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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SwissProt-module.html">Package SwissProt</a> ::
Module SProt
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module SProt</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SwissProt.SProt-pysrc.html">source code</a></span></p>
<p>This module provides code to work with the sprotXX.dat file from
SwissProt. http://www.expasy.ch/sprot/sprot-top.html</p>
<p>Tested with: Release 37, Release 38, Release 39</p>
<p>Limited testing with: Release 51, 54</p>
<p>Classes: Record Holds SwissProt data. Reference
Holds reference data from a SwissProt entry. Iterator Iterates
over entries in a SwissProt file. Dictionary Accesses a SwissProt
file using a dictionary interface. RecordParser Parses a SwissProt
record into a Record object. SequenceParser Parses a SwissProt record
into a SeqRecord object.</p>
<p>_Scanner Scans SwissProt-formatted data. _RecordConsumer
Consumes SwissProt data to a SProt.Record object. _SequenceConsumer
Consumes SwissProt data to a SeqRecord object.</p>
<p>Functions: index_file Index a SwissProt file for a
Dictionary.</p>
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<a href="Bio.SwissProt.SProt.Record-class.html" class="summary-name">Record</a><br />
Holds information from a SwissProt record.
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<a href="Bio.SwissProt.SProt.Reference-class.html" class="summary-name">Reference</a><br />
Holds information from 1 references in a SwissProt entry.
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<a href="Bio.SwissProt.SProt.Iterator-class.html" class="summary-name">Iterator</a><br />
Returns one record at a time from a SwissProt file.
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<a href="Bio.SwissProt.SProt.Dictionary-class.html" class="summary-name">Dictionary</a><br />
Accesses a SwissProt file using a dictionary interface.
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<span class="summary-type"> </span>
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<a href="Bio.SwissProt.SProt.ExPASyDictionary-class.html" class="summary-name">ExPASyDictionary</a><br />
Access SwissProt at ExPASy using a read-only dictionary interface.
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<a href="Bio.SwissProt.SProt.RecordParser-class.html" class="summary-name">RecordParser</a><br />
Parses SwissProt data into a Record object.
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<a href="Bio.SwissProt.SProt.SequenceParser-class.html" class="summary-name">SequenceParser</a><br />
Parses SwissProt data into a standard SeqRecord object.
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<a href="Bio.SwissProt.SProt._Scanner-class.html" class="summary-name" onclick="show_private();">_Scanner</a><br />
Scans SwissProt-formatted data.
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<a href="Bio.SwissProt.SProt._RecordConsumer-class.html" class="summary-name" onclick="show_private();">_RecordConsumer</a><br />
Consumer that converts a SwissProt record to a Record object.
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<a href="Bio.SwissProt.SProt._SequenceConsumer-class.html" class="summary-name" onclick="show_private();">_SequenceConsumer</a><br />
Consumer that converts a SwissProt record to a SeqRecord object.
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<td><span class="summary-sig"><a href="Bio.SwissProt.SProt-module.html#index_file" class="summary-sig-name">index_file</a>(<span class="summary-sig-arg">filename</span>,
<span class="summary-sig-arg">indexname</span>,
<span class="summary-sig-arg">rec2key</span>=<span class="summary-sig-default">None</span>)</span><br />
Index a SwissProt file.</td>
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<span class="codelink"><a href="Bio.SwissProt.SProt-pysrc.html#index_file">source code</a></span>
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<a name="_CHOMP"></a><span class="summary-name">_CHOMP</span> = <code title="'''
\r\t.,;'''"><code class="variable-quote">'</code><code class="variable-string"> \n\r\t.,;</code><code class="variable-quote">'</code></code>
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<a name="xml_support"></a><span class="summary-name">xml_support</span> = <code title="1">1</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">index_file</span>(<span class="sig-arg">filename</span>,
<span class="sig-arg">indexname</span>,
<span class="sig-arg">rec2key</span>=<span class="sig-default">None</span>)</span>
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<p>Index a SwissProt file. filename is the name of the file. indexname
is the name of the dictionary. rec2key is an optional callback that
takes a Record and generates a unique key (e.g. the accession number) for
the record. If not specified, the entry name will be used.</p>
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