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Package Bio
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<h1 class="epydoc">Source Code for <a href="Bio-module.html">Package Bio</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""Collection of modules for dealing with biological data in Python.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">The Biopython Project is an international association of developers </tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">of freely available Python tools for computational molecular biology.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">http://biopython.org</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="MissingExternalDependencyError"></a><div id="MissingExternalDependencyError-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="MissingExternalDependencyError-toggle" onclick="return toggle('MissingExternalDependencyError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MissingExternalDependencyError-class.html">MissingExternalDependencyError</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MissingExternalDependencyError-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="MissingExternalDependencyError-expanded"><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt>
<a name="_load_registries"></a><div id="_load_registries-def"><a name="L16"></a><tt class="py-lineno">16</tt> <a class="py-toggle" href="#" id="_load_registries-toggle" onclick="return toggle('_load_registries');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio-module.html#_load_registries">_load_registries</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_load_registries-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="_load_registries-expanded"><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</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-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.Registry=Bio.config.Registry-module.html,Class Bio.config.Registry.Registry=Bio.config.Registry.Registry-class.html"><a title="Bio.config.Registry
Bio.config.Registry.Registry" class="py-name" href="#" onclick="return doclink('link-2', 'Registry', 'link-2');">Registry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.config.Registry
Bio.config.Registry.Registry" class="py-name" href="#" onclick="return doclink('link-3', 'Registry', 'link-2');">Registry</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> </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">getattr</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-string">"version_info"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op"><</tt> <tt class="py-op">(</tt><tt class="py-number">2</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="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">self</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">modules</tt><tt class="py-op">[</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt> <tt class="py-comment"># self refers to this module.</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-comment"># Load the registries. Look in all the '.py' files in Bio.config</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"># for Registry objects. Save them all into the local namespace.</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"># Import code changed to allow for compilation with py2exe from distutils</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"># import Bio.config</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">config_imports</tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.config"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">"Bio"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-comment"># in a zipfile</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">config_imports</tt><tt class="py-op">,</tt> <tt class="py-string">'__loader__'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">zipfiles</tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.config"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">"Bio"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">__loader__</tt><tt class="py-op">.</tt><tt class="py-name">_files</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-comment"># Get only Bio.config modules</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-4" 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-4', 'x', 'link-4');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">zipfiles</tt><tt class="py-op">[</tt><tt class="py-name">file</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zipfiles</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'keys', 'link-5');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> \ </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'Bio\\config'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">file</tt><tt class="py-op">]</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-6', 'x', 'link-4');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-7" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-7');">name</a></tt><tt class="py-op">.</tt><tt id="link-8" 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-8', 'split', 'link-8');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\\"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-9" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-9', 'name', 'link-7');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-10" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-10', 'x', 'link-4');">x</a></tt><tt class="py-op">]</tt> <tt class="py-comment"># Get module name</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</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-4');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-12" 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-12', 'map', 'link-12');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-13" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-13', 'x', 'link-4');">x</a></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-4');">x</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-15', 'x', 'link-4');">x</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># chop off '.pyc'</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-comment"># not in a zipfile, get files normally</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt id="link-16" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-16', 'x', 'link-4');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">(</tt><tt class="py-name">config_imports</tt><tt class="py-op">.</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-17', 'x', 'link-4');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-18', 'filter', 'link-18');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-19" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-19', 'x', 'link-4');">x</a></tt><tt class="py-op">:</tt> <tt class="py-keyword">not</tt> <tt id="link-20" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-20', 'x', 'link-4');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</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-4');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">".py"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-22', 'x', 'link-4');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-23', 'x', 'link-4');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-24', 'map', 'link-12');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-25" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-25', 'x', 'link-4');">x</a></tt><tt class="py-op">:</tt> <tt id="link-26" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-26', 'x', 'link-4');">x</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</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-4');">x</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># chop off '.py'</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">module</tt> <tt class="py-keyword">in</tt> <tt id="link-28" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-4');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.config.%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">module</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">"Bio"</tt><tt class="py-op">,</tt><tt class="py-string">"config"</tt><tt class="py-op">]</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">for</tt> <tt id="link-29" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-29', 'name', 'link-7');">name</a></tt><tt class="py-op">,</tt> <tt id="link-30" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.obj=Bio.Encodings.IUPACEncoding-module.html#obj"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-30', 'obj', 'link-30');">obj</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'items', 'link-31');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-32" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-32', 'name', 'link-7');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-33', 'obj', 'link-30');">obj</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.config.Registry
Bio.config.Registry.Registry" class="py-name" href="#" onclick="return doclink('link-34', 'Registry', 'link-2');">Registry</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-35', 'name', 'link-7');">name</a></tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-36', 'obj', 'link-30');">obj</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-comment"># Put the registry loading code in a function so we don't polute the</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># module namespace with local variables.</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-comment"># WARNING:</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The call to _load_registries is being skipped as part of deprecating</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.expressions, which does not function properly with the new version</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># of mxTextTools. If at some point we decide to revive Bio.expressions,</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># this line should be reinstated.</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"><tt class="py-comment"># _load_registries()</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-keyword">del</tt> <tt class="py-name">_load_registries</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> </tt><script type="text/javascript">
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