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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.EUtils-module.html">Package EUtils</a> ::
Module parse
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<h1 class="epydoc">Source Code for <a href="Bio.EUtils.parse-module.html">Module Bio.EUtils.parse</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">codecs</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-0', 'time', 'link-0');">time</a></tt><tt class="py-op">,</tt> <tt class="py-name">urllib</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">,</tt> <tt class="py-name">htmlentitydefs</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">xmlreader</tt><tt class="py-op">,</tt> <tt class="py-name">SAXException</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.EUtils.Datatypes=Bio.EUtils.Datatypes-module.html"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-1', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Module Bio.EUtils.ReseekFile=Bio.EUtils.ReseekFile-module.html,Class Bio.EUtils.ReseekFile.ReseekFile=Bio.EUtils.ReseekFile.ReseekFile-class.html"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-2', 'ReseekFile', 'link-2');">ReseekFile</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Module Bio.EUtils.MultiDict=Bio.EUtils.MultiDict-module.html"><a title="Bio.EUtils.MultiDict" class="py-name" href="#" onclick="return doclink('link-3', 'MultiDict', 'link-3');">MultiDict</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt class="py-name">handler</tt> <tt class="py-keyword">import</tt> <tt class="py-name">feature_external_ges</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.EUtils.POM=Bio.EUtils.POM-module.html"><a title="Bio.EUtils.POM" class="py-name" href="#" onclick="return doclink('link-4', 'POM', 'link-4');">POM</a></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="_construct_pattern"></a><div id="_construct_pattern-def"><a name="L7"></a><tt class="py-lineno"> 7</tt> <a class="py-toggle" href="#" id="_construct_pattern-toggle" onclick="return toggle('_construct_pattern');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_construct_pattern">_construct_pattern</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_construct_pattern-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_construct_pattern-expanded"><a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-5" 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-5', 'x', 'link-5');">x</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <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-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">htmlentitydefs</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Variable Bio.EUtils.parse.entitydefs=Bio.EUtils.parse-module.html#entitydefs"><a title="Bio.EUtils.parse.entitydefs" class="py-name" href="#" onclick="return doclink('link-7', 'entitydefs', 'link-7');">entitydefs</a></tt><tt class="py-op">.</tt><tt id="link-8" 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-8', 'keys', 'link-8');">keys</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="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-name">entity_pattern</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-9', 'compile', 'link-9');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"&([a-zA-Z]{1,%d});"</tt> <tt class="py-op">%</tt> <tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-name">defs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-10" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-10', 'v', 'link-10');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">htmlentitydefs</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.EUtils.parse.entitydefs" class="py-name" href="#" onclick="return doclink('link-11', 'entitydefs', 'link-7');">entitydefs</a></tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'items', 'link-12');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-13', 'v', 'link-10');">v</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-name">defs</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">unicode</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-14', 'v', 'link-10');">v</a></tt><tt class="py-op">,</tt> <tt class="py-string">"latin-1"</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-15" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-15', 'v', 'link-10');">v</a></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-string">"&#"</tt> <tt class="py-keyword">and</tt> <tt id="link-16" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-16', 'v', 'link-10');">v</a></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-op">==</tt> <tt class="py-string">";"</tt><tt class="py-op">:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-name">defs</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">unichr</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-17', 'v', 'link-10');">v</a></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-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt><tt class="py-string">"Unexpected entitydef value: %r"</tt> <tt class="py-op">%</tt> <tt id="link-18" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-18', 'v', 'link-10');">v</a></tt><tt class="py-op">)</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">return</tt> <tt class="py-name">entity_pattern</tt><tt class="py-op">,</tt> <tt class="py-name">defs</tt> </tt>
</div><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt id="link-19" class="py-name" targets="Variable Bio.EUtils.parse._entity_pattern=Bio.EUtils.parse-module.html#_entity_pattern"><a title="Bio.EUtils.parse._entity_pattern" class="py-name" href="#" onclick="return doclink('link-19', '_entity_pattern', 'link-19');">_entity_pattern</a></tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name"><a title="Bio.EUtils.parse.entitydefs" class="py-name" href="#" onclick="return doclink('link-20', 'entitydefs', 'link-7');">entitydefs</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name" targets="Function Bio.EUtils.parse._construct_pattern()=Bio.EUtils.parse-module.html#_construct_pattern"><a title="Bio.EUtils.parse._construct_pattern" class="py-name" href="#" onclick="return doclink('link-21', '_construct_pattern', 'link-21');">_construct_pattern</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="_load_module"></a><div id="_load_module-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="_load_module-toggle" onclick="return toggle('_load_module');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_load_module">_load_module</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_load_module-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_load_module-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-name">mod</tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt id="link-22" 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-22', 'name', 'link-22');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt id="link-23" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-23', 'name', 'link-22');">name</a></tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'split', 'link-24');">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-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">mod</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">mod</tt><tt class="py-op">,</tt> <tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mod</tt> </tt>
</div><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="GetObject"></a><div id="GetObject-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="GetObject-toggle" onclick="return toggle('GetObject');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.parse.GetObject-class.html">GetObject</a><tt class="py-op">:</tt> </tt>
</div><div id="GetObject-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetObject-expanded"><a name="GetObject.__call__"></a><div id="GetObject.__call__-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="GetObject.__call__-toggle" onclick="return toggle('GetObject.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse.GetObject-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GetObject.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GetObject.__call__-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'obj', 'link-25');">obj</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-26', 'obj', 'link-25');">obj</a></tt> </tt>
</div></div><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="UsePOMParser"></a><div id="UsePOMParser-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="UsePOMParser-toggle" onclick="return toggle('UsePOMParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.parse.UsePOMParser-class.html">UsePOMParser</a><tt class="py-op">:</tt> </tt>
</div><div id="UsePOMParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UsePOMParser-expanded"><a name="UsePOMParser.__init__"></a><div id="UsePOMParser.__init__-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="UsePOMParser.__init__-toggle" onclick="return toggle('UsePOMParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse.UsePOMParser-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">module_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UsePOMParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UsePOMParser.__init__-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module_name</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.EUtils.DTDs."</tt> <tt class="py-op">+</tt> <tt class="py-name">module_name</tt> </tt>
</div><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="UsePOMParser.parse_using_dtd"></a><div id="UsePOMParser.parse_using_dtd-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="UsePOMParser.parse_using_dtd-toggle" onclick="return toggle('UsePOMParser.parse_using_dtd');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse.UsePOMParser-class.html#parse_using_dtd">parse_using_dtd</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UsePOMParser.parse_using_dtd-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UsePOMParser.parse_using_dtd-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Function Bio.EUtils.parse._load_module()=Bio.EUtils.parse-module.html#_load_module"><a title="Bio.EUtils.parse._load_module" class="py-name" href="#" onclick="return doclink('link-27', '_load_module', 'link-27');">_load_module</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module_name</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">cb</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name" targets="Class Bio.EUtils.parse.GetObject=Bio.EUtils.parse.GetObject-class.html"><a title="Bio.EUtils.parse.GetObject" class="py-name" href="#" onclick="return doclink('link-28', 'GetObject', 'link-28');">GetObject</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.EUtils.POM" class="py-name" href="#" onclick="return doclink('link-29', 'POM', 'link-4');">POM</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.get_parser()=Bio.EUtils.POM.POMDocument-class.html#get_parser"><a title="Bio.EUtils.POM.POMDocument.get_parser" class="py-name" href="#" onclick="return doclink('link-30', 'get_parser', 'link-30');">get_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">callback</tt> <tt class="py-op">=</tt> <tt class="py-name">cb</tt><tt class="py-op">,</tt> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt class="py-name">module</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-comment"># This tells the parser to not resolve the NCBI DTDs</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setFeature</tt><tt class="py-op">(</tt><tt class="py-name">feature_external_ges</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">SAXException</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">SAXException</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-31', 'parse', 'link-31');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cb</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-32', 'obj', 'link-25');">obj</a></tt> </tt>
</div></div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"># Pull out the "ERROR", "ErrorList", and "WarningList" terms</tt> </tt>
<a name="_check_for_errors"></a><div id="_check_for_errors-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="_check_for_errors-toggle" onclick="return toggle('_check_for_errors');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_check_for_errors">_check_for_errors</a><tt class="py-op">(</tt><tt class="py-param">pom</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_check_for_errors-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_check_for_errors-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">errmsg</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt id="link-33" class="py-name" targets="Variable Bio.Entrez.SerialSet.errors=Bio.Entrez.SerialSet-module.html#errors"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-33', 'errors', 'link-33');">errors</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 class="py-name">warnings</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-34', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">err</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</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">errmsg</tt> <tt class="py-op">=</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-35', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">for</tt> <tt id="link-36" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-36', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-37', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"ErrorList"</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>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt id="link-38" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-38', 'errors', 'link-33');">errors</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-39', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-40', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Variable Bio.EUtils.Datatypes.problem_category_mapping=Bio.EUtils.Datatypes-module.html#problem_category_mapping"><a title="Bio.EUtils.Datatypes.problem_category_mapping" class="py-name" href="#" onclick="return doclink('link-41', 'problem_category_mapping', 'link-41');">problem_category_mapping</a></tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-42', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt><tt class="py-op">(</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-43', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-44', 'tostring', 'link-35');">tostring</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="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-45" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-45', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-46', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"WarningList"</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>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-47', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-48', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.EUtils.Datatypes.problem_category_mapping" class="py-name" href="#" onclick="return doclink('link-49', 'problem_category_mapping', 'link-41');">problem_category_mapping</a></tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-50', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt><tt class="py-op">(</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-51', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-52', 'tostring', 'link-35');">tostring</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="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">errmsg</tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-53', 'errors', 'link-33');">errors</a></tt><tt class="py-op">,</tt> <tt class="py-name">warnings</tt> </tt>
</div><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="_check_for_bad_input_stream"></a><div id="_check_for_bad_input_stream-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="_check_for_bad_input_stream-toggle" onclick="return toggle('_check_for_bad_input_stream');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_check_for_bad_input_stream">_check_for_bad_input_stream</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">force_encoding</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_check_for_bad_input_stream-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_check_for_bad_input_stream-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">reseekfile</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-54', 'ReseekFile', 'link-2');">ReseekFile</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-55', 'ReseekFile', 'link-2');">ReseekFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt id="link-56" 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-56', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reseekfile</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-57', 'read', 'link-57');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">500</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">reseekfile</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-58', 'seek', 'link-58');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">reseekfile</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.nobuffer()=Bio.EUtils.ReseekFile.ReseekFile-class.html#nobuffer"><a title="Bio.EUtils.ReseekFile.ReseekFile.nobuffer" class="py-name" href="#" onclick="return doclink('link-59', 'nobuffer', 'link-59');">nobuffer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-60', 's', 'link-56');">s</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-61', 'split', 'link-24');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lines</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-string">"<Html>"</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-62', 'find', 'link-62');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"<h2>Error occured:"</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt id="link-63" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-63', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">r"Error occured:([^<]+)"</tt><tt class="py-op">,</tt> <tt class="py-name">lines</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">0</tt><tt class="py-op">]</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-64', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-65', 's', 'link-56');">s</a></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">raise</tt> <tt id="link-66" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-66', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Class Bio.EUtils.Datatypes.EUtilsError=Bio.EUtils.Datatypes.EUtilsError-class.html"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-67', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-68', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-69" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-69', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-70', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-string">"Unknown error:\n"</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">reseekfile</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-71', 'read', 'link-57');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-comment"># On error, fetch can return a valid XML document, but not one</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># which matches the DTD. Rather than change the DTD (which is</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># pubmed_020114.dtd) I'll check it here to raise the error.</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># XXX HACK!</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">lines</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-string">"<pmFetchResult>"</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># <pmFetchResult></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># \t<ERROR>Empty id list - nothing todo</ERROR></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </pmFetchResult></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-72" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-72', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Unable to parse pmFetchResult error message"</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-73', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-string">r"<ERROR>([^>]+)</ERROR>"</tt><tt class="py-op">,</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-74" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-74', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-75', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-76', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment"># This happens when you choose a database which doesn't exist</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Are there other reasons? Probably yes, if you choose</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># other illegal parameters.</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">lines</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-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"<!doctype"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-77" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-77', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-78', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-string">"Parameter not allowed"</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">force_encoding</tt> <tt class="py-keyword">and</tt> <tt class="py-name">lines</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-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'<?xml version="1.0"?>'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment"># Doesn't use an encoding, which means the XML is supposed</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># to be in UTF-8 encoding. However, it seems NCBI uses</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Latin-1 so we need to translate the Latin-1 input to</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># UTF-8 output else the XML parsers will fail for non-ASCII</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># characters.</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">reseekfile</tt> <tt class="py-op">=</tt> <tt class="py-name">codecs</tt><tt class="py-op">.</tt><tt class="py-name">EncodedFile</tt><tt class="py-op">(</tt><tt class="py-name">reseekfile</tt><tt class="py-op">,</tt> <tt class="py-string">"utf-8"</tt><tt class="py-op">,</tt> <tt class="py-string">"iso-8859-1"</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reseekfile</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment">##############################</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="parse_search"></a><div id="parse_search-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="parse_search-toggle" onclick="return toggle('parse_search');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_search">parse_search</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">webenv_ref</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_search-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_search-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-comment"># Need to pull out the webenv from the input stream</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name" targets="Function Bio.EUtils.parse._check_for_bad_input_stream()=Bio.EUtils.parse-module.html#_check_for_bad_input_stream"><a title="Bio.EUtils.parse._check_for_bad_input_stream" class="py-name" href="#" onclick="return doclink('link-79', '_check_for_bad_input_stream', 'link-79');">_check_for_bad_input_stream</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">xml_parser</tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name" targets="Class Bio.EUtils.parse.UsePOMParser=Bio.EUtils.parse.UsePOMParser-class.html"><a title="Bio.EUtils.parse.UsePOMParser" class="py-name" href="#" onclick="return doclink('link-80', 'UsePOMParser', 'link-80');">UsePOMParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"eSearch_020511"</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt class="py-name">xml_parser</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name" targets="Method Bio.EUtils.parse.UsePOMParser.parse_using_dtd()=Bio.EUtils.parse.UsePOMParser-class.html#parse_using_dtd"><a title="Bio.EUtils.parse.UsePOMParser.parse_using_dtd" class="py-name" href="#" onclick="return doclink('link-81', 'parse_using_dtd', 'link-81');">parse_using_dtd</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">errmsg</tt><tt class="py-op">,</tt> <tt id="link-82" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-82', 'errors', 'link-33');">errors</a></tt><tt class="py-op">,</tt> <tt class="py-name">warnings</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name" targets="Function Bio.EUtils.parse._check_for_errors()=Bio.EUtils.parse-module.html#_check_for_errors,Method Bio.config.DBRegistry.TextLikeMixin._check_for_errors()=Bio.config.DBRegistry.TextLikeMixin-class.html#_check_for_errors"><a title="Bio.EUtils.parse._check_for_errors
Bio.config.DBRegistry.TextLikeMixin._check_for_errors" class="py-name" href="#" onclick="return doclink('link-83', '_check_for_errors', 'link-83');">_check_for_errors</a></tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># ErrorList (PhraseNotFound*,FieldNotFound*)></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># WarningList (PhraseIgnored*,</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># QuotedPhraseNotFound*,</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># OutputMessage*)></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-comment"># If it's only "PhraseNotFound" erros, with an</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># OutputMessage of "No items found." then personally</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># think that should be considered the same as a search</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># which returned no results.</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment"># Set things up for an empty match</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt id="link-84" 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-84', 'count', 'link-84');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt id="link-85" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-85', 'ids', 'link-85');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">translation_set</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">nothing_matched</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">errmsg</tt> <tt class="py-op">==</tt> <tt class="py-string">"Can't run executor"</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-comment"># Check that the error list only contains PhraseNotFound terms</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">flg</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-86" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-86', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-87" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-87', 'errors', 'link-33');">errors</a></tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-88" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-88', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Variable Bio.EUtils.Datatypes.FieldNotFound.category=Bio.EUtils.Datatypes.FieldNotFound-class.html#category,Variable Bio.EUtils.Datatypes.OutputMessage.category=Bio.EUtils.Datatypes.OutputMessage-class.html#category,Variable Bio.EUtils.Datatypes.PhraseIgnored.category=Bio.EUtils.Datatypes.PhraseIgnored-class.html#category,Variable Bio.EUtils.Datatypes.PhraseNotFound.category=Bio.EUtils.Datatypes.PhraseNotFound-class.html#category,Variable Bio.EUtils.Datatypes.QuotedPhraseNotFound.category=Bio.EUtils.Datatypes.QuotedPhraseNotFound-class.html#category"><a title="Bio.EUtils.Datatypes.FieldNotFound.category
Bio.EUtils.Datatypes.OutputMessage.category
Bio.EUtils.Datatypes.PhraseIgnored.category
Bio.EUtils.Datatypes.PhraseNotFound.category
Bio.EUtils.Datatypes.QuotedPhraseNotFound.category" class="py-name" href="#" onclick="return doclink('link-89', 'category', 'link-89');">category</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">"PhraseNotFound"</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">flg</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">flg</tt><tt class="py-op">:</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-comment"># Okay, only PhraseNotFound. Make sure there is</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># only one OutputMessage, with the text "No items found."</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># (Eg, an OutputMessage of 'Query syntax error.' means</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># there was a real problem.)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">msgs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-90" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-90', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">for</tt> <tt id="link-91" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-91', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">warnings</tt> <tt class="py-keyword">if</tt> <tt id="link-92" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-92', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.EUtils.Datatypes.FieldNotFound.category
Bio.EUtils.Datatypes.OutputMessage.category
Bio.EUtils.Datatypes.PhraseIgnored.category
Bio.EUtils.Datatypes.PhraseNotFound.category
Bio.EUtils.Datatypes.QuotedPhraseNotFound.category" class="py-name" href="#" onclick="return doclink('link-93', 'category', 'link-89');">category</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"OutputMessage"</tt><tt class="py-op">]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">msgs</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">msgs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-94', 'text', 'link-94');">text</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"No items found."</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">nothing_matched</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">nothing_matched</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment"># This is an error</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt id="link-95" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-95', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Class Bio.EUtils.Datatypes.EUtilsSearchError=Bio.EUtils.Datatypes.EUtilsSearchError-class.html"><a title="Bio.EUtils.Datatypes.EUtilsSearchError" class="py-name" href="#" onclick="return doclink('link-96', 'EUtilsSearchError', 'link-96');">EUtilsSearchError</a></tt><tt class="py-op">(</tt><tt class="py-name">errmsg</tt><tt class="py-op">,</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-97" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-97', 'errors', 'link-33');">errors</a></tt><tt class="py-op">,</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-comment"># In other words, check if something matched</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">nothing_matched</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-comment">## Get WebEnv, if it exists</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.get_element()=Bio.EUtils.POM.ElementNode-class.html#get_element,Function Martel.test.test_attrs.get_element()=Martel.test.test_attrs-module.html#get_element"><a title="Bio.EUtils.POM.ElementNode.get_element
Martel.test.test_attrs.get_element" class="py-name" href="#" onclick="return doclink('link-98', 'get_element', 'link-98');">get_element</a></tt><tt class="py-op">(</tt><tt class="py-string">"WebEnv"</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt id="link-99" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-99', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"WebEnv"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-100', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote</tt><tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-101', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-comment"># ONLY change webenv_ref if there's a new one</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">webenv_ref</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-name">webenv</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment"># Other simple fields</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Bio.EUtils.POM.ElementNode.get_element
Martel.test.test_attrs.get_element" class="py-name" href="#" onclick="return doclink('link-102', 'get_element', 'link-98');">get_element</a></tt><tt class="py-op">(</tt><tt class="py-string">"QueryKey"</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"QueryKey"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-103', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt id="link-104" 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-104', 'count', 'link-84');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"Count"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-105', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"RetMax"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-106', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"RetStart"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-107', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># The identifiers (if any)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># NOTE: not a DBIds because the search result doesn't list the</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># database searched!</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-108" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-108', 'ids', 'link-85');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-109" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-109', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-110', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-111" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-111', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"IdList"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find_elements()=Bio.EUtils.POM.ElementNode-class.html#find_elements"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-112', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Id"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment"># TranslationSet</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">translation_set</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ele</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"TranslationSet"</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">translation_set</tt><tt class="py-op">[</tt><tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote_plus</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"From"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-113', 'tostring', 'link-35');">tostring</a></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>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote_plus</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"To"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-114', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-comment"># Convert the RPN TranslationStack into an Expression</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">stack</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">translation_stack</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"TranslationStack"</tt><tt class="py-op">]</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">translation_stack</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ele</tt> <tt class="py-keyword">in</tt> <tt class="py-name">translation_stack</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ele</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"TermSet"</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">stack</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-115', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-116" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-116', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-117" class="py-name" targets="Class Bio.EUtils.DTDs.eSearch_020511.Term=Bio.EUtils.DTDs.eSearch_020511.Term-class.html,Class Bio.EUtils.Datatypes.Term=Bio.EUtils.Datatypes.Term-class.html"><a title="Bio.EUtils.DTDs.eSearch_020511.Term
Bio.EUtils.Datatypes.Term" class="py-name" href="#" onclick="return doclink('link-117', 'Term', 'link-117');">Term</a></tt><tt class="py-op">(</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote_plus</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"Term"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-118', 'tostring', 'link-35');">tostring</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="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote_plus</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"Field"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-119', 'tostring', 'link-35');">tostring</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="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt id="link-120" 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-120', 'count', 'link-84');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"Count"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-121', 'tostring', 'link-35');">tostring</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="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">explode</tt> <tt class="py-op">=</tt> <tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"Explode"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-122', 'tostring', 'link-35');">tostring</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="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">ele</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"OP"</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt id="link-123" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-123', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ele</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-124', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-125" 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-125', 'strip', 'link-125');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-126" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-126', 's', 'link-56');">s</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"AND"</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">stack</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-op">[</tt><tt class="py-name">stack</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-name">stack</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-op">]</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-127" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-127', 's', 'link-56');">s</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"OR"</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">stack</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-op">[</tt><tt class="py-name">stack</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-name">stack</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-op">]</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-128" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-128', 's', 'link-56');">s</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"RANGE"</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">stack</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-op">[</tt><tt id="link-129" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-129', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name" targets="Class Bio.EUtils.Datatypes.Range=Bio.EUtils.Datatypes.Range-class.html,Class Bio.GenBank.LocationParser.Range=Bio.GenBank.LocationParser.Range-class.html"><a title="Bio.EUtils.Datatypes.Range
Bio.GenBank.LocationParser.Range" class="py-name" href="#" onclick="return doclink('link-130', 'Range', 'link-130');">Range</a></tt><tt class="py-op">(</tt><tt class="py-name">stack</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-name">stack</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-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-131" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-131', 's', 'link-56');">s</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"NOT"</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">stack</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-op">[</tt><tt id="link-132" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-132', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name" targets="Class Bio.EUtils.Datatypes.Not=Bio.EUtils.Datatypes.Not-class.html"><a title="Bio.EUtils.Datatypes.Not" class="py-name" href="#" onclick="return doclink('link-133', 'Not', 'link-133');">Not</a></tt><tt class="py-op">(</tt><tt class="py-name">stack</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-name">stack</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-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-134" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-134', 's', 'link-56');">s</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"GROUP"</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-comment"># GROUP doesn't appear to do any more than put an extra</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># parenthesis around ANDs and ORs -- can't find any</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># specific documentation on its role</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># So right now it is redundant and just ignore it</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown OP code: %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-135" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-135', 's', 'link-56');">s</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown TranslationStack element: %r"</tt> <tt class="py-op">%</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-comment"># hack -- it appears as if the translation stack is sometimes missing</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># an AND at the end, which I guess is supposed to be implicit. For</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># instance, doing a text word search plus date range leaves off a</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># trailing and to link the final elements.</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">stack</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">stack</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-op">[</tt><tt class="py-name">stack</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-name">stack</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-op">]</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">stack</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Incomplete TranslationStack: %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">stack</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">stack</tt><tt class="py-op">:</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">stack</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-name">stack</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-comment"># Return either our synthesized query or </tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">search_result</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-136', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name" targets="Class Bio.EUtils.Datatypes.SearchResult=Bio.EUtils.Datatypes.SearchResult-class.html"><a title="Bio.EUtils.Datatypes.SearchResult" class="py-name" href="#" onclick="return doclink('link-137', 'SearchResult', 'link-137');">SearchResult</a></tt><tt class="py-op">(</tt><tt id="link-138" 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-138', 'count', 'link-84');">count</a></tt><tt class="py-op">,</tt> <tt class="py-name">retmax</tt><tt class="py-op">,</tt> <tt class="py-name">retstart</tt><tt class="py-op">,</tt> <tt id="link-139" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-139', 'ids', 'link-85');">ids</a></tt><tt class="py-op">,</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">translation_set</tt><tt class="py-op">,</tt> <tt class="py-name">expression</tt><tt class="py-op">,</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">webenv</tt><tt class="py-op">,</tt> <tt class="py-name">query_key</tt><tt class="py-op">,</tt> <tt id="link-140" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-140', 'errors', 'link-33');">errors</a></tt><tt class="py-op">,</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">,</tt> <tt id="link-141" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-141', 'time', 'link-0');">time</a></tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-142', 'time', 'link-0');">time</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">search_result</tt> </tt>
</div><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-comment">###########################</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="parse_post"></a><div id="parse_post-def"><a name="L258"></a><tt class="py-lineno">258</tt> <a class="py-toggle" href="#" id="parse_post-toggle" onclick="return toggle('parse_post');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_post">parse_post</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">webenv_ref</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_post-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_post-expanded"><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-comment"># It doesn't look like I need check for a bad input stream</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># since I can only generate two types of error messages</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-comment"># ePost_020511.dtd</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">xml_parser</tt> <tt class="py-op">=</tt> <tt id="link-143" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser" class="py-name" href="#" onclick="return doclink('link-143', 'UsePOMParser', 'link-80');">UsePOMParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"ePost_020511"</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt class="py-name">xml_parser</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser.parse_using_dtd" class="py-name" href="#" onclick="return doclink('link-144', 'parse_using_dtd', 'link-81');">parse_using_dtd</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-comment"># If there was an ERROR, raise it now</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">errmsg</tt><tt class="py-op">,</tt> <tt id="link-145" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-145', 'errors', 'link-33');">errors</a></tt><tt class="py-op">,</tt> <tt class="py-name">warnings</tt> <tt class="py-op">=</tt> <tt id="link-146" class="py-name"><a title="Bio.EUtils.parse._check_for_errors
Bio.config.DBRegistry.TextLikeMixin._check_for_errors" class="py-name" href="#" onclick="return doclink('link-146', '_check_for_errors', 'link-83');">_check_for_errors</a></tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">errmsg</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-147" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-147', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-148', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-name">errmsg</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-comment"># Get any invalid identifies</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">invalid_ids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-149" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-149', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-150', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-151" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-151', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-152', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"InvalidIdList"</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>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-comment"># Otherwise, get the WebEnv string</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-153" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-153', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"WebEnv"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-154', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">webenv</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">unquote</tt><tt class="py-op">(</tt><tt id="link-155" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-155', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">webenv_ref</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-name">webenv</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">query_key</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"QueryKey"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-156', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-157" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-157', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name" targets="Class Bio.EUtils.Datatypes.PostResult=Bio.EUtils.Datatypes.PostResult-class.html"><a title="Bio.EUtils.Datatypes.PostResult" class="py-name" href="#" onclick="return doclink('link-158', 'PostResult', 'link-158');">PostResult</a></tt><tt class="py-op">(</tt><tt class="py-name">webenv</tt><tt class="py-op">,</tt> <tt class="py-name">query_key</tt><tt class="py-op">,</tt> <tt class="py-name">invalid_ids</tt><tt class="py-op">,</tt> <tt id="link-159" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-159', 'time', 'link-0');">time</a></tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-160', 'time', 'link-0');">time</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-comment">###############################</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-comment"># PubDate: '2000 Feb 1' or '1975 Jun' or '1995'</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># BLAH! PubMed 8318652 also has "1993 May-Jun" for </tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-161" class="py-name" targets="Variable Bio.EUtils.parse._pubdate_format1=Bio.EUtils.parse-module.html#_pubdate_format1"><a title="Bio.EUtils.parse._pubdate_format1" class="py-name" href="#" onclick="return doclink('link-161', '_pubdate_format1', 'link-161');">_pubdate_format1</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-162', 'compile', 'link-9');">compile</a></tt><tt class="py-op">(</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-string">r"(?P<year>\d{4})( (?P<month>[A-Za-z]{3})( (?P<day>\d+))?)?$"</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt id="link-163" class="py-name" targets="Variable Bio.EUtils.parse._pubdate_format2=Bio.EUtils.parse-module.html#_pubdate_format2"><a title="Bio.EUtils.parse._pubdate_format2" class="py-name" href="#" onclick="return doclink('link-163', '_pubdate_format2', 'link-163');">_pubdate_format2</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-164', 'compile', 'link-9');">compile</a></tt><tt class="py-op">(</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-string">r"(?P<year>\d{4}) (?P<month1>[A-Za-z]{3})-(?P<month2>[A-Za-z]{3})"</tt><tt class="py-op">)</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt id="link-165" class="py-name" targets="Variable Bio.EUtils.parse._month_names_to_number=Bio.EUtils.parse-module.html#_month_names_to_number"><a title="Bio.EUtils.parse._month_names_to_number" class="py-name" href="#" onclick="return doclink('link-165', '_month_names_to_number', 'link-165');">_month_names_to_number</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-string">"Jan"</tt><tt class="py-op">:</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-string">"Feb"</tt><tt class="py-op">:</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-string">"Mar"</tt><tt class="py-op">:</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-string">"Apr"</tt><tt class="py-op">:</tt> <tt class="py-number">4</tt><tt class="py-op">,</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-string">"May"</tt><tt class="py-op">:</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-string">"Jun"</tt><tt class="py-op">:</tt> <tt class="py-number">6</tt><tt class="py-op">,</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-string">"Jul"</tt><tt class="py-op">:</tt> <tt class="py-number">7</tt><tt class="py-op">,</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-string">"Aug"</tt><tt class="py-op">:</tt> <tt class="py-number">8</tt><tt class="py-op">,</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-string">"Sep"</tt><tt class="py-op">:</tt> <tt class="py-number">9</tt><tt class="py-op">,</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-string">"Oct"</tt><tt class="py-op">:</tt> <tt class="py-number">10</tt><tt class="py-op">,</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-string">"Nov"</tt><tt class="py-op">:</tt> <tt class="py-number">11</tt><tt class="py-op">,</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-string">"Dec"</tt><tt class="py-op">:</tt> <tt class="py-number">12</tt><tt class="py-op">,</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-comment"># Ignoring the hour and minute parts -- they seem to be either</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># midnight or 09:00 and since I don't know the timezone it seems</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># rather pointless</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># EntrezDate: 2000/02/17 09:00</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-166" class="py-name" targets="Variable Bio.EUtils.parse._entrezdate_format=Bio.EUtils.parse-module.html#_entrezdate_format"><a title="Bio.EUtils.parse._entrezdate_format" class="py-name" href="#" onclick="return doclink('link-166', '_entrezdate_format', 'link-166');">_entrezdate_format</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-167', 'compile', 'link-9');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(?P<year>\d+)/(?P<month>\d+)/(?P<day>\d+)"</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"># This may not be the right way to do this.</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Perhaps should keep the string and only translate upon request</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># to a given time format?</tt> </tt>
<a name="convert_summary_Date"></a><div id="convert_summary_Date-def"><a name="L320"></a><tt class="py-lineno">320</tt> <a class="py-toggle" href="#" id="convert_summary_Date-toggle" onclick="return toggle('convert_summary_Date');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_Date">convert_summary_Date</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_Date-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_Date-expanded"><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-168" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_Date_string()=Bio.EUtils.parse-module.html#convert_summary_Date_string"><a title="Bio.EUtils.parse.convert_summary_Date_string" class="py-name" href="#" onclick="return doclink('link-168', 'convert_summary_Date_string', 'link-168');">convert_summary_Date_string</a></tt><tt class="py-op">(</tt><tt id="link-169" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-169', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-170', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="convert_summary_Date_string"></a><div id="convert_summary_Date_string-def"><a name="L323"></a><tt class="py-lineno">323</tt> <a class="py-toggle" href="#" id="convert_summary_Date_string-toggle" onclick="return toggle('convert_summary_Date_string');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_Date_string">convert_summary_Date_string</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_Date_string-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_Date_string-expanded"><a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-comment"># Can be in one of several different formats</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-171" class="py-name"><a title="Bio.EUtils.parse._pubdate_format1" class="py-name" href="#" onclick="return doclink('link-171', '_pubdate_format1', 'link-161');">_pubdate_format1</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-172', 'match', 'link-172');">match</a></tt><tt class="py-op">(</tt><tt id="link-173" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-173', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-comment"># 2000 Feb 15</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-174" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-174', 'd', 'link-174');">d</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt id="link-175" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-175', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"year"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-176', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"year"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt id="link-177" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-177', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"month"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-178" class="py-name"><a title="Bio.EUtils.parse._month_names_to_number" class="py-name" href="#" onclick="return doclink('link-178', '_month_names_to_number', 'link-165');">_month_names_to_number</a></tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-179', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"month"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt id="link-180" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-180', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"day"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-181', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"day"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">TypeError</tt><tt class="py-op">:</tt> <tt class="py-comment"># if this is None</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt id="link-182" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-182', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"day"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-183" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-183', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-184" class="py-name" targets="Class Bio.EUtils.Datatypes.Date=Bio.EUtils.Datatypes.Date-class.html"><a title="Bio.EUtils.Datatypes.Date" class="py-name" href="#" onclick="return doclink('link-184', 'Date', 'link-184');">Date</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt id="link-185" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-185', 'd', 'link-174');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-186" class="py-name"><a title="Bio.EUtils.parse._pubdate_format2" class="py-name" href="#" onclick="return doclink('link-186', '_pubdate_format2', 'link-163');">_pubdate_format2</a></tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-187', 'match', 'link-172');">match</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-188', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-comment"># 1993 May-Jun</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-189" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-189', 'd', 'link-174');">d</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt id="link-190" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-190', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"year"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-191', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"year"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt id="link-192" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-192', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"month"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-193" class="py-name"><a title="Bio.EUtils.parse._month_names_to_number" class="py-name" href="#" onclick="return doclink('link-193', '_month_names_to_number', 'link-165');">_month_names_to_number</a></tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-194', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"month1"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt id="link-195" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-195', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"day"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-196" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-196', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.EUtils.Datatypes.Date" class="py-name" href="#" onclick="return doclink('link-197', 'Date', 'link-184');">Date</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt id="link-198" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-198', 'd', 'link-174');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-199" class="py-name"><a title="Bio.EUtils.parse._entrezdate_format" class="py-name" href="#" onclick="return doclink('link-199', '_entrezdate_format', 'link-166');">_entrezdate_format</a></tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-200', 'match', 'link-172');">match</a></tt><tt class="py-op">(</tt><tt id="link-201" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-201', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-202" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-202', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.EUtils.Datatypes.Date" class="py-name" href="#" onclick="return doclink('link-203', 'Date', 'link-184');">Date</a></tt><tt class="py-op">(</tt><tt id="link-204" class="py-name" targets="Method Bio.Medline._RecordConsumer.year()=Bio.Medline._RecordConsumer-class.html#year"><a title="Bio.Medline._RecordConsumer.year" class="py-name" href="#" onclick="return doclink('link-204', 'year', 'link-204');">year</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-205', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"year"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">month</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-206', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"month"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">day</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-207', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">"day"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown date format: %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-208', 's', 'link-56');">s</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="unescape_entities"></a><div id="unescape_entities-def"><a name="L353"></a><tt class="py-lineno">353</tt> <a class="py-toggle" href="#" id="unescape_entities-toggle" onclick="return toggle('unescape_entities');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#unescape_entities">unescape_entities</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="unescape_entities-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="unescape_entities-expanded"><a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"&"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-209" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-209', 's', 'link-56');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">unicode</tt><tt class="py-op">(</tt><tt id="link-210" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-210', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">terms</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt id="link-211" 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-211', 'i', 'link-211');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">defs</tt> <tt class="py-op">=</tt> <tt id="link-212" class="py-name"><a title="Bio.EUtils.parse.entitydefs" class="py-name" href="#" onclick="return doclink('link-212', 'entitydefs', 'link-7');">entitydefs</a></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt id="link-213" class="py-name"><a title="Bio.EUtils.parse._entity_pattern" class="py-name" href="#" onclick="return doclink('link-213', '_entity_pattern', 'link-19');">_entity_pattern</a></tt><tt class="py-op">.</tt><tt id="link-214" class="py-name" targets="Method Bio.Restriction.Restriction.FormattedSeq.finditer()=Bio.Restriction.Restriction.FormattedSeq-class.html#finditer"><a title="Bio.Restriction.Restriction.FormattedSeq.finditer" class="py-name" href="#" onclick="return doclink('link-214', 'finditer', 'link-214');">finditer</a></tt><tt class="py-op">(</tt><tt id="link-215" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-215', 's', 'link-56');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-name">terms</tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-216', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-217" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-217', 's', 'link-56');">s</a></tt><tt class="py-op">[</tt><tt id="link-218" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-218', 'i', 'link-211');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-219', 'start', 'link-219');">start</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="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">terms</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-220', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">defs</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-221', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">terms</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-222', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-223', 'group', 'link-176');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt id="link-224" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-224', 'i', 'link-211');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-225', 'end', 'link-225');">end</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">terms</tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-226', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-227" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-227', 's', 'link-56');">s</a></tt><tt class="py-op">[</tt><tt id="link-228" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-228', 'i', 'link-211');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">terms</tt><tt class="py-op">)</tt> </tt>
</div><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="convert_summary_String"></a><div id="convert_summary_String-def"><a name="L370"></a><tt class="py-lineno">370</tt> <a class="py-toggle" href="#" id="convert_summary_String-toggle" onclick="return toggle('convert_summary_String');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_String">convert_summary_String</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_String-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_String-expanded"><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-comment"># The text may have HTML entity definitions .. convert as needed</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># XXX Is this correct? Most other characters are properly</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># encoded. This may mean that that data provider messed up and</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sent data in the wrong format.</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-229" class="py-name" targets="Function Bio.EUtils.parse.unescape_entities()=Bio.EUtils.parse-module.html#unescape_entities"><a title="Bio.EUtils.parse.unescape_entities" class="py-name" href="#" onclick="return doclink('link-229', 'unescape_entities', 'link-229');">unescape_entities</a></tt><tt class="py-op">(</tt><tt id="link-230" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-230', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-231', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> </tt>
<a name="convert_summary_Integer"></a><div id="convert_summary_Integer-def"><a name="L378"></a><tt class="py-lineno">378</tt> <a class="py-toggle" href="#" id="convert_summary_Integer-toggle" onclick="return toggle('convert_summary_Integer');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_Integer">convert_summary_Integer</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_Integer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_Integer-expanded"><a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-232" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-232', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-233', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> </tt>
<a name="convert_summary_Unknown"></a><div id="convert_summary_Unknown-def"><a name="L381"></a><tt class="py-lineno">381</tt> <a class="py-toggle" href="#" id="convert_summary_Unknown-toggle" onclick="return toggle('convert_summary_Unknown');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_Unknown">convert_summary_Unknown</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_Unknown-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_Unknown-expanded"><a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-234" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-234', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-235', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> </tt>
<a name="convert_summary_List"></a><div id="convert_summary_List-def"><a name="L384"></a><tt class="py-lineno">384</tt> <a class="py-toggle" href="#" id="convert_summary_List-toggle" onclick="return toggle('convert_summary_List');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_List">convert_summary_List</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_List-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_List-expanded"><a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-comment"># XXX I'm not doing this as a list.. Should I?</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-236" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_Items()=Bio.EUtils.parse-module.html#convert_summary_Items"><a title="Bio.EUtils.parse.convert_summary_Items" class="py-name" href="#" onclick="return doclink('link-236', 'convert_summary_Items', 'link-236');">convert_summary_Items</a></tt><tt class="py-op">(</tt><tt id="link-237" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-237', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-238" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-238', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Item"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="convert_summary_Items"></a><div id="convert_summary_Items-def"><a name="L388"></a><tt class="py-lineno">388</tt> <a class="py-toggle" href="#" id="convert_summary_Items-toggle" onclick="return toggle('convert_summary_Items');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#convert_summary_Items">convert_summary_Items</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_summary_Items-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert_summary_Items-expanded"><a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt id="link-239" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-239', 'd', 'link-174');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-240" class="py-name"><a title="Bio.EUtils.MultiDict" class="py-name" href="#" onclick="return doclink('link-240', 'MultiDict', 'link-3');">MultiDict</a></tt><tt class="py-op">.</tt><tt id="link-241" class="py-name" targets="Class Bio.EUtils.MultiDict.OrderedMultiDict=Bio.EUtils.MultiDict.OrderedMultiDict-class.html"><a title="Bio.EUtils.MultiDict.OrderedMultiDict" class="py-name" href="#" onclick="return doclink('link-241', 'OrderedMultiDict', 'link-241');">OrderedMultiDict</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-242" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-242', 'item', 'link-242');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-243" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-243', 'x', 'link-5');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt id="link-244" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-244', 'name', 'link-22');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-245" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-245', 'item', 'link-242');">item</a></tt><tt class="py-op">.</tt><tt id="link-246" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.Name=Bio.EUtils.DTDs.LinkOut.Name-class.html,Class Bio.EUtils.DTDs.eInfo_020511.Name=Bio.EUtils.DTDs.eInfo_020511.Name-class.html,Class Bio.EUtils.DTDs.eLink_020511.Name=Bio.EUtils.DTDs.eLink_020511.Name-class.html"><a title="Bio.EUtils.DTDs.LinkOut.Name
Bio.EUtils.DTDs.eInfo_020511.Name
Bio.EUtils.DTDs.eLink_020511.Name" class="py-name" href="#" onclick="return doclink('link-246', 'Name', 'link-246');">Name</a></tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-247" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-247', 'name', 'link-22');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-248" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-248', 'd', 'link-174');">d</a></tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Found multiple Items named %r!"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-249" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-249', 'name', 'link-22');">name</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt id="link-250" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-250', 'd', 'link-174');">d</a></tt><tt class="py-op">[</tt><tt id="link-251" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-251', 'name', 'link-22');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-252" class="py-name" targets="Variable Bio.EUtils.parse.summary_type_parser_table=Bio.EUtils.parse-module.html#summary_type_parser_table"><a title="Bio.EUtils.parse.summary_type_parser_table" class="py-name" href="#" onclick="return doclink('link-252', 'summary_type_parser_table', 'link-252');">summary_type_parser_table</a></tt><tt class="py-op">[</tt><tt id="link-253" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-253', 'item', 'link-242');">item</a></tt><tt class="py-op">.</tt><tt class="py-name">Type</tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt id="link-254" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-254', 'item', 'link-242');">item</a></tt><tt class="py-op">)</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-255" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-255', 'd', 'link-174');">d</a></tt> </tt>
</div><a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt id="link-256" class="py-name"><a title="Bio.EUtils.parse.summary_type_parser_table" class="py-name" href="#" onclick="return doclink('link-256', 'summary_type_parser_table', 'link-252');">summary_type_parser_table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-string">"String"</tt><tt class="py-op">:</tt> <tt id="link-257" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_String()=Bio.EUtils.parse-module.html#convert_summary_String"><a title="Bio.EUtils.parse.convert_summary_String" class="py-name" href="#" onclick="return doclink('link-257', 'convert_summary_String', 'link-257');">convert_summary_String</a></tt><tt class="py-op">,</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-string">"Integer"</tt><tt class="py-op">:</tt> <tt id="link-258" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_Integer()=Bio.EUtils.parse-module.html#convert_summary_Integer"><a title="Bio.EUtils.parse.convert_summary_Integer" class="py-name" href="#" onclick="return doclink('link-258', 'convert_summary_Integer', 'link-258');">convert_summary_Integer</a></tt><tt class="py-op">,</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-string">"Unknown"</tt><tt class="py-op">:</tt> <tt id="link-259" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_Unknown()=Bio.EUtils.parse-module.html#convert_summary_Unknown"><a title="Bio.EUtils.parse.convert_summary_Unknown" class="py-name" href="#" onclick="return doclink('link-259', 'convert_summary_Unknown', 'link-259');">convert_summary_Unknown</a></tt><tt class="py-op">,</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-string">"Date"</tt><tt class="py-op">:</tt> <tt id="link-260" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_Date()=Bio.EUtils.parse-module.html#convert_summary_Date"><a title="Bio.EUtils.parse.convert_summary_Date" class="py-name" href="#" onclick="return doclink('link-260', 'convert_summary_Date', 'link-260');">convert_summary_Date</a></tt><tt class="py-op">,</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-string">"List"</tt><tt class="py-op">:</tt> <tt id="link-261" class="py-name" targets="Function Bio.EUtils.parse.convert_summary_List()=Bio.EUtils.parse-module.html#convert_summary_List"><a title="Bio.EUtils.parse.convert_summary_List" class="py-name" href="#" onclick="return doclink('link-261', 'convert_summary_List', 'link-261');">convert_summary_List</a></tt><tt class="py-op">,</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> </tt>
<a name="parse_summary_xml"></a><div id="parse_summary_xml-def"><a name="L405"></a><tt class="py-lineno">405</tt> <a class="py-toggle" href="#" id="parse_summary_xml-toggle" onclick="return toggle('parse_summary_xml');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_summary_xml">parse_summary_xml</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_summary_xml-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_summary_xml-expanded"><a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-262" class="py-name"><a title="Bio.EUtils.parse._check_for_bad_input_stream" class="py-name" href="#" onclick="return doclink('link-262', '_check_for_bad_input_stream', 'link-79');">_check_for_bad_input_stream</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">xml_parser</tt> <tt class="py-op">=</tt> <tt id="link-263" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser" class="py-name" href="#" onclick="return doclink('link-263', 'UsePOMParser', 'link-80');">UsePOMParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"eSummary_020511"</tt><tt class="py-op">)</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt class="py-name">xml_parser</tt><tt class="py-op">.</tt><tt id="link-264" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser.parse_using_dtd" class="py-name" href="#" onclick="return doclink('link-264', 'parse_using_dtd', 'link-81');">parse_using_dtd</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-name">errmsg</tt><tt class="py-op">,</tt> <tt id="link-265" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-265', 'errors', 'link-33');">errors</a></tt><tt class="py-op">,</tt> <tt class="py-name">warnings</tt> <tt class="py-op">=</tt> <tt id="link-266" class="py-name"><a title="Bio.EUtils.parse._check_for_errors
Bio.config.DBRegistry.TextLikeMixin._check_for_errors" class="py-name" href="#" onclick="return doclink('link-266', '_check_for_errors', 'link-83');">_check_for_errors</a></tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">errmsg</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-267" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-267', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-268', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-name">errmsg</tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">docsum</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom</tt><tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt id="link-269" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-269', 'id', 'link-269');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">docsum</tt><tt class="py-op">[</tt><tt class="py-string">"Id"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-270', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt id="link-271" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-271', 'd', 'link-174');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-272" class="py-name"><a title="Bio.EUtils.parse.convert_summary_Items" class="py-name" href="#" onclick="return doclink('link-272', 'convert_summary_Items', 'link-236');">convert_summary_Items</a></tt><tt class="py-op">(</tt><tt class="py-name">docsum</tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-273', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Item"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-274" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-274', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-275" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-275', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-276" class="py-name" targets="Class Bio.EUtils.Datatypes.Summary=Bio.EUtils.Datatypes.Summary-class.html"><a title="Bio.EUtils.Datatypes.Summary" class="py-name" href="#" onclick="return doclink('link-276', 'Summary', 'link-276');">Summary</a></tt><tt class="py-op">(</tt><tt id="link-277" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-277', 'id', 'link-269');">id</a></tt><tt class="py-op">,</tt> <tt id="link-278" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-278', 'd', 'link-174');">d</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">results</tt> </tt>
</div><a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-comment">###############################</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-comment"># XML</tt> </tt>
<a name="parse_fetch_publication_xml"></a><div id="parse_fetch_publication_xml-def"><a name="L424"></a><tt class="py-lineno">424</tt> <a class="py-toggle" href="#" id="parse_fetch_publication_xml-toggle" onclick="return toggle('parse_fetch_publication_xml');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_fetch_publication_xml">parse_fetch_publication_xml</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_fetch_publication_xml-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_fetch_publication_xml-expanded"><a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-279" class="py-name"><a title="Bio.EUtils.parse._check_for_bad_input_stream" class="py-name" href="#" onclick="return doclink('link-279', '_check_for_bad_input_stream', 'link-79');">_check_for_bad_input_stream</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">force_encoding</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">xml_parser</tt> <tt class="py-op">=</tt> <tt id="link-280" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser" class="py-name" href="#" onclick="return doclink('link-280', 'UsePOMParser', 'link-80');">UsePOMParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"pubmed_020114"</tt><tt class="py-op">)</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">xml_parser</tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser.parse_using_dtd" class="py-name" href="#" onclick="return doclink('link-281', 'parse_using_dtd', 'link-81');">parse_using_dtd</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> </tt>
<a name="parse_fetch_sequence_xml"></a><div id="parse_fetch_sequence_xml-def"><a name="L429"></a><tt class="py-lineno">429</tt> <a class="py-toggle" href="#" id="parse_fetch_sequence_xml-toggle" onclick="return toggle('parse_fetch_sequence_xml');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_fetch_sequence_xml">parse_fetch_sequence_xml</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_fetch_sequence_xml-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_fetch_sequence_xml-expanded"><a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt> </tt>
</div><a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt class="py-comment"># Identifer list ("\n" separated)</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Useful for "uilist", "acc", and a few others</tt> </tt>
<a name="parse_fetch_identifiers"></a><div id="parse_fetch_identifiers-def"><a name="L434"></a><tt class="py-lineno">434</tt> <a class="py-toggle" href="#" id="parse_fetch_identifiers-toggle" onclick="return toggle('parse_fetch_identifiers');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_fetch_identifiers">parse_fetch_identifiers</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_fetch_identifiers-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_fetch_identifiers-expanded"><a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-282" class="py-name"><a title="Bio.EUtils.parse._check_for_bad_input_stream" class="py-name" href="#" onclick="return doclink('link-282', '_check_for_bad_input_stream', 'link-79');">_check_for_bad_input_stream</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-283" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-283', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-284" 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-284', 'strip', 'link-125');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-285" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-285', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-286" 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-286', 'readlines', 'link-286');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt id="link-287" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-287', 'x', 'link-5');">x</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">"\n"</tt><tt class="py-op">]</tt> </tt>
</div><a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-comment">###############################</tt> </tt>
<a name="_check_for_link_errors"></a><div id="_check_for_link_errors-def"><a name="L439"></a><tt class="py-lineno">439</tt> <a class="py-toggle" href="#" id="_check_for_link_errors-toggle" onclick="return toggle('_check_for_link_errors');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_check_for_link_errors">_check_for_link_errors</a><tt class="py-op">(</tt><tt class="py-param">pom</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_check_for_link_errors-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_check_for_link_errors-expanded"><a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-288" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-288', 'has_key', 'link-288');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"LinkSet"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-289', 'has_key', 'link-288');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-290" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-290', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-291', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-292', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-293" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-293', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-294', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-string">"Server failed to process request"</tt><tt class="py-op">)</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">.</tt><tt id="link-295" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-295', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"LinkSet"</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>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-string">"Did not expect to find more than one LinkSet in the XML"</tt><tt class="py-op">)</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-name">linkset</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"LinkSet"</tt><tt class="py-op">]</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">linkset</tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-296', 'has_key', 'link-288');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-297" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-297', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-298', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-name">linkset</tt><tt class="py-op">[</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-299', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> </tt>
<a name="_parse_link"></a><div id="_parse_link-def"><a name="L451"></a><tt class="py-lineno">451</tt> <a class="py-toggle" href="#" id="_parse_link-toggle" onclick="return toggle('_parse_link');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_parse_link">_parse_link</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_link-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_link-expanded"><a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-comment">#infile = _check_for_bad_input_stream(infile)</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Need this, as seen in</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=llinks&db=pubmed&id=10611131%2C12085853</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># which has an a-with-umlaut in Latin-1 encoding</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">codecs</tt><tt class="py-op">.</tt><tt class="py-name">EncodedFile</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"utf-8"</tt><tt class="py-op">,</tt> <tt class="py-string">"iso-8859-1"</tt><tt class="py-op">)</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-name">xml_parser</tt> <tt class="py-op">=</tt> <tt id="link-300" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser" class="py-name" href="#" onclick="return doclink('link-300', 'UsePOMParser', 'link-80');">UsePOMParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"eLink_020511"</tt><tt class="py-op">)</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt class="py-name">xml_parser</tt><tt class="py-op">.</tt><tt id="link-301" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser.parse_using_dtd" class="py-name" href="#" onclick="return doclink('link-301', 'parse_using_dtd', 'link-81');">parse_using_dtd</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt id="link-302" class="py-name" targets="Function Bio.EUtils.parse._check_for_link_errors()=Bio.EUtils.parse-module.html#_check_for_link_errors"><a title="Bio.EUtils.parse._check_for_link_errors" class="py-name" href="#" onclick="return doclink('link-302', '_check_for_link_errors', 'link-302');">_check_for_link_errors</a></tt><tt class="py-op">(</tt><tt class="py-name">pom</tt><tt class="py-op">)</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">pom</tt> </tt>
</div><a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> </tt>
<a name="parse_neighbor_links"></a><div id="parse_neighbor_links-def"><a name="L463"></a><tt class="py-lineno">463</tt> <a class="py-toggle" href="#" id="parse_neighbor_links-toggle" onclick="return toggle('parse_neighbor_links');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_neighbor_links">parse_neighbor_links</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_neighbor_links-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_neighbor_links-expanded"><a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt id="link-303" class="py-name" targets="Function Bio.EUtils.parse._parse_link()=Bio.EUtils.parse-module.html#_parse_link"><a title="Bio.EUtils.parse._parse_link" class="py-name" href="#" onclick="return doclink('link-303', '_parse_link', 'link-303');">_parse_link</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">pom_linkset</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"LinkSet"</tt><tt class="py-op">]</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-name">dbfrom</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">[</tt><tt class="py-string">"DbFrom"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-304" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-304', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">idlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-305" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-305', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-306" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-306', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-307" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-307', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">[</tt><tt class="py-string">"IdList"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-308', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Id"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-name">linksetdbs</tt> <tt class="py-op">=</tt> <tt id="link-309" class="py-name"><a title="Bio.EUtils.MultiDict" class="py-name" href="#" onclick="return doclink('link-309', 'MultiDict', 'link-3');">MultiDict</a></tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Bio.EUtils.MultiDict.OrderedMultiDict" class="py-name" href="#" onclick="return doclink('link-310', 'OrderedMultiDict', 'link-241');">OrderedMultiDict</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pom_linksetdb</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">.</tt><tt id="link-311" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-311', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"LinkSetDb"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pom_linksetdb</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-312', 'has_key', 'link-288');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-313" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-313', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-314" class="py-name"><a title="Bio.EUtils.Datatypes.EUtilsError" class="py-name" href="#" onclick="return doclink('link-314', 'EUtilsError', 'link-67');">EUtilsError</a></tt><tt class="py-op">(</tt><tt class="py-name">pom_linksetdb</tt><tt class="py-op">[</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-315', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-name">dbto</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_linksetdb</tt><tt class="py-op">[</tt><tt class="py-string">"DbTo"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-316" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-316', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">linkname</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_linksetdb</tt><tt class="py-op">[</tt><tt class="py-string">"LinkName"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-317" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-317', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-name">links</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pom_link</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom_linksetdb</tt><tt class="py-op">.</tt><tt id="link-318" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-318', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Link"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt id="link-319" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-319', 'score', 'link-319');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">pom_link</tt><tt class="py-op">.</tt><tt id="link-320" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-320', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"Score"</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-321" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-321', 'score', 'link-319');">score</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt id="link-322" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-322', 'score', 'link-319');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-323" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-323', 'score', 'link-319');">score</a></tt><tt class="py-op">.</tt><tt id="link-324" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-324', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">links</tt><tt class="py-op">.</tt><tt id="link-325" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-325', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-326" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-326', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-327" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.Link=Bio.EUtils.DTDs.LinkOut.Link-class.html,Class Bio.EUtils.DTDs.eInfo_020511.Link=Bio.EUtils.DTDs.eInfo_020511.Link-class.html,Class Bio.EUtils.DTDs.eLink_020511.Link=Bio.EUtils.DTDs.eLink_020511.Link-class.html,Class Bio.EUtils.Datatypes.Link=Bio.EUtils.Datatypes.Link-class.html"><a title="Bio.EUtils.DTDs.LinkOut.Link
Bio.EUtils.DTDs.eInfo_020511.Link
Bio.EUtils.DTDs.eLink_020511.Link
Bio.EUtils.Datatypes.Link" class="py-name" href="#" onclick="return doclink('link-327', 'Link', 'link-327');">Link</a></tt><tt class="py-op">(</tt><tt class="py-name">pom_link</tt><tt class="py-op">[</tt><tt class="py-string">"Id"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-328', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-329" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-329', 'score', 'link-319');">score</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-name">linksetdbs</tt><tt class="py-op">[</tt><tt class="py-name">linkname</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-330" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-330', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-331" class="py-name" targets="Class Bio.EUtils.DTDs.eLink_020511.LinkSetDb=Bio.EUtils.DTDs.eLink_020511.LinkSetDb-class.html,Class Bio.EUtils.Datatypes.LinkSetDb=Bio.EUtils.Datatypes.LinkSetDb-class.html"><a title="Bio.EUtils.DTDs.eLink_020511.LinkSetDb
Bio.EUtils.Datatypes.LinkSetDb" class="py-name" href="#" onclick="return doclink('link-331', 'LinkSetDb', 'link-331');">LinkSetDb</a></tt><tt class="py-op">(</tt><tt class="py-name">dbto</tt><tt class="py-op">,</tt> <tt class="py-name">linkname</tt><tt class="py-op">,</tt> <tt class="py-name">links</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-332" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-332', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-333" class="py-name" targets="Class Bio.EUtils.Datatypes.NeighborLinkSet=Bio.EUtils.Datatypes.NeighborLinkSet-class.html"><a title="Bio.EUtils.Datatypes.NeighborLinkSet" class="py-name" href="#" onclick="return doclink('link-333', 'NeighborLinkSet', 'link-333');">NeighborLinkSet</a></tt><tt class="py-op">(</tt><tt id="link-334" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-334', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-335" class="py-name" targets="Class Bio.EUtils.Datatypes.DBIds=Bio.EUtils.Datatypes.DBIds-class.html"><a title="Bio.EUtils.Datatypes.DBIds" class="py-name" href="#" onclick="return doclink('link-335', 'DBIds', 'link-335');">DBIds</a></tt><tt class="py-op">(</tt><tt class="py-name">dbfrom</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">idlist</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-name">linksetdbs</tt><tt class="py-op">)</tt> </tt>
</div><a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> </tt>
<a name="parse_lcheck"></a><div id="parse_lcheck-def"><a name="L486"></a><tt class="py-lineno">486</tt> <a class="py-toggle" href="#" id="parse_lcheck-toggle" onclick="return toggle('parse_lcheck');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_lcheck">parse_lcheck</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_lcheck-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_lcheck-expanded"><a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt id="link-336" class="py-name"><a title="Bio.EUtils.parse._parse_link" class="py-name" href="#" onclick="return doclink('link-336', '_parse_link', 'link-303');">_parse_link</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-name">pom_linkset</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"LinkSet"</tt><tt class="py-op">]</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-name">dbfrom</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">[</tt><tt class="py-string">"DbFrom"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-337" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-337', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-name">idchecks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ele</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">[</tt><tt class="py-string">"IdCheckList"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-338" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-338', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Id"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-name">has_linkout</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">,</tt> <tt class="py-string">"HasLinkOut"</tt><tt class="py-op">,</tt> <tt class="py-string">"N"</tt><tt class="py-op">)</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-name">has_linkout</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-number">1</tt><tt class="py-op">}</tt><tt class="py-op">.</tt><tt id="link-339" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-339', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">has_linkout</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-name">has_neighbor</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">,</tt> <tt class="py-string">"HasNeighbor"</tt><tt class="py-op">,</tt> <tt class="py-string">"N"</tt><tt class="py-op">)</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">has_neighbor</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-number">1</tt><tt class="py-op">}</tt><tt class="py-op">.</tt><tt id="link-340" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-340', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">has_neighbor</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-name">idchecks</tt><tt class="py-op">.</tt><tt id="link-341" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-341', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-342" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-342', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-343" class="py-name" targets="Class Bio.EUtils.Datatypes.IdCheck=Bio.EUtils.Datatypes.IdCheck-class.html"><a title="Bio.EUtils.Datatypes.IdCheck" class="py-name" href="#" onclick="return doclink('link-343', 'IdCheck', 'link-343');">IdCheck</a></tt><tt class="py-op">(</tt><tt class="py-name">ele</tt><tt class="py-op">.</tt><tt id="link-344" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-344', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-name">has_linkout</tt><tt class="py-op">,</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-name">has_neighbor</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-345" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-345', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-346" class="py-name" targets="Class Bio.EUtils.Datatypes.CheckLinkSet=Bio.EUtils.Datatypes.CheckLinkSet-class.html"><a title="Bio.EUtils.Datatypes.CheckLinkSet" class="py-name" href="#" onclick="return doclink('link-346', 'CheckLinkSet', 'link-346');">CheckLinkSet</a></tt><tt class="py-op">(</tt><tt class="py-name">dbfrom</tt><tt class="py-op">,</tt> <tt class="py-name">idchecks</tt><tt class="py-op">)</tt> </tt>
</div><a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-name">parse_ncheck</tt> <tt class="py-op">=</tt> <tt id="link-347" class="py-name" targets="Function Bio.EUtils.parse.parse_lcheck()=Bio.EUtils.parse-module.html#parse_lcheck"><a title="Bio.EUtils.parse.parse_lcheck" class="py-name" href="#" onclick="return doclink('link-347', 'parse_lcheck', 'link-347');">parse_lcheck</a></tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> </tt>
<a name="_get_opt_string"></a><div id="_get_opt_string-def"><a name="L503"></a><tt class="py-lineno">503</tt> <a class="py-toggle" href="#" id="_get_opt_string-toggle" onclick="return toggle('_get_opt_string');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#_get_opt_string">_get_opt_string</a><tt class="py-op">(</tt><tt class="py-param">ele</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_opt_string-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_opt_string-expanded"><a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt id="link-348" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-348', 'x', 'link-5');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ele</tt><tt class="py-op">.</tt><tt id="link-349" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-349', 'get', 'link-34');">get</a></tt><tt class="py-op">(</tt><tt id="link-350" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-350', 'name', 'link-22');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-351" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-351', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt id="link-352" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-352', 's', 'link-56');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-353" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-353', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-354" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-354', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-355" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-355', 's', 'link-56');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-356" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-356', 's', 'link-56');">s</a></tt> </tt>
</div><a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> </tt>
<a name="parse_llinks"></a><div id="parse_llinks-def"><a name="L512"></a><tt class="py-lineno">512</tt> <a class="py-toggle" href="#" id="parse_llinks-toggle" onclick="return toggle('parse_llinks');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_llinks">parse_llinks</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_llinks-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_llinks-expanded"><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">pom</tt> <tt class="py-op">=</tt> <tt id="link-357" class="py-name"><a title="Bio.EUtils.parse._parse_link" class="py-name" href="#" onclick="return doclink('link-357', '_parse_link', 'link-303');">_parse_link</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-name">pom_linkset</tt> <tt class="py-op">=</tt> <tt class="py-name">pom</tt><tt class="py-op">[</tt><tt class="py-string">"LinkSet"</tt><tt class="py-op">]</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-name">dbfrom</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">[</tt><tt class="py-string">"DbFrom"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-358" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-358', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-name">idurlsets</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ele</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom_linkset</tt><tt class="py-op">[</tt><tt class="py-string">"IdUrlList"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-359" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-359', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"IdUrlSet"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt id="link-360" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-360', 'id', 'link-269');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ele</tt><tt class="py-op">[</tt><tt class="py-string">"Id"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-361" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-361', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-name">objurls</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pom_objurl</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ele</tt><tt class="py-op">.</tt><tt id="link-362" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-362', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"ObjUrl"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt id="link-363" class="py-name" targets="Function Bio.EUtils.parse._get_opt_string()=Bio.EUtils.parse-module.html#_get_opt_string"><a title="Bio.EUtils.parse._get_opt_string" class="py-name" href="#" onclick="return doclink('link-363', '_get_opt_string', 'link-363');">_get_opt_string</a></tt><tt class="py-op">(</tt><tt class="py-name">pom_objurl</tt><tt class="py-op">,</tt> <tt class="py-string">"Url"</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-name">linkname</tt> <tt class="py-op">=</tt> <tt id="link-364" class="py-name"><a title="Bio.EUtils.parse._get_opt_string" class="py-name" href="#" onclick="return doclink('link-364', '_get_opt_string', 'link-363');">_get_opt_string</a></tt><tt class="py-op">(</tt><tt class="py-name">pom_objurl</tt><tt class="py-op">,</tt> <tt class="py-string">"LinkName"</tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-name">subject_types</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-365" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-365', 'x', 'link-5');">x</a></tt><tt class="py-op">.</tt><tt id="link-366" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-366', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-367" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-367', 'x', 'link-5');">x</a></tt> <tt class="py-keyword">in</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-name">pom_objurl</tt><tt class="py-op">.</tt><tt id="link-368" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-368', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"SubjectType"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt id="link-369" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.attributes()=Bio.EUtils.POM.ElementNode-class.html#attributes"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-369', 'attributes', 'link-369');">attributes</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-370" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-370', 's', 'link-56');">s</a></tt><tt class="py-op">.</tt><tt id="link-371" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-371', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-372" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-372', 's', 'link-56');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">pom_objurl</tt><tt class="py-op">.</tt><tt id="link-373" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find_elements" class="py-name" href="#" onclick="return doclink('link-373', 'find_elements', 'link-112');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-string">"Attribute"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-name">pom_provider</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_objurl</tt><tt class="py-op">[</tt><tt class="py-string">"Provider"</tt><tt class="py-op">]</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-name">provider_name</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_provider</tt><tt class="py-op">[</tt><tt class="py-string">"Name"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-374" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-374', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-name">provider_name_abbr</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_provider</tt><tt class="py-op">[</tt><tt class="py-string">"NameAbbr"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-375" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-375', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-name">provider_id</tt> <tt class="py-op">=</tt> <tt class="py-name">pom_provider</tt><tt class="py-op">[</tt><tt class="py-string">"Id"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-376" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-376', 'tostring', 'link-35');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-name">provider_url</tt> <tt class="py-op">=</tt> <tt id="link-377" class="py-name"><a title="Bio.EUtils.parse._get_opt_string" class="py-name" href="#" onclick="return doclink('link-377', '_get_opt_string', 'link-363');">_get_opt_string</a></tt><tt class="py-op">(</tt><tt class="py-name">pom_provider</tt><tt class="py-op">,</tt> <tt class="py-string">"Url"</tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-name">provider_icon_url</tt> <tt class="py-op">=</tt> <tt id="link-378" class="py-name"><a title="Bio.EUtils.parse._get_opt_string" class="py-name" href="#" onclick="return doclink('link-378', '_get_opt_string', 'link-363');">_get_opt_string</a></tt><tt class="py-op">(</tt><tt class="py-name">pom_provider</tt><tt class="py-op">,</tt> <tt class="py-string">"IconUrl"</tt><tt class="py-op">)</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-name">provider</tt> <tt class="py-op">=</tt> <tt id="link-379" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-379', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-380" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.Provider=Bio.EUtils.DTDs.LinkOut.Provider-class.html,Class Bio.EUtils.DTDs.eLink_020511.Provider=Bio.EUtils.DTDs.eLink_020511.Provider-class.html,Class Bio.EUtils.Datatypes.Provider=Bio.EUtils.Datatypes.Provider-class.html"><a title="Bio.EUtils.DTDs.LinkOut.Provider
Bio.EUtils.DTDs.eLink_020511.Provider
Bio.EUtils.Datatypes.Provider" class="py-name" href="#" onclick="return doclink('link-380', 'Provider', 'link-380');">Provider</a></tt><tt class="py-op">(</tt><tt class="py-name">provider_name</tt><tt class="py-op">,</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-name">provider_name_abbr</tt><tt class="py-op">,</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-name">provider_id</tt><tt class="py-op">,</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-name">provider_url</tt><tt class="py-op">,</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-name">provider_icon_url</tt><tt class="py-op">)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-name">objurl</tt> <tt class="py-op">=</tt> <tt id="link-381" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-381', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-382" class="py-name" targets="Class Bio.EUtils.DTDs.eLink_020511.ObjUrl=Bio.EUtils.DTDs.eLink_020511.ObjUrl-class.html,Class Bio.EUtils.Datatypes.ObjUrl=Bio.EUtils.Datatypes.ObjUrl-class.html"><a title="Bio.EUtils.DTDs.eLink_020511.ObjUrl
Bio.EUtils.Datatypes.ObjUrl" class="py-name" href="#" onclick="return doclink('link-382', 'ObjUrl', 'link-382');">ObjUrl</a></tt><tt class="py-op">(</tt><tt class="py-name">subject_types</tt><tt class="py-op">,</tt> <tt class="py-name">provider</tt><tt class="py-op">,</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">linkname</tt><tt class="py-op">,</tt> <tt class="py-name">url</tt><tt class="py-op">,</tt> <tt id="link-383" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-383', 'attributes', 'link-369');">attributes</a></tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">objurls</tt><tt class="py-op">.</tt><tt id="link-384" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-384', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">objurl</tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-name">idurlsets</tt><tt class="py-op">.</tt><tt id="link-385" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-385', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt id="link-386" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-386', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-387" class="py-name" targets="Class Bio.EUtils.DTDs.eLink_020511.IdUrlSet=Bio.EUtils.DTDs.eLink_020511.IdUrlSet-class.html,Class Bio.EUtils.Datatypes.IdUrlSet=Bio.EUtils.Datatypes.IdUrlSet-class.html"><a title="Bio.EUtils.DTDs.eLink_020511.IdUrlSet
Bio.EUtils.Datatypes.IdUrlSet" class="py-name" href="#" onclick="return doclink('link-387', 'IdUrlSet', 'link-387');">IdUrlSet</a></tt><tt class="py-op">(</tt><tt id="link-388" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-388', 'id', 'link-269');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">objurls</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-389" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-389', 'Datatypes', 'link-1');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-390" class="py-name" targets="Class Bio.EUtils.Datatypes.LinksLinkSet=Bio.EUtils.Datatypes.LinksLinkSet-class.html"><a title="Bio.EUtils.Datatypes.LinksLinkSet" class="py-name" href="#" onclick="return doclink('link-390', 'LinksLinkSet', 'link-390');">LinksLinkSet</a></tt><tt class="py-op">(</tt><tt class="py-name">dbfrom</tt><tt class="py-op">,</tt> <tt class="py-name">idurlsets</tt><tt class="py-op">)</tt> </tt>
</div><a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"><tt class="py-name">parse_prlinks</tt> <tt class="py-op">=</tt> <tt id="link-391" class="py-name" targets="Function Bio.EUtils.parse.parse_llinks()=Bio.EUtils.parse-module.html#parse_llinks"><a title="Bio.EUtils.parse.parse_llinks" class="py-name" href="#" onclick="return doclink('link-391', 'parse_llinks', 'link-391');">parse_llinks</a></tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> </tt>
<a name="parse_link_xml"></a><div id="parse_link_xml-def"><a name="L549"></a><tt class="py-lineno">549</tt> <a class="py-toggle" href="#" id="parse_link_xml-toggle" onclick="return toggle('parse_link_xml');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.parse-module.html#parse_link_xml">parse_link_xml</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_link_xml-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_link_xml-expanded"><a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-392" class="py-name"><a title="Bio.EUtils.parse._check_for_bad_input_stream" class="py-name" href="#" onclick="return doclink('link-392', '_check_for_bad_input_stream', 'link-79');">_check_for_bad_input_stream</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-name">xml_parser</tt> <tt class="py-op">=</tt> <tt id="link-393" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser" class="py-name" href="#" onclick="return doclink('link-393', 'UsePOMParser', 'link-80');">UsePOMParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"eLink_020511"</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">xml_parser</tt><tt class="py-op">.</tt><tt id="link-394" class="py-name"><a title="Bio.EUtils.parse.UsePOMParser.parse_using_dtd" class="py-name" href="#" onclick="return doclink('link-394', 'parse_using_dtd', 'link-81');">parse_using_dtd</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> </tt><script type="text/javascript">
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