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<a href="Bio-module.html">Package Bio</a> ::
Package Rebase
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package Rebase</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Rebase-pysrc.html">source code</a></span></p>
<p>This module provides code to work with files from Rebase.
http://rebase.neb.com/rebase/rebase.html</p>
<p>Classes: Record Holds rebase sequence data. Iterator
Iterates over sequence data in a rebase file. Dictionary Accesses
a rebase file using a dictionary interface. RecordParser Parses
rebase sequence data into a Record object.</p>
<p>_Scanner Scans a rebase-format stream. _RecordConsumer
Consumes rebase data to a Record object.</p>
<p>Functions: index_file Index a FASTA file for a Dictionary.</p>
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<a href="Bio.Rebase.Record-class.html" class="summary-name">Record</a><br />
Holds information from a FASTA record.
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Returns one record at a time from a Rebase file.
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Accesses a rebase file using a dictionary interface.
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Parses FASTA sequence data into a Record object.
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Scans a rebase file.
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<a href="Bio.Rebase._RecordConsumer-class.html" class="summary-name" onclick="show_private();">_RecordConsumer</a><br />
Consumer that converts a rebase record to a Record object.
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<td><span class="summary-sig"><a href="Bio.Rebase-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_file(filename, ind/exname, rec2key=None)</td>
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<span class="codelink"><a href="Bio.Rebase-pysrc.html#index_file">source code</a></span>
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<a href="Bio.Rebase-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.Rebase was deprecated, as it does not seem to be able to parse \
recent HTML files from Rebase. If you want to continue to use this mod\
ule, please get in contact with the Biopython developers at biopython-\
dev@biopython.org to avoid permanent removal of this module from Biopy\
thon',
<type 'exceptions.DeprecationWarning'>,
27): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.Rebase was deprecated, as it does</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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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>
</h3>
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><span class="codelink"><a href="Bio.Rebase-pysrc.html#index_file">source code</a></span>
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<p>index_file(filename, ind/exname, rec2key=None)</p>
<p>Index a rebase 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 sequence title will be used.</p>
<dl class="fields">
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<h3 class="epydoc">__warningregistry__</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.Rebase was deprecated, as it does not seem to be able to parse </code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">recent HTML files from Rebase. If you want to continue to use this mod</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">ule, please get in contact with the Biopython developers at biopython-</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">dev@biopython.org to avoid permanent removal of this module from Biopy</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">thon</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.DeprecationWarning'><code class="variable-op">,</code>
27<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code>
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