Automated update 86c189c43d1e8c9e9a17e8b9ffb314718b39aa27

dev/api/Bio.SeqIO.UniprotIO.html

@@ -139,37 +139,45 @@
 <a class="reference external" href="http://www.uniprot.org">http://www.uniprot.org</a></p>
 <p>The UniProt XML format essentially replaces the old plain text file format
 originally introduced by SwissProt (“swiss” format in Bio.SeqIO).</p>
-<dl class="py function">
+<dl class="py class">
 <dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.UniprotIterator">
-<span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.UniprotIO.</span></span><span class="sig-name descname"><span class="pre">UniprotIterator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_raw_comments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.UniprotIO.</span></span><span class="sig-name descname"><span class="pre">UniprotIterator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="p"><span class="pre">[</span></span><span class="pre">bytes</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_raw_comments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator" title="Link to this definition"></a></dt>
+<dd><p>Bases: <a class="reference internal" href="Bio.SeqIO.Interfaces.html#Bio.SeqIO.Interfaces.SequenceIterator" title="Bio.SeqIO.Interfaces.SequenceIterator"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceIterator</span></code></a></p>
+<p>Parser for UniProt XML files, returning SeqRecord objects.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.UniprotIterator.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">IO</span><span class="p"><span class="pre">[</span></span><span class="pre">bytes</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bytes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_raw_comments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator.__init__" title="Link to this definition"></a></dt>
 <dd><p>Iterate over UniProt XML as SeqRecord objects.</p>
 <p>parses an XML entry at a time from any UniProt XML file
 returns a SeqRecord for each iteration</p>
-<p>This generator can be used in Bio.SeqIO</p>
-<p>Argument source is a file-like object or a path to a file.</p>
-<p>Optional argument alphabet should not be used anymore.</p>
-<p>return_raw_comments = True –&gt; comment fields are returned as complete XML to allow further processing
-skip_parsing_errors = True –&gt; if parsing errors are found, skip to next entry</p>
+<dl class="simple">
+<dt>Arguments:</dt><dd><ul class="simple">
+<li><p>source   - input stream opened in binary mode, or a path to a file</p></li>
+<li><p>alphabet - optional alphabet, not used. Leave as None.</p></li>
+<li><p>return_raw_comments - if True, return comment fields as complete XML
+to allow further processing.</p></li>
+</ul>
+</dd>
+</dl>
+<p>This generator can be used in Bio.SeqIO.</p>
 </dd></dl>
 
-<dl class="py class">
-<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.Parser">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.SeqIO.UniprotIO.</span></span><span class="sig-name descname"><span class="pre">Parser</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elem</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_raw_comments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.Parser" title="Link to this definition"></a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Parse a UniProt XML entry to a SeqRecord.</p>
-<p>Optional argument alphabet is no longer used.</p>
-<p>return_raw_comments=True to get back the complete comment field in XML format</p>
 <dl class="py method">
-<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.Parser.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elem</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_raw_comments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.Parser.__init__" title="Link to this definition"></a></dt>
-<dd><p>Initialize the class.</p>
+<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.UniprotIterator.__next__">
+<span class="sig-name descname"><span class="pre">__next__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator.__next__" title="Link to this definition"></a></dt>
+<dd><p>Return the next SeqRecord.</p>
+<p>This method must be implemented by the subclass.</p>
 </dd></dl>
 
-<dl class="py method">
-<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.Parser.parse">
-<span class="sig-name descname"><span class="pre">parse</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqIO.UniprotIO.Parser.parse" title="Link to this definition"></a></dt>
-<dd><p>Parse the input.</p>
-</dd></dl>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.UniprotIterator.__abstractmethods__">
+<span class="sig-name descname"><span class="pre">__abstractmethods__</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">frozenset({})</span></em><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator.__abstractmethods__" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.UniprotIterator.__parameters__">
+<span class="sig-name descname"><span class="pre">__parameters__</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">()</span></em><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator.__parameters__" title="Link to this definition"></a></dt>
+<dd></dd></dl>
 
 </dd></dl>
 

dev/api/Bio.SeqIO.html

@@ -578,10 +578,11 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html">Bio.SeqIO.UniprotIO module</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator"><code class="docutils literal notranslate"><span class="pre">UniprotIterator()</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser"><code class="docutils literal notranslate"><span class="pre">Parser</span></code></a><ul>
-<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser.__init__"><code class="docutils literal notranslate"><span class="pre">Parser.__init__()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser.parse"><code class="docutils literal notranslate"><span class="pre">Parser.parse()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator"><code class="docutils literal notranslate"><span class="pre">UniprotIterator</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__init__"><code class="docutils literal notranslate"><span class="pre">UniprotIterator.__init__()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__next__"><code class="docutils literal notranslate"><span class="pre">UniprotIterator.__next__()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">UniprotIterator.__abstractmethods__</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__parameters__"><code class="docutils literal notranslate"><span class="pre">UniprotIterator.__parameters__</span></code></a></li>
 </ul>
 </li>
 </ul>

dev/api/Bio.html

@@ -1841,8 +1841,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html">Bio.SeqIO.UniprotIO module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator"><code class="docutils literal notranslate"><span class="pre">UniprotIterator()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser"><code class="docutils literal notranslate"><span class="pre">Parser</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator"><code class="docutils literal notranslate"><span class="pre">UniprotIterator</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="Bio.SeqIO.XdnaIO.html">Bio.SeqIO.XdnaIO module</a><ul>

dev/genindex.html

@@ -325,6 +325,8 @@ <h2 id="_">_</h2>
         <li><a href="api/Bio.SeqIO.TabIO.html#Bio.SeqIO.TabIO.TabIterator.__abstractmethods__">(Bio.SeqIO.TabIO.TabIterator attribute)</a>
 </li>
         <li><a href="api/Bio.SeqIO.TwoBitIO.html#Bio.SeqIO.TwoBitIO.TwoBitIterator.__abstractmethods__">(Bio.SeqIO.TwoBitIO.TwoBitIterator attribute)</a>
+</li>
+        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__abstractmethods__">(Bio.SeqIO.UniprotIO.UniprotIterator attribute)</a>
 </li>
         <li><a href="api/Bio.SeqIO.XdnaIO.html#Bio.SeqIO.XdnaIO.XdnaIterator.__abstractmethods__">(Bio.SeqIO.XdnaIO.XdnaIterator attribute)</a>
 </li>
@@ -1598,7 +1600,7 @@ <h2 id="_">_</h2>
 </li>
         <li><a href="api/Bio.SeqIO.TwoBitIO.html#Bio.SeqIO.TwoBitIO.TwoBitIterator.__init__">(Bio.SeqIO.TwoBitIO.TwoBitIterator method)</a>
 </li>
-        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser.__init__">(Bio.SeqIO.UniprotIO.Parser method)</a>
+        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__init__">(Bio.SeqIO.UniprotIO.UniprotIterator method)</a>
 </li>
         <li><a href="api/Bio.SeqIO.XdnaIO.html#Bio.SeqIO.XdnaIO.XdnaIterator.__init__">(Bio.SeqIO.XdnaIO.XdnaIterator method)</a>
 </li>
@@ -2059,6 +2061,8 @@ <h2 id="_">_</h2>
         <li><a href="api/Bio.SeqIO.TabIO.html#Bio.SeqIO.TabIO.TabIterator.__next__">(Bio.SeqIO.TabIO.TabIterator method)</a>
 </li>
         <li><a href="api/Bio.SeqIO.TwoBitIO.html#Bio.SeqIO.TwoBitIO.TwoBitIterator.__next__">(Bio.SeqIO.TwoBitIO.TwoBitIterator method)</a>
+</li>
+        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__next__">(Bio.SeqIO.UniprotIO.UniprotIterator method)</a>
 </li>
         <li><a href="api/Bio.SeqIO.XdnaIO.html#Bio.SeqIO.XdnaIO.XdnaIterator.__next__">(Bio.SeqIO.XdnaIO.XdnaIterator method)</a>
 </li>
@@ -2161,6 +2165,8 @@ <h2 id="_">_</h2>
         <li><a href="api/Bio.SeqIO.TabIO.html#Bio.SeqIO.TabIO.TabIterator.__parameters__">(Bio.SeqIO.TabIO.TabIterator attribute)</a>
 </li>
         <li><a href="api/Bio.SeqIO.TwoBitIO.html#Bio.SeqIO.TwoBitIO.TwoBitIterator.__parameters__">(Bio.SeqIO.TwoBitIO.TwoBitIterator attribute)</a>
+</li>
+        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator.__parameters__">(Bio.SeqIO.UniprotIO.UniprotIterator attribute)</a>
 </li>
         <li><a href="api/Bio.SeqIO.XdnaIO.html#Bio.SeqIO.XdnaIO.XdnaIterator.__parameters__">(Bio.SeqIO.XdnaIO.XdnaIterator attribute)</a>
 </li>
@@ -10951,8 +10957,6 @@ <h2 id="P">P</h2>
         <li><a href="api/Bio.Phylo.NeXMLIO.html#Bio.Phylo.NeXMLIO.Parser.parse">(Bio.Phylo.NeXMLIO.Parser method)</a>
 </li>
         <li><a href="api/Bio.Phylo.PhyloXMLIO.html#Bio.Phylo.PhyloXMLIO.Parser.parse">(Bio.Phylo.PhyloXMLIO.Parser method)</a>
-</li>
-        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser.parse">(Bio.SeqIO.UniprotIO.Parser method)</a>
 </li>
         <li><a href="api/Bio.Align.html#Bio.Align.parse">(in module Bio.Align)</a>
 </li>
@@ -11121,8 +11125,6 @@ <h2 id="P">P</h2>
         <li><a href="api/Bio.Phylo.NeXMLIO.html#Bio.Phylo.NeXMLIO.Parser">(class in Bio.Phylo.NeXMLIO)</a>
 </li>
         <li><a href="api/Bio.Phylo.PhyloXMLIO.html#Bio.Phylo.PhyloXMLIO.Parser">(class in Bio.Phylo.PhyloXMLIO)</a>
-</li>
-        <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.Parser">(class in Bio.SeqIO.UniprotIO)</a>
 </li>
       </ul></li>
       <li><a href="api/Bio.Affy.CelFile.html#Bio.Affy.CelFile.ParserError">ParserError</a>
@@ -11177,10 +11179,10 @@ <h2 id="P">P</h2>
 </li>
       <li><a href="api/Bio.PDB.PDBExceptions.html#Bio.PDB.PDBExceptions.PDBIOException">PDBIOException</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/Bio.PDB.PDBList.html#Bio.PDB.PDBList.PDBList">PDBList (class in Bio.PDB.PDBList)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/Bio.PDB.PDBMLParser.html#Bio.PDB.PDBMLParser.PDBMLParser">PDBMLParser (class in Bio.PDB.PDBMLParser)</a>
 </li>
       <li><a href="api/Bio.PDB.PDBParser.html#Bio.PDB.PDBParser.PDBParser">PDBParser (class in Bio.PDB.PDBParser)</a>
@@ -13859,7 +13861,7 @@ <h2 id="U">U</h2>
       </ul></li>
       <li><a href="api/Bio.Emboss.Applications.html#Bio.Emboss.Applications.ETandemCommandline.uniform">uniform (Bio.Emboss.Applications.ETandemCommandline property)</a>
 </li>
-      <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator">UniprotIterator() (in module Bio.SeqIO.UniprotIO)</a>
+      <li><a href="api/Bio.SeqIO.UniprotIO.html#Bio.SeqIO.UniprotIO.UniprotIterator">UniprotIterator (class in Bio.SeqIO.UniprotIO)</a>
 </li>
       <li><a href="api/Bio.PDB.Selection.html#Bio.PDB.Selection.uniqueify">uniqueify() (in module Bio.PDB.Selection)</a>
 </li>