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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 StockholmWriter
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class StockholmWriter</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a> --+
|
<a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Interfaces.SequentialSequenceWriter</a> --+
|
<strong class="uidshort">StockholmWriter</strong>
</pre>
<hr />
<p>Class to write PFAM style Stockholm format files.</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>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.StockholmIO.StockholmWriter-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handle</span>)</span><br />
Creates the writer object.</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.StockholmIO.StockholmWriter-class.html#write_header" class="summary-sig-name">write_header</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">count</span>)</span><br />
Must supply the number of records (count).</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_header">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.StockholmWriter-class.html#write_file" class="summary-sig-name">write_file</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">records</span>)</span><br />
Use this to write an entire file containing the given records.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_file">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.StockholmWriter-class.html#write_record" class="summary-sig-name">write_record</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Write a single Stockholm record to the file.</td>
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<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_record">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.StockholmWriter-class.html#write_footer" class="summary-sig-name">write_footer</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_footer">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Interfaces.SequentialSequenceWriter</a></code></b>:
<code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_records">write_records</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a></code></b>:
<code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean">clean</a></code>
</p>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO.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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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.SeqIO.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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<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>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.__init__">source code</a></span>
</td>
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<p>Creates the writer object.</p>
<p>Use the method write_file() to actually record your sequence
records.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#__init__">Interfaces.SequenceWriter.__init__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="write_header"></a>
<div>
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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">write_header</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">count</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_header">source code</a></span>
</td>
</tr></table>
<p>Must supply the number of records (count).</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_header">Interfaces.SequentialSequenceWriter.write_header</a>
</dt>
</dl>
</td></tr></table>
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<a name="write_file"></a>
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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">write_file</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">records</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_file">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Use this to write an entire file containing the given records.
records - A list or iterator returning SeqRecord objects.
If len(records) is not supported, then it will be
converted into a list.
This method should only be called once for each file.
</pre>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#write_file">Interfaces.SequenceWriter.write_file</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="write_record"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">write_record</span>(<span class="sig-arg">self</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#StockholmWriter.write_record">source code</a></span>
</td>
</tr></table>
<p>Write a single Stockholm record to the file.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_record">Interfaces.SequentialSequenceWriter.write_record</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="write_footer"></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">write_footer</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.StockholmIO-pysrc.html#StockholmWriter.write_footer">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_footer">Interfaces.SequentialSequenceWriter.write_footer</a>
</dt>
</dl>
</td></tr></table>
</div>
<br />
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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>
</dd>
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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">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>
</pre></td></tr></table>
</dd>
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