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‎dev/api/Bio.Entrez.html‎

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</dl>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="Bio.Entrez.egquery">
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<span class="sig-prename descclassname"><span class="pre">Bio.Entrez.</span></span><span class="sig-name descname"><span class="pre">egquery</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">keywds</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.Entrez.egquery" title="Link to this definition"></a></dt>
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<dd><p>Provide Entrez database counts for a global search (DEPRECATED).</p>
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<p>EGQuery provided Entrez database counts in XML for a single search
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using Global Query. However, the NCBI are no longer maintaining this
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function and suggest using esearch on each database of interest.</p>
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<p>See the online documentation for an explanation of the parameters:
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<a class="reference external" href="http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EGQuery">http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EGQuery</a></p>
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<p>This quick example based on a longer version from the Biopython
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Tutorial just checks there are over 60 matches for ‘Biopython’
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in PubMedCentral:</p>
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<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">Bio</span><span class="w"> </span><span class="kn">import</span> <span class="n">Entrez</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">Entrez</span><span class="o">.</span><span class="n">email</span> <span class="o">=</span> <span class="s2">&quot;Your.Name.Here@example.org&quot;</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">handle</span> <span class="o">=</span> <span class="n">Entrez</span><span class="o">.</span><span class="n">egquery</span><span class="p">(</span><span class="n">term</span><span class="o">=</span><span class="s2">&quot;biopython&quot;</span><span class="p">)</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">record</span> <span class="o">=</span> <span class="n">Entrez</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">handle</span><span class="p">)</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">handle</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">record</span><span class="p">[</span><span class="s2">&quot;eGQueryResult&quot;</span><span class="p">]:</span>
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<span class="gp">... </span> <span class="k">if</span> <span class="s2">&quot;pmc&quot;</span> <span class="ow">in</span> <span class="n">row</span><span class="p">[</span><span class="s2">&quot;DbName&quot;</span><span class="p">]:</span>
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<span class="gp">... </span> <span class="nb">print</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s2">&quot;Count&quot;</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">60</span><span class="p">)</span>
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<span class="go">True</span>
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</pre></div>
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</div>
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<dl class="field-list simple">
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<dt class="field-odd">Returns<span class="colon">:</span></dt>
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<dd class="field-odd"><p>Handle to the results, by default in XML format.</p>
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</dd>
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<dt class="field-even">Raises<span class="colon">:</span></dt>
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<dd class="field-even"><p><strong>urllib.error.URLError</strong> – If there’s a network error.</p>
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</dd>
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</dl>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="Bio.Entrez.espell">
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<span class="sig-prename descclassname"><span class="pre">Bio.Entrez.</span></span><span class="sig-name descname"><span class="pre">espell</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">keywds</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.Entrez.espell" title="Link to this definition"></a></dt>

‎dev/api/Bio.SeqIO.UniprotIO.html‎

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<p>Parser for UniProt XML files, returning SeqRecord objects.</p>
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<dl class="py attribute">
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<dt class="sig sig-object py" id="Bio.SeqIO.UniprotIO.UniprotIterator.modes">
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<span class="sig-name descname"><span class="pre">modes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'bt'</span></em><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator.modes" title="Link to this definition"></a></dt>
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<span class="sig-name descname"><span class="pre">modes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'b'</span></em><a class="headerlink" href="#Bio.SeqIO.UniprotIO.UniprotIterator.modes" title="Link to this definition"></a></dt>
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<dd></dd></dl>
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<dl class="py method">

‎dev/api/Bio.SeqUtils.ProtParam.html‎

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It is not recalculated upon subsequent calls.</p>
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</dd></dl>
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<dl class="py method">
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<dt class="sig sig-object py" id="Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent">
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<span class="sig-name descname"><span class="pre">get_amino_acids_percent</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent" title="Link to this definition"></a></dt>
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<dd><p>Included for backwards compatibility (DEPRECATED).</p>
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</dd></dl>
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<dl class="py property">
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<dt class="sig sig-object py" id="Bio.SeqUtils.ProtParam.ProteinAnalysis.amino_acids_percent">
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<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">amino_acids_percent</span></span><a class="headerlink" href="#Bio.SeqUtils.ProtParam.ProteinAnalysis.amino_acids_percent" title="Link to this definition"></a></dt>
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<dd><p>Get the amino acid content in percentages.</p>
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<p>The same as count_amino_acids only returns the Number in percentage of
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entire sequence. Returns a dictionary of {AminoAcid:percentage}.</p>
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<p>Unlike the deprecated get_amino_acids_percent method, this attribute
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returns percentages in the range 0-100.</p>
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<p>The same as count_amino_acids, but returns the number as a percentage
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of the sequence length. Returns a dictionary of {AminoAcid:percentage},
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where the percentage is in the range 0-100.</p>
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</dd></dl>
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<dl class="py method">

‎dev/api/Bio.SeqUtils.html‎

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<li class="toctree-l2"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis</span></code></a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis.__init__()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.count_amino_acids"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis.count_amino_acids()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis.get_amino_acids_percent()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.amino_acids_percent"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis.amino_acids_percent</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.molecular_weight"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis.molecular_weight()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.aromaticity"><code class="docutils literal notranslate"><span class="pre">ProteinAnalysis.aromaticity()</span></code></a></li>

‎dev/api/Bio.html‎

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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.elink"><code class="docutils literal notranslate"><span class="pre">elink()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.einfo"><code class="docutils literal notranslate"><span class="pre">einfo()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.esummary"><code class="docutils literal notranslate"><span class="pre">esummary()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.egquery"><code class="docutils literal notranslate"><span class="pre">egquery()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.espell"><code class="docutils literal notranslate"><span class="pre">espell()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.ecitmatch"><code class="docutils literal notranslate"><span class="pre">ecitmatch()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.Entrez.html#Bio.Entrez.read"><code class="docutils literal notranslate"><span class="pre">read()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html">Bio.motifs.meme module</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.read"><code class="docutils literal notranslate"><span class="pre">read()</span></code></a></li>
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<li class="toctree-l4"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Motif"><code class="docutils literal notranslate"><span class="pre">Motif</span></code></a></li>
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<li class="toctree-l4"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Instance"><code class="docutils literal notranslate"><span class="pre">Instance</span></code></a></li>
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<li class="toctree-l4"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Record"><code class="docutils literal notranslate"><span class="pre">Record</span></code></a></li>
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</ul>
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‎dev/api/Bio.motifs.html‎

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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Motif.__annotations__"><code class="docutils literal notranslate"><span class="pre">Motif.__annotations__</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Instance"><code class="docutils literal notranslate"><span class="pre">Instance</span></code></a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Instance.__init__"><code class="docutils literal notranslate"><span class="pre">Instance.__init__()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Instance.__abstractmethods__"><code class="docutils literal notranslate"><span class="pre">Instance.__abstractmethods__</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Instance.__annotations__"><code class="docutils literal notranslate"><span class="pre">Instance.__annotations__</span></code></a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Record"><code class="docutils literal notranslate"><span class="pre">Record</span></code></a><ul>
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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Record.__init__"><code class="docutils literal notranslate"><span class="pre">Record.__init__()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="Bio.motifs.meme.html#Bio.motifs.meme.Record.__getitem__"><code class="docutils literal notranslate"><span class="pre">Record.__getitem__()</span></code></a></li>

‎dev/api/Bio.motifs.meme.html‎

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</dd></dl>
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<dl class="py class">
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<dt class="sig sig-object py" id="Bio.motifs.meme.Instance">
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<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.motifs.meme.</span></span><span class="sig-name descname"><span class="pre">Instance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwds</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.motifs.meme.Instance" title="Link to this definition"></a></dt>
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<dd><p>Bases: <a class="reference internal" href="Bio.Seq.html#Bio.Seq.Seq" title="Bio.Seq.Seq"><code class="xref py py-class docutils literal notranslate"><span class="pre">Seq</span></code></a></p>
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<p>A class describing the instances of a MEME motif, and the data thereof.</p>
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<dl class="py method">
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<dt class="sig sig-object py" id="Bio.motifs.meme.Instance.__init__">
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<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwds</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.motifs.meme.Instance.__init__" title="Link to this definition"></a></dt>
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<dd><p>Initialize the class.</p>
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</dd></dl>
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<dl class="py attribute">
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<dt class="sig sig-object py" id="Bio.motifs.meme.Instance.__abstractmethods__">
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<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.motifs.meme.Instance.__abstractmethods__" title="Link to this definition"></a></dt>
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<dd></dd></dl>
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<dl class="py attribute">
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<dt class="sig sig-object py" id="Bio.motifs.meme.Instance.__annotations__">
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<span class="sig-name descname"><span class="pre">__annotations__</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'_data':</span> <span class="pre">'bytes</span> <span class="pre">|</span> <span class="pre">SequenceDataAbstractBaseClass'}</span></em><a class="headerlink" href="#Bio.motifs.meme.Instance.__annotations__" title="Link to this definition"></a></dt>
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<dd></dd></dl>
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</dd></dl>
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<dl class="py class">
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<dt class="sig sig-object py" id="Bio.motifs.meme.Record">
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<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.motifs.meme.</span></span><span class="sig-name descname"><span class="pre">Record</span></span><a class="headerlink" href="#Bio.motifs.meme.Record" title="Link to this definition"></a></dt>

‎dev/genindex.html‎

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<li><a href="api/Bio.Blast.html#Bio.Blast.Records.__abstractmethods__">(Bio.Blast.Records attribute)</a>
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<li><a href="api/Bio.codonalign.codonseq.html#Bio.codonalign.codonseq.CodonSeq.__abstractmethods__">(Bio.codonalign.codonseq.CodonSeq attribute)</a>
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</li>
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<li><a href="api/Bio.motifs.meme.html#Bio.motifs.meme.Instance.__abstractmethods__">(Bio.motifs.meme.Instance attribute)</a>
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<li><a href="api/Bio.SearchIO.BlastIO.blast_tab.html#Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer.__abstractmethods__">(Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer attribute)</a>
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<li><a href="api/Bio.motifs.matrix.html#Bio.motifs.matrix.PositionSpecificScoringMatrix.__annotations__">(Bio.motifs.matrix.PositionSpecificScoringMatrix attribute)</a>
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<li><a href="api/Bio.motifs.matrix.html#Bio.motifs.matrix.PositionWeightMatrix.__annotations__">(Bio.motifs.matrix.PositionWeightMatrix attribute)</a>
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</li>
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<li><a href="api/Bio.motifs.meme.html#Bio.motifs.meme.Instance.__annotations__">(Bio.motifs.meme.Instance attribute)</a>
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<li><a href="api/Bio.motifs.meme.html#Bio.motifs.meme.Motif.__annotations__">(Bio.motifs.meme.Motif attribute)</a>
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<li><a href="api/Bio.motifs.matrix.html#Bio.motifs.matrix.GenericPositionMatrix.__init__">(Bio.motifs.matrix.GenericPositionMatrix method)</a>
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<li><a href="api/Bio.motifs.matrix.html#Bio.motifs.matrix.PositionWeightMatrix.__init__">(Bio.motifs.matrix.PositionWeightMatrix method)</a>
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<li><a href="api/Bio.motifs.meme.html#Bio.motifs.meme.Instance.__init__">(Bio.motifs.meme.Instance method)</a>
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<li><a href="api/Bio.motifs.meme.html#Bio.motifs.meme.Motif.__init__">(Bio.motifs.meme.Motif method)</a>
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<li><a href="api/Bio.PDB.internal_coords.html#Bio.PDB.internal_coords.Edron.edron_re">edron_re (Bio.PDB.internal_coords.Edron attribute)</a>
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<li><a href="api/Bio.Entrez.html#Bio.Entrez.efetch">efetch() (in module Bio.Entrez)</a>
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<li><a href="api/Bio.Entrez.html#Bio.Entrez.egquery">egquery() (in module Bio.Entrez)</a>
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<li><a href="api/Bio.Entrez.html#Bio.Entrez.einfo">einfo() (in module Bio.Entrez)</a>
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<li><a href="api/Bio.codonalign.codonalignment.html#Bio.codonalign.codonalignment.CodonAlignment.get_aln_length">get_aln_length() (Bio.codonalign.codonalignment.CodonAlignment method)</a>
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<li><a href="api/Bio.PDB.Atom.html#Bio.PDB.Atom.Atom.get_altloc">get_altloc() (Bio.PDB.Atom.Atom method)</a>
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</li>
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<li><a href="api/Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent">get_amino_acids_percent() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)</a>
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<li><a href="api/Bio.PDB.internal_coords.html#Bio.PDB.internal_coords.IC_Residue.get_angle">get_angle() (Bio.PDB.internal_coords.IC_Residue method)</a>
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<li><a href="api/Bio.Nexus.Nexus.html#Bio.Nexus.Nexus.Nexus.insert_gap">insert_gap() (Bio.Nexus.Nexus.Nexus method)</a>
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<li><a href="api/Bio.SeqUtils.ProtParam.html#Bio.SeqUtils.ProtParam.ProteinAnalysis.instability_index">instability_index() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)</a>
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<li><a href="api/Bio.motifs.meme.html#Bio.motifs.meme.Instance">Instance (class in Bio.motifs.meme)</a>
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<li><a href="api/Bio.Graphics.GenomeDiagram.html#Bio.Graphics.GenomeDiagram.ColorTranslator.int255_color">int255_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method)</a>
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‎dev/objects.inv‎

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‎dev/searchindex.js‎

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