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Bio ::
GenBank ::
NCBIDictionary ::
Class NCBIDictionary
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class NCBIDictionary</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary">source code</a></span></p>
<p>Access GenBank using a read-only dictionary interface.</p>
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<td><span class="summary-sig"><a href="Bio.GenBank.NCBIDictionary-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">format</span>,
<span class="summary-sig-arg">parser</span>=<span class="summary-sig-default">None</span>)</span><br />
Initialize an NCBI dictionary to retrieve sequences.</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.__len__">source code</a></span>
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<td><span class="summary-sig"><a name="clear"></a><span class="summary-sig-name">clear</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__setitem__"></a><span class="summary-sig-name">__setitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>,
<span class="summary-sig-arg">item</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.__setitem__">source code</a></span>
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<td><span class="summary-sig"><a name="update"></a><span class="summary-sig-name">update</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.update">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="keys"></a><span class="summary-sig-name">keys</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.keys">source code</a></span>
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<td><span class="summary-sig"><a name="items"></a><span class="summary-sig-name">items</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.items">source code</a></span>
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<td><span class="summary-sig"><a name="values"></a><span class="summary-sig-name">values</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="summary-type">bool</span>
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<td><span class="summary-sig"><a name="has_key"></a><span class="summary-sig-name">has_key</span>(<span class="summary-sig-arg">S</span>,
<span class="summary-sig-arg">id</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.has_key">source code</a></span>
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<td><span class="summary-sig"><a name="get"></a><span class="summary-sig-name">get</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>,
<span class="summary-sig-arg">failobj</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.get">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.GenBank.NCBIDictionary-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
Return the GenBank entry specified by the GenBank ID.</td>
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<a name="VALID_DATABASES"></a><span class="summary-name">VALID_DATABASES</span> = <code title="['nucleotide', 'protein', 'genome']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">nucleotide</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">protein</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">genome</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<a name="VALID_FORMATS"></a><span class="summary-name">VALID_FORMATS</span> = <code title="['genbank', 'fasta']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">genbank</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">fasta</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">format</span>,
<span class="sig-arg">parser</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
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><span class="codelink"><a href="Bio.GenBank-pysrc.html#NCBIDictionary.__init__">source code</a></span>
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<p>Initialize an NCBI dictionary to retrieve sequences.</p>
<p>Create a new Dictionary to access GenBank. Valid values for database
are 'nucleotide' and 'protein'. Valid values for format are 'genbank'
(for nucleotide genbank and protein genpept) and 'fasta'. dely and retmax
are old options kept only for compatibility -- do not bother to set them.
parser is an optional parser object to change the results into another
form. If unspecified, then the raw contents of the file will be
returned.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
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<p>Return the GenBank entry specified by the GenBank ID.</p>
<p>Raises a KeyError if there's an error.</p>
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