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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.SubsMat-module.html">Package&nbsp;SubsMat</a> ::
        Module&nbsp;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">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</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="L3"></a><tt class="py-lineno"> 3</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="L4"></a><tt class="py-lineno"> 4</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="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-comment">##################################################################</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># A class to handle frequency tables</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright Iddo Friedberg idoerg@cc.huji.ac.il</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Biopython (http://biopython.org) license applies</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Methods to read a letter frequency or a letter count file:</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Example files for a DNA alphabet:</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># A count file (whitespace seperated):</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># A  50</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># C  37</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># G  23</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># T  58</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The same info as a frequency file:</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># A 0.2976</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># C 0.2202</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"># G 0.1369</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># T 0.3452</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Functions:</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   read_count(f): read a count file from stream f. Then convert to</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   frequencies</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   read_freq(f): read a frequency data file from stream f. Of course, we then</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">#   don't have the counts, but it is usually the letter frquencies which are</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">#   interesting.</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Methods:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   (all internal)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Attributes:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   alphabet: The IUPAC alphabet set (or any other) whose letters you are</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   using. Common sets are: IUPAC.protein (20-letter protein),</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   IUPAC.unambiguous_dna (4-letter DNA). See Bio/alphabet for more.</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   data: frequency dictionary.</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">#   count: count dictionary. Empty if no counts are provided.</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Example of use:</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   &gt;&gt;&gt; from SubsMat import FreqTable</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   &gt;&gt;&gt; ftab = FreqTable.FreqTable(my_frequency_dictionary,FreqTable.FREQ)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   &gt;&gt;&gt; ftab = FreqTable.FreqTable(my_count_dictionary,FreqTable.COUNT)</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   &gt;&gt;&gt; ftab = FreqTable.read_count(open('myDNACountFile'))</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt>  <tt class="py-line"><tt class="py-comment"></tt><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 class="py-comment">#  </tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##################################################################</tt> </tt>
<a name="FreqTable"></a><div id="FreqTable-def"><a name="L50"></a><tt class="py-lineno">50</tt> <a class="py-toggle" href="#" id="FreqTable-toggle" onclick="return toggle('FreqTable');">-</a><tt class="py-line"><tt class="py-comment"></tt><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="L51"></a><tt class="py-lineno">51</tt>  <tt class="py-line">     </tt>
<a name="FreqTable._freq_from_count"></a><div id="FreqTable._freq_from_count-def"><a name="L52"></a><tt class="py-lineno">52</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="L53"></a><tt class="py-lineno">53</tt>  <tt class="py-line">        <tt id="link-4" 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-4', 'sum', 'link-4');">sum</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-5" 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-5', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" 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,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-6', 'count', 'link-6');">count</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-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,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-7', 'values', 'link-7');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt>  <tt class="py-line">            <tt id="link-8" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-8', 'sum', 'link-4');">sum</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-9', 'sum', 'link-4');">sum</a></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-5');">i</a></tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</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-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-12', 'count', 'link-6');">count</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-13', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-14" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-14', 'i', 'link-5');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-15', 'count', 'link-6');">count</a></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-5');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">/</tt> <tt id="link-17" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-17', 'sum', 'link-4');">sum</a></tt> </tt>
</div><a name="L58"></a><tt class="py-lineno">58</tt>  <tt class="py-line"> </tt>
<a name="FreqTable._alphabet_from_input"></a><div id="FreqTable._alphabet_from_input-def"><a name="L59"></a><tt class="py-lineno">59</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="L60"></a><tt class="py-lineno">60</tt>  <tt class="py-line">        <tt id="link-18" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-18', 's', 'link-18');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt>  <tt class="py-line">        <tt class="py-name">letters_list</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-19', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt>  <tt class="py-line">        <tt class="py-name">letters_list</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'sort', 'link-20');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-21" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-21', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">letters_list</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt>  <tt class="py-line">            <tt id="link-22" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-22', 's', 'link-18');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-23', 's', 'link-18');">s</a></tt> <tt class="py-op">+</tt> <tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-5');">i</a></tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-25', 's', 'link-18');">s</a></tt> </tt>
</div><a name="L66"></a><tt class="py-lineno">66</tt>  <tt class="py-line"> </tt>
<a name="FreqTable.__init__"></a><div id="FreqTable.__init__-def"><a name="L67"></a><tt class="py-lineno">67</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="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-26" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-26', 'alphabet', 'link-26');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-27', 'alphabet', 'link-26');">alphabet</a></tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</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-28" class="py-name"><a title="Bio.SubsMat.FreqTable.COUNT" class="py-name" href="#" onclick="return doclink('link-28', 'COUNT', 'link-2');">COUNT</a></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">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-29', 'count', 'link-6');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">in_dict</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', '_freq_from_count', 'link-30');">_freq_from_count</a></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-keyword">elif</tt> <tt class="py-name">dict_type</tt> <tt class="py-op">==</tt> <tt id="link-31" class="py-name"><a title="Bio.SubsMat.FreqTable.FREQ" class="py-name" href="#" onclick="return doclink('link-31', 'FREQ', 'link-3');">FREQ</a></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 id="link-32" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-32', 'count', 'link-6');">count</a></tt> <tt class="py-op">=</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 id="link-33" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,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.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-33', 'update', 'link-33');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">in_dict</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt><tt class="py-string">"bad dict_type"</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-34" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-34', 'alphabet', 'link-26');">alphabet</a></tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-35', 'alphabet', 'link-26');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-36', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-37', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">(</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">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-38', 'alphabet', 'link-26');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-39" 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,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-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
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-39', 'letters', 'link-39');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', '_alphabet_from_input', 'link-40');">_alphabet_from_input</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L80"></a><tt class="py-lineno">80</tt>  <tt class="py-line"> </tt>
<a name="read_count"></a><div id="read_count-def"><a name="L81"></a><tt class="py-lineno">81</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="L82"></a><tt class="py-lineno">82</tt>  <tt class="py-line">    <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-41', 'map', 'link-41');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-42', 'split', 'link-42');">split</a></tt><tt class="py-op">,</tt><tt id="link-43" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-43', 'map', 'link-41');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-44', 'strip', 'link-44');">strip</a></tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-45', 'readlines', 'link-45');">readlines</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="L83"></a><tt class="py-lineno">83</tt>  <tt class="py-line">    <tt id="link-46" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-46', 'count', 'link-6');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt>  <tt class="py-line">        <tt id="link-48" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-48', 'count', 'link-6');">count</a></tt><tt class="py-op">[</tt><tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-49', 'i', 'link-5');">i</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-5');">i</a></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="L86"></a><tt class="py-lineno">86</tt>  <tt class="py-line">    <tt class="py-name">freq_table</tt> <tt class="py-op">=</tt> <tt id="link-51" 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-51', 'FreqTable', 'link-51');">FreqTable</a></tt><tt class="py-op">(</tt><tt id="link-52" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-52', 'count', 'link-6');">count</a></tt><tt class="py-op">,</tt><tt id="link-53" class="py-name"><a title="Bio.SubsMat.FreqTable.COUNT" class="py-name" href="#" onclick="return doclink('link-53', 'COUNT', 'link-2');">COUNT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">freq_table</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno">88</tt>  <tt class="py-line"> </tt>
<a name="read_freq"></a><div id="read_freq-def"><a name="L89"></a><tt class="py-lineno">89</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="L90"></a><tt class="py-lineno">90</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="L91"></a><tt class="py-lineno">91</tt>  <tt class="py-line">    <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-54', 'map', 'link-41');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-55', 'split', 'link-42');">split</a></tt><tt class="py-op">,</tt><tt id="link-56" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-56', 'map', 'link-41');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-57', 'strip', 'link-44');">strip</a></tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-58', 'readlines', 'link-45');">readlines</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="L92"></a><tt class="py-lineno">92</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-59', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno">93</tt>  <tt class="py-line">        <tt class="py-name">freq_dict</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-60', 'i', 'link-5');">i</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-61', 'i', 'link-5');">i</a></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="L94"></a><tt class="py-lineno">94</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-62" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-62', 'FreqTable', 'link-51');">FreqTable</a></tt><tt class="py-op">(</tt><tt class="py-name">freq_dict</tt><tt class="py-op">,</tt><tt id="link-63" class="py-name"><a title="Bio.SubsMat.FreqTable.FREQ" class="py-name" href="#" onclick="return doclink('link-63', 'FREQ', 'link-3');">FREQ</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L95"></a><tt class="py-lineno">95</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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