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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.StockholmIO-module.html">Module StockholmIO</a> ::
Class StockholmIterator
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class StockholmIterator</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.SeqIO.Interfaces.SequenceIterator-class.html">Interfaces.SequenceIterator</a> --+
|
<a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html">Interfaces.InterlacedSequenceIterator</a> --+
|
<strong class="uidshort">StockholmIterator</strong>
</pre>
<hr />
<p>Loads a Stockholm file from PFAM into SeqRecord objects.</p>
<p>The entire file is loaded, and any sequence can be accessed using the
[index] notation.</p>
<p>This parser will detect if the Stockholm file follows the PFAM
conventions for sequence specific meta-data (lines starting #=GS and
#=GR) and populates the SeqRecord fields accordingly.</p>
<p>Any annotation which does not follow the PFAM conventions is currently
ignored.</p>
<p>If an accession is provided for an entry in the meta data, IT WILL NOT
be used as the record.id (it will be recorded in the record's
annotations). This is because some files have (sub) sequences from
different parts of the same accession (differentiated by different
start-end positions).</p>
<p>Wrap-around alignments are not supported - each sequences must be on a
single line. However, interlaced sequences should work.</p>
<p>For more information on the file format, please see:
http://www.bioperl.org/wiki/Stockholm_multiple_alignment_format
http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html</p>
<p>For consistency with BioPerl and EMBOSS we call this the
"stockholm" format.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">SingleLetterAlphabet()</span>)</span><br />
Create a StockholmIterator object (which returns SeqRecord objects).</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator.__init__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="ParseAlignment"></a><span class="summary-sig-name">ParseAlignment</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator.ParseAlignment">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.StockholmIO.StockholmIterator-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the number of records.</td>
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<td><span class="summary-sig"><a name="_identifier_split"></a><span class="summary-sig-name">_identifier_split</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">identifier</span>)</span><br />
Returns (name,start,end) string tuple from an identier</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator._identifier_split">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html#_get_meta_data" class="summary-sig-name" onclick="show_private();">_get_meta_data</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">identifier</span>,
<span class="summary-sig-arg">meta_dict</span>)</span><br />
Takes an itentifier and returns dict of all meta-data matching it.</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator._get_meta_data">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html#_populate_meta_data" class="summary-sig-name" onclick="show_private();">_populate_meta_data</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">identifier</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Adds meta-date to a SecRecord's annotations dictionary.</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator._populate_meta_data">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">i</span>)</span><br />
Provides random access to the SeqRecords.</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator.__getitem__">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html">Interfaces.InterlacedSequenceIterator</a></code></b>:
<code><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__iter__">__iter__</a></code>,
<code><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#move_start">move_start</a></code>,
<code><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next">next</a></code>
</p>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<td align="left"><span class="table-header">Class Variables</span></td>
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html#pfam_gr_mapping" class="summary-name">pfam_gr_mapping</a> = <code title="{'AS': 'active_site',
'IN': 'intron',
'LI': 'ligand_binding',
'PP': 'posterior_probability',
'SA': 'surface_accessibility',
'SS': 'secondary_structure',
'TM': 'transmembrane'}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">active_site</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">IN</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">intron</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">LI</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html#pfam_gs_mapping" class="summary-name">pfam_gs_mapping</a> = <code title="{'LO': 'look', 'OC': 'organism_classification', 'OS': 'organism'}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">LO</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">look</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">OC</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">organism_classificatio</code><code class="variable-ellipsis">...</code></code>
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<!-- ==================== METHOD DETAILS ==================== -->
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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">handle</span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">SingleLetterAlphabet()</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator.__init__">source code</a></span>
</td>
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<p>Create a StockholmIterator object (which returns SeqRecord
objects).</p>
<p>handle - input file alphabet - optional alphabet</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequenceIterator-class.html#__init__">Interfaces.SequenceIterator.__init__</a>
</dt>
</dl>
</td></tr></table>
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<a name="__len__"></a>
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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.StockholmIO-pysrc.html#StockholmIterator.__len__">source code</a></span>
</td>
</tr></table>
<p>Return the number of records.</p>
<p>This method should be replaced by any derived class to do something
useful.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__len__">Interfaces.InterlacedSequenceIterator.__len__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
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<a name="_get_meta_data"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_get_meta_data</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">identifier</span>,
<span class="sig-arg">meta_dict</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator._get_meta_data">source code</a></span>
</td>
</tr></table>
<p>Takes an itentifier and returns dict of all meta-data matching it.</p>
<p>For example, given "Q9PN73_CAMJE/149-220" will return all
matches to this or "Q9PN73_CAMJE" which the identifier without
its /start-end suffix.</p>
<p>In the example below, the suffix is required to match the AC, but must
be removed to match the OS and OC meta-data.</p>
<p># STOCKHOLM 1.0 #=GS Q9PN73_CAMJE/149-220 AC Q9PN73 ...
Q9PN73_CAMJE/149-220 NKA... ... #=GS Q9PN73_CAMJE OS
Campylobacter jejuni #=GS Q9PN73_CAMJE OC Bacteria</p>
<p>This function will return an empty dictionary if no data is found</p>
<dl class="fields">
</dl>
</td></tr></table>
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<a name="_populate_meta_data"></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">_populate_meta_data</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">identifier</span>,
<span class="sig-arg">record</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator._populate_meta_data">source code</a></span>
</td>
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<p>Adds meta-date to a SecRecord's annotations dictionary.</p>
<p>This function applies the PFAM conventions.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__getitem__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">i</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmIterator.__getitem__">source code</a></span>
</td>
</tr></table>
<p>Provides random access to the SeqRecords.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__getitem__">Interfaces.InterlacedSequenceIterator.__getitem__</a>
</dt>
</dl>
</td></tr></table>
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class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc">pfam_gr_mapping</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">active_site</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">IN</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">intron</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">LI</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">ligand_binding</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">PP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">posterior_probability</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">SA</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">surface_accessibility</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">SS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">secondary_structure</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">TM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">transmembrane</code><code class="variable-quote">'</code><code class="variable-group">}</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="pfam_gs_mapping"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc">pfam_gs_mapping</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">LO</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">look</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">OC</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">organism_classification</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">OS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">organism</code><code class="variable-quote">'</code><code class="variable-group">}</code>
</pre></td></tr></table>
</dd>
</dl>
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