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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
<a href="Bio.SeqIO._index-module.html">Module _index</a> ::
Class _SQLiteManySeqFilesDict
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class _SQLiteManySeqFilesDict</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict">source code</a></span></p>
<pre class="base-tree">
UserDict.DictMixin --+
|
<a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html" onclick="show_private();">_IndexedSeqFileDict</a> --+
|
<strong class="uidshort">_SQLiteManySeqFilesDict</strong>
</pre>
<hr />
<p>Read only dictionary interface to many sequential sequence files.</p>
<p>Keeps the keys, file-numbers and offsets in an SQLite database. To
access a record by key, reads from the offset in the approapriate file
using Bio.SeqIO for parsing.</p>
<p>There are OS limits on the number of files that can be open at once,
so a pool are kept. If a record is required from a closed file, then one
of the open handles is closed first.</p>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index_filename</span>,
<span class="summary-sig-arg">filenames</span>,
<span class="summary-sig-arg">format</span>,
<span class="summary-sig-arg">alphabet</span>,
<span class="summary-sig-arg">key_function</span>,
<span class="summary-sig-arg">max_open</span>=<span class="summary-sig-default">10</span>)</span></td>
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<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__repr__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__contains__" class="summary-sig-name">__contains__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
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<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__contains__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
How many records are there?</td>
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<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__len__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over the keys.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__iter__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#keys" class="summary-sig-name">keys</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return a list of all the keys (SeqRecord identifiers).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.keys">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
x[y]</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__getitem__">source code</a></span>
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<span class="summary-type">D[k] if k in D, else d</span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get" class="summary-sig-name">get</a>(<span class="summary-sig-arg">D</span>,
<span class="summary-sig-arg">k</span>,
<span class="summary-sig-arg">d</span>=<span class="summary-sig-default">...</span>)</span><br />
d defaults to None.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.get">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get_raw" class="summary-sig-name">get_raw</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span><br />
Similar to the get method, but returns the record as a raw string.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.get_raw">source code</a></span>
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<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a name="close"></a><span class="summary-sig-name">close</span>(<span class="summary-sig-arg">self</span>)</span><br />
Close any open file handles.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.close">source code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html" onclick="show_private();">_IndexedSeqFileDict</a></code></b>:
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#__setitem__">__setitem__</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#__str__">__str__</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#clear">clear</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#copy">copy</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#fromkeys">fromkeys</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#items">items</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#iteritems">iteritems</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#iterkeys">iterkeys</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#itervalues">itervalues</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#pop">pop</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#popitem">popitem</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#update">update</a></code>,
<code><a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#values">values</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>UserDict.DictMixin</code></b>:
<code>__cmp__</code>,
<code>has_key</code>,
<code>setdefault</code>
</p>
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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">index_filename</span>,
<span class="sig-arg">filenames</span>,
<span class="sig-arg">format</span>,
<span class="sig-arg">alphabet</span>,
<span class="sig-arg">key_function</span>,
<span class="sig-arg">max_open</span>=<span class="sig-default">10</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__init__">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#__init__">_IndexedSeqFileDict.__init__</a>
</dt>
</dl>
</td></tr></table>
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<a name="__repr__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__repr__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__repr__">source code</a></span>
</td>
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<dl class="fields">
<dt>Overrides:
UserDict.DictMixin.__repr__
</dt>
</dl>
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<a name="__contains__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__contains__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">key</span>)</span>
<br /><em class="fname">(In operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__contains__">source code</a></span>
</td>
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<dl class="fields">
<dt>Overrides:
UserDict.DictMixin.__contains__
</dt>
</dl>
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<a name="__len__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__len__">source code</a></span>
</td>
</tr></table>
<p>How many records are there?</p>
<dl class="fields">
<dt>Overrides:
UserDict.DictMixin.__len__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__iter__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__iter__">source code</a></span>
</td>
</tr></table>
<p>Iterate over the keys.</p>
<dl class="fields">
<dt>Overrides:
UserDict.DictMixin.__iter__
</dt>
</dl>
</td></tr></table>
</div>
<a name="keys"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">keys</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.keys">source code</a></span>
</td>
</tr></table>
<p>Return a list of all the keys (SeqRecord identifiers).</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys">_IndexedSeqFileDict.keys</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__getitem__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">x</span>,
<span class="sig-arg">y</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.__getitem__">source code</a></span>
</td>
</tr></table>
<p>x[y]</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#__getitem__">_IndexedSeqFileDict.__getitem__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="get"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get</span>(<span class="sig-arg">D</span>,
<span class="sig-arg">k</span>,
<span class="sig-arg">d</span>=<span class="sig-default">...</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.get">source code</a></span>
</td>
</tr></table>
<p>d defaults to None.</p>
<dl class="fields">
<dt>Returns: D[k] if k in D, else d</dt>
<dt>Overrides:
UserDict.DictMixin.get
</dt>
</dl>
</td></tr></table>
</div>
<a name="get_raw"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">get_raw</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">key</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO._index-pysrc.html#_SQLiteManySeqFilesDict.get_raw">source code</a></span>
</td>
</tr></table>
<p>Similar to the get method, but returns the record as a raw string.</p>
<p>If the key is not found, a KeyError exception is raised.</p>
<p>Note that on Python 3 a bytes string is returned, not a typical
unicode string.</p>
<p>NOTE - This functionality is not supported for every file format.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO._index._IndexedSeqFileDict-class.html#get_raw">_IndexedSeqFileDict.get_raw</a>
</dt>
</dl>
</td></tr></table>
</div>
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