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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignIO-module.html">Package AlignIO</a> ::
<a href="Bio.AlignIO.StockholmIO-module.html">Module StockholmIO</a> ::
Class StockholmWriter
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class StockholmWriter</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html">Interfaces.AlignmentWriter</a> --+
|
<a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html">Interfaces.SequentialAlignmentWriter</a> --+
|
<strong class="uidshort">StockholmWriter</strong>
</pre>
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<p>Stockholm/PFAM alignment writer.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#write_alignment" class="summary-sig-name">write_alignment</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">alignment</span>)</span><br />
Use this to write (another) single alignment to an open file.</td>
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<span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter.write_alignment">source code</a></span>
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<td><span class="summary-sig"><a name="_write_record"></a><span class="summary-sig-name">_write_record</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Write a single SeqRecord to the file</td>
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<span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter._write_record">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html">Interfaces.SequentialAlignmentWriter</a></code></b>:
<code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__">__init__</a></code>,
<code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_file">write_file</a></code>,
<code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_footer">write_footer</a></code>,
<code><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_header">write_header</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html">Interfaces.AlignmentWriter</a></code></b>:
<code><a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean">clean</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#pfam_gr_mapping" class="summary-name">pfam_gr_mapping</a> = <code title="{'active_site': 'AS',
'intron': 'IN',
'ligand_binding': 'LI',
'posterior_probability': 'PP',
'secondary_structure': 'SS',
'surface_accessibility': 'SA',
'transmembrane': 'TM'}"><code class="variable-group">{</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">AS</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">IN</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ligan</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#pfam_gs_mapping" class="summary-name">pfam_gs_mapping</a> = <code title="{'look': 'LO', 'organism': 'OS', 'organism_classification': 'OC'}"><code class="variable-group">{</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">LO</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-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_c</code><code class="variable-ellipsis">...</code></code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">write_alignment</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">alignment</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignIO.StockholmIO-pysrc.html#StockholmWriter.write_alignment">source code</a></span>
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<p>Use this to write (another) single alignment to an open file.</p>
<p>Note that sequences and their annotation are recorded together (rather
than having a block of annotation followed by a block of aligned
sequences).</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_alignment">Interfaces.SequentialAlignmentWriter.write_alignment</a>
</dt>
</dl>
</td></tr></table>
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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">active_site</code><code class="variable-quote">'</code><code class="variable-op">: </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">intron</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">ligand_binding</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">posterior_probability</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">secondary_structure</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">surface_accessibility</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">transmembrane</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-group">}</code>
</pre></td></tr></table>
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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">look</code><code class="variable-quote">'</code><code class="variable-op">: </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">organism</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_classification</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-group">}</code>
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