f. Of course, we then</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-comment"># don't have the counts, but it is usually the letter frquencies which are</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-comment"># interesting.</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-comment"># Methods:</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-comment"># (all internal)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-comment"># Attributes:</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-comment"># alphabet: The IUPAC alphabet set (or any other) whose letters you are</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-comment"># using. Common sets are: IUPAC.protein (20-letter protein),</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-comment"># IUPAC.unambiguous_dna (4-letter DNA). See Bio/alphabet for more.</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-comment"># data: frequency dictionary.</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-comment"># count: count dictionary. Empty if no counts are provided.</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-comment"># Example of use:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-comment"># >>> from SubsMat import FreqTable</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-comment"># >>> ftab = FreqTable.FreqTable(my_frequency_dictionary,FreqTable.FREQ)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-comment"># >>> ftab = FreqTable.FreqTable(my_count_dictionary,FreqTable.COUNT)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"># >>> ftab = FreqTable.read_count(open('myDNACountFile'))</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"># </tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-comment">##################################################################</tt> </tt>
<a name="FreqTable"></a><div id="FreqTable-def"><a name="L49"></a><tt class="py-lineno">49</tt> <a class="py-toggle" href="#" id="FreqTable-toggle" onclick="return toggle('FreqTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SubsMat.FreqTable.FreqTable-class.html">FreqTable</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FreqTable-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="FreqTable-expanded"><a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> </tt>
<a name="FreqTable._freq_from_count"></a><div id="FreqTable._freq_from_count-def"><a name="L51"></a><tt class="py-lineno">51</tt> <a class="py-toggle" href="#" id="FreqTable._freq_from_count-toggle" onclick="return toggle('FreqTable._freq_from_count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SubsMat.FreqTable.FreqTable-class.html#_freq_from_count">_freq_from_count</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="FreqTable._freq_from_count-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FreqTable._freq_from_count-expanded"><a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">total</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-4" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Method Bio.SubsMat.SeqMat.sum()=Bio.SubsMat.SeqMat-class.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-4', 'sum', 'link-4');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Method Bio.Seq.UnknownSeq.count()=Bio.Seq.UnknownSeq-class.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-5', 'count', 'link-5');">count</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.Phylo.PhyloXML.Events.values()=Bio.Phylo.PhyloXML.Events-class.html#values,Method Bio.SeqIO._index._IndexedSeqFileDict.values()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-6', 'values', 'link-6');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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-keyword">for</tt> <tt id="link-7" 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-7', 'i', 'link-7');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-8', 'count', 'link-5');">count</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.SeqIO._index._IndexedSeqFileDict.iteritems()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#iteritems,Method BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#iteritems,Method BioSQL.BioSeqDatabase.DBServer.iteritems()=BioSQL.BioSeqDatabase.DBServer-class.html#iteritems"><a title="Bio.SeqIO._index._IndexedSeqFileDict.iteritems
BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems
BioSQL.BioSeqDatabase.DBServer.iteritems" class="py-name" href="#" onclick="return doclink('link-9', 'iteritems', 'link-9');">iteritems</a></tt><tt class="py-op">(</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 id="link-10" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-10', 'i', 'link-7');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">v</tt> <tt class="py-op">/</tt> <tt class="py-name">total</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> </tt>
<a name="FreqTable._alphabet_from_input"></a><div id="FreqTable._alphabet_from_input-def"><a name="L56"></a><tt class="py-lineno">56</tt> <a class="py-toggle" href="#" id="FreqTable._alphabet_from_input-toggle" onclick="return toggle('FreqTable._alphabet_from_input');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SubsMat.FreqTable.FreqTable-class.html#_alphabet_from_input">_alphabet_from_input</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="FreqTable._alphabet_from_input-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FreqTable._alphabet_from_input-expanded"><a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-11" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-11', 'i', 'link-7');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt class="py-name">self</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">s</tt> <tt class="py-op">+=</tt> <tt id="link-12" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-12', 'i', 'link-7');">i</a></tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">s</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> </tt>
<a name="FreqTable.__init__"></a><div id="FreqTable.__init__-def"><a name="L62"></a><tt class="py-lineno">62</tt> <a class="py-toggle" href="#" id="FreqTable.__init__-toggle" onclick="return toggle('FreqTable.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SubsMat.FreqTable.FreqTable-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">in_dict</tt><tt class="py-op">,</tt><tt class="py-param">dict_type</tt><tt class="py-op">,</tt><tt class="py-param">alphabet</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="FreqTable.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FreqTable.__init__-expanded"><a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">alphabet</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dict_type</tt> <tt class="py-op">==</tt> <tt id="link-13" class="py-name"><a title="Bio.SubsMat.FreqTable.COUNT" class="py-name" href="#" onclick="return doclink('link-13', 'COUNT', 'link-2');">COUNT</a></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">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-14', 'count', 'link-5');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">in_dict</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.SubsMat.FreqTable.FreqTable._freq_from_count()=Bio.SubsMat.FreqTable.FreqTable-class.html#_freq_from_count"><a title="Bio.SubsMat.FreqTable.FreqTable._freq_from_count" class="py-name" href="#" onclick="return doclink('link-15', '_freq_from_count', 'link-15');">_freq_from_count</a></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-keyword">elif</tt> <tt class="py-name">dict_type</tt> <tt class="py-op">==</tt> <tt id="link-16" class="py-name"><a title="Bio.SubsMat.FreqTable.FREQ" class="py-name" href="#" onclick="return doclink('link-16', 'FREQ', 'link-3');">FREQ</a></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">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-17', 'count', 'link-5');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</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">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SeqIO._index._IndexedSeqFileDict.update()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#update,Method Bio.SeqRecord._RestrictedDict.update()=Bio.SeqRecord._RestrictedDict-class.html#update"><a title="Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SeqIO._index._IndexedSeqFileDict.update
Bio.SeqRecord._RestrictedDict.update" class="py-name" href="#" onclick="return doclink('link-18', 'update', 'link-18');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">in_dict</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</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">"bad dict_type"</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">alphabet</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-19', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-20', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">(</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">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-21', 'letters', 'link-21');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.SubsMat.FreqTable.FreqTable._alphabet_from_input()=Bio.SubsMat.FreqTable.FreqTable-class.html#_alphabet_from_input"><a title="Bio.SubsMat.FreqTable.FreqTable._alphabet_from_input" class="py-name" href="#" onclick="return doclink('link-22', '_alphabet_from_input', 'link-22');">_alphabet_from_input</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> </tt>
<a name="read_count"></a><div id="read_count-def"><a name="L76"></a><tt class="py-lineno">76</tt> <a class="py-toggle" href="#" id="read_count-toggle" onclick="return toggle('read_count');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SubsMat.FreqTable-module.html#read_count">read_count</a><tt class="py-op">(</tt><tt class="py-param">f</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_count-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="read_count-expanded"><a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-23', 'count', 'link-5');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</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">f</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-24" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-24', 'value', 'link-24');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-25', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-26', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-27', 'count', 'link-5');">count</a></tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-28', 'value', 'link-24');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt class="py-name">freq_table</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Module Bio.SubsMat.FreqTable=Bio.SubsMat.FreqTable-module.html,Class Bio.SubsMat.FreqTable.FreqTable=Bio.SubsMat.FreqTable.FreqTable-class.html"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-29', 'FreqTable', 'link-29');">FreqTable</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-30', 'count', 'link-5');">count</a></tt><tt class="py-op">,</tt><tt id="link-31" class="py-name"><a title="Bio.SubsMat.FreqTable.COUNT" class="py-name" href="#" onclick="return doclink('link-31', 'COUNT', 'link-2');">COUNT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">freq_table</tt> </tt>
</div><a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> </tt>
<a name="read_freq"></a><div id="read_freq-def"><a name="L84"></a><tt class="py-lineno">84</tt> <a class="py-toggle" href="#" id="read_freq-toggle" onclick="return toggle('read_freq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SubsMat.FreqTable-module.html#read_freq">read_freq</a><tt class="py-op">(</tt><tt class="py-param">f</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_freq-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="read_freq-expanded"><a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-name">freq_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</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">f</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-32', 'value', 'link-24');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-33', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-34', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> <tt class="py-name">freq_dict</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-35', 'value', 'link-24');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-36" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-36', 'FreqTable', 'link-29');">FreqTable</a></tt><tt class="py-op">(</tt><tt class="py-name">freq_dict</tt><tt class="py-op">,</tt><tt id="link-37" class="py-name"><a title="Bio.SubsMat.FreqTable.FREQ" class="py-name" href="#" onclick="return doclink('link-37', 'FREQ', 'link-3');">FREQ</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno">90</tt> <tt class="py-line"> </tt><script type="text/javascript">
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