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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
Module UniprotIO
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<h1 class="epydoc">Module UniprotIO</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.UniprotIO-pysrc.html">source code</a></span></p>
<p>Bio.SeqIO support for the "uniprot-xml" file format.</p>
<p>See also:</p>
<p>http://www.uniprot.org</p>
<p>The UniProt XML format essentially replaces the old plain text file
format originally introduced by SwissProt ("swiss" format in
Bio.SeqIO).</p>
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<a href="Bio.SeqIO.UniprotIO.Parser-class.html" class="summary-name">Parser</a><br />
Parse a UniProt XML entry to a SeqRecord.
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<td><span class="summary-sig"><a href="Bio.SeqIO.UniprotIO-module.html#UniprotIterator" class="summary-sig-name">UniprotIterator</a>(<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">ProteinAlphabet()</span>,
<span class="summary-sig-arg">return_raw_comments</span>=<span class="summary-sig-default">False</span>)</span><br />
Generator function to parse UniProt XML as SeqRecord objects.</td>
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<span class="codelink"><a href="Bio.SeqIO.UniprotIO-pysrc.html#UniprotIterator">source code</a></span>
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<a name="NS"></a><span class="summary-name">NS</span> = <code title="'{http://uniprot.org/uniprot}'"><code class="variable-quote">'</code><code class="variable-string">{http://uniprot.org/uniprot}</code><code class="variable-quote">'</code></code>
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<a href="Bio.SeqIO.UniprotIO-module.html#REFERENCE_JOURNAL" class="summary-name">REFERENCE_JOURNAL</a> = <code title="'%(name)s %(volume)s:%(first)s-%(last)s(%(pub_date)s)'"><code class="variable-quote">'</code><code class="variable-string">%(name)s %(volume)s:%(first)s-%(last)s(%(</code><code class="variable-ellipsis">...</code></code>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.SeqIO'"><code class="variable-quote">'</code><code class="variable-string">Bio.SeqIO</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">UniprotIterator</span>(<span class="sig-arg">handle</span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">ProteinAlphabet()</span>,
<span class="sig-arg">return_raw_comments</span>=<span class="sig-default">False</span>)</span>
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><span class="codelink"><a href="Bio.SeqIO.UniprotIO-pysrc.html#UniprotIterator">source code</a></span>
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<p>Generator function to parse 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>return_raw_comments = True --> comment fields are returned as
complete xml to allow further processing skip_parsing_errors = True
--> if parsing errors are found, skip to next entry</p>
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<h3 class="epydoc">REFERENCE_JOURNAL</h3>
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<dt>Value:</dt>
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<code class="variable-quote">'</code><code class="variable-string">%(name)s %(volume)s:%(first)s-%(last)s(%(pub_date)s)</code><code class="variable-quote">'</code>
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