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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Phylo-module.html">Package Phylo</a> ::
<a href="Bio.Phylo.PhyloXML-module.html">Module PhyloXML</a> ::
Class Sequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Sequence</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Sequence">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a> --+
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<a href="Bio.Phylo.PhyloXML.PhyloElement-class.html">PhyloElement</a> --+
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<strong class="uidshort">Sequence</strong>
</pre>
<hr />
<p>A molecular sequence (Protein, DNA, RNA) associated with a node.</p>
<p>One intended use for <tt class="rst-docutils literal">id_ref</tt> is to link a sequence to a taxonomy (via the
taxonomy's <tt class="rst-docutils literal">id_source</tt>) in case of multiple sequences and taxonomies per
node.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Sequence-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">type</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id_ref</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id_source</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">symbol</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">accession</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">location</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">mol_seq</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">uri</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">domain_architecture</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">annotations</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">other</span>=<span class="summary-sig-default">None</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
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<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Sequence.__init__">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.Phylo.PhyloXML.Sequence-class.html#to_seqrecord" class="summary-sig-name">to_seqrecord</a>(<span class="summary-sig-arg">self</span>)</span><br />
Create a SeqRecord object from this Sequence instance.</td>
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<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Sequence.to_seqrecord">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="get_alphabet"></a><span class="summary-sig-name">get_alphabet</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Sequence.get_alphabet">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.TreeElement-class.html#__repr__">__repr__</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeElement-class.html#__str__">__str__</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>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
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<!-- ==================== CLASS METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="from_seqrecord"></a><span class="summary-sig-name">from_seqrecord</span>(<span class="summary-sig-arg">cls</span>,
<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">is_aligned</span>=<span class="summary-sig-default">None</span>)</span><br />
Create a new PhyloXML Sequence from a SeqRecord object.</td>
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<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Sequence.from_seqrecord">source code</a></span>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Phylo.PhyloXML.Sequence-class.html#alphabets" class="summary-name">alphabets</a> = <code title="{'dna': DNAAlphabet(),
'protein': ProteinAlphabet(),
'rna': RNAAlphabet()}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">dna</code><code class="variable-quote">'</code><code class="variable-op">: </code>DNAAlphabet()<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">protein</code><code class="variable-quote">'</code><code class="variable-op">: </code>ProteinAlphabet(<code class="variable-ellipsis">...</code></code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="re_symbol"></a><span class="summary-name">re_symbol</span> = <code title="re.compile(r'\S{1,10}')">re.compile(r'\S<code class="re-op">{1,10}</code>')</code>
</td>
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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</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">type</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id_ref</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id_source</span>=<span class="sig-default">None</span>,
<span class="sig-arg">symbol</span>=<span class="sig-default">None</span>,
<span class="sig-arg">accession</span>=<span class="sig-default">None</span>,
<span class="sig-arg">name</span>=<span class="sig-default">None</span>,
<span class="sig-arg">location</span>=<span class="sig-default">None</span>,
<span class="sig-arg">mol_seq</span>=<span class="sig-default">None</span>,
<span class="sig-arg">uri</span>=<span class="sig-default">None</span>,
<span class="sig-arg">domain_architecture</span>=<span class="sig-default">None</span>,
<span class="sig-arg">annotations</span>=<span class="sig-default">None</span>,
<span class="sig-arg">other</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Sequence.__init__">source code</a></span>
</td>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>type</code></strong> ({'dna', 'rna', 'protein'}) - type of molecule this sequence represents</li>
<li><strong class="pname"><code>id_ref</code></strong> (string) - reference to another resource</li>
<li><strong class="pname"><code>id_source</code></strong> (string) - source for the reference</li>
<li><strong class="pname"><code>symbol</code></strong> (string) - short symbol of the sequence, e.g. 'ACTM' (max. 10 chars)</li>
<li><strong class="pname"><code>accession</code></strong> (Accession) - accession code for this sequence.</li>
<li><strong class="pname"><code>name</code></strong> (string) - full name of the sequence, e.g. 'muscle Actin'</li>
<li><strong class="pname"><code>location</code></strong> - location of a sequence on a genome/chromosome.</li>
<li><strong class="pname"><code>mol_seq</code></strong> (MolSeq) - the molecular sequence itself</li>
<li><strong class="pname"><code>uri</code></strong> (Uri) - link</li>
<li><strong class="pname"><code>annotations</code></strong> (list of Annotation objects) - annotations on this sequence</li>
<li><strong class="pname"><code>domain_architecture</code></strong> (DomainArchitecture) - protein domains on this sequence</li>
<li><strong class="pname"><code>other</code></strong> (list of Other objects) - non-phyloXML elements</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<a name="to_seqrecord"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">to_seqrecord</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
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<p>Create a SeqRecord object from this Sequence instance.</p>
<p>The seqrecord.annotations dictionary is packed like so:</p>
<pre class="rst-literal-block">
{ # Sequence attributes with no SeqRecord equivalent:
'id_ref': self.id_ref,
'id_source': self.id_source,
'location': self.location,
'uri': { 'value': self.uri.value,
'desc': self.uri.desc,
'type': self.uri.type },
# Sequence.annotations attribute (list of Annotations)
'annotations': [{ 'ref': ann.ref,
'source': ann.source,
'evidence': ann.evidence,
'type': ann.type,
'confidence': [ ann.confidence.value,
ann.confidence.type ],
'properties': [{ 'value': prop.value,
'ref': prop.ref,
'applies_to': prop.applies_to,
'datatype': prop.datatype,
'unit': prop.unit,
'id_ref': prop.id_ref }
for prop in ann.properties],
} for ann in self.annotations],
}
</pre>
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</dl>
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<!-- ==================== CLASS VARIABLE DETAILS ==================== -->
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<h3 class="epydoc">alphabets</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">dna</code><code class="variable-quote">'</code><code class="variable-op">: </code>DNAAlphabet()<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">protein</code><code class="variable-quote">'</code><code class="variable-op">: </code>ProteinAlphabet()<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">rna</code><code class="variable-quote">'</code><code class="variable-op">: </code>RNAAlphabet()<code class="variable-group">}</code>
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