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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GFF-module.html">Package GFF</a> ::
Class Feature
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Feature</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GFF-pysrc.html#Feature">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Feature</strong>
</pre>
<hr />
<p>strand may be: +/0 = Watson -/1 = Crick</p>
<p>I propose that we start calling these the Rosalind and Franklin
strands</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>RetrieveSeqname._dir = <span class="py-string">'GFF'</span>
<span class="py-prompt">>>> </span>feature = Feature(<span class="py-string">"NC_001802x.fna"</span>, 73, 78) <span class="py-comment"># not having the x will interfere with the RetrieveSequence test</span>
<span class="py-prompt">>>> </span>feature.seq()
<span class="py-output">Seq('AATAAA', Alphabet())</span>
<span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">print</span> feature.location()
<span class="py-output">NC_001802x.fna:73..78</span>
<span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio <span class="py-keyword">import</span> SeqIO
<span class="py-prompt">>>> </span>record = feature.record()
<span class="py-prompt">>>> </span>records = [record]
<span class="py-prompt">>>> </span>SeqIO.write(records, sys.stdout, <span class="py-string">'fasta'</span>)
<span class="py-output">> NC_001802x.fna:73..78</span>
<span class="py-output">AATAAA</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>feature2 = Feature(location=easy.LocationFromString(<span class="py-string">"NC_001802x.fna:73..78"</span>))
<span class="py-prompt">>>> </span>writer.write(feature2.record())
<span class="py-output">> NC_001802x.fna:73..78</span>
<span class="py-output">AATAAA</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>location3 = easy.LocationFromString(<span class="py-string">"NC_001802x.fna:complement(73..78)"</span>)
<span class="py-prompt">>>> </span>feature3 = Feature(location=location3)
<span class="py-prompt">>>> </span>writer.write(feature3.record())
<span class="py-output">> NC_001802x.fna:complement(73..78)</span>
<span class="py-output">TTTATT</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>location4 = easy.LocationFromString(<span class="py-string">"NC_001802x.fna:336..1631"</span>)
<span class="py-prompt">>>> </span>feature4 = Feature(location=location4, frame=0)
<span class="py-prompt">>>> </span>feature4.frame
<span class="py-output">0</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>feature4.translate()[:7]
<span class="py-output">Seq('MGARASV', HasStopCodon(IUPACProtein(), '*'))</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>feature4.frame = 6 <span class="py-comment"># can't happen, but a useful demonstration</span>
<span class="py-prompt">>>> </span>feature4.translate()[:5]
<span class="py-output">Seq('ARASV', HasStopCodon(IUPACProtein(), '*'))</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>feature4.frame = 1
<span class="py-prompt">>>> </span>feature4.translate()[:5]
<span class="py-output">Seq('WVRER', HasStopCodon(IUPACProtein(), '*'))</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>location5 = easy.LocationFromString(<span class="py-string">"NC_001802lc.fna:336..1631"</span>) <span class="py-comment"># lowercase data</span>
<span class="py-prompt">>>> </span>feature5 = Feature(location=location5, frame=0)
<span class="py-prompt">>>> </span>feature5.translate()[:7]
<span class="py-output">Seq('MGARASV', HasStopCodon(IUPACProtein(), '*'))</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>location6 = easy.LocationFromString(<span class="py-string">"NC_001802lc.fna:335..351"</span>)
<span class="py-prompt">>>> </span>feature6 = Feature(location=location6, frame=1)
<span class="py-prompt">>>> </span>feature6.translate()
<span class="py-output">Seq('MGARA', HasStopCodon(IUPACProtein(), '*'))</span></pre>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GFF.Feature-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seqname</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">end</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">strand</span>=<span class="summary-sig-default">"+"</span>,
<span class="summary-sig-arg">frame</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">alphabet</span>=<span class="summary-sig-default">DEFAULT_ALPHABET</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
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<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.__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.GFF.Feature-class.html#__hash__" class="summary-sig-name">__hash__</a>(<span class="summary-sig-arg">self</span>)</span><br />
hash(x)</td>
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<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.__hash__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="seq"></a><span class="summary-sig-name">seq</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.seq">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="translate"></a><span class="summary-sig-name">translate</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.translate">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="location"></a><span class="summary-sig-name">location</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.location">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="target_location"></a><span class="summary-sig-name">target_location</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.target_location">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="id"></a><span class="summary-sig-name">id</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.id">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="record"></a><span class="summary-sig-name">record</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.record">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="xrange"></a><span class="summary-sig-name">xrange</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.xrange">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.GFF.Feature-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
str(x)</td>
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<span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.__str__">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__getattribute__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>
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<!-- ==================== PROPERTIES ==================== -->
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<td align="left"><span class="table-header">Properties</span></td>
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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">seqname</span>=<span class="sig-default">None</span>,
<span class="sig-arg">start</span>=<span class="sig-default">None</span>,
<span class="sig-arg">end</span>=<span class="sig-default">None</span>,
<span class="sig-arg">strand</span>=<span class="sig-default">"+"</span>,
<span class="sig-arg">frame</span>=<span class="sig-default">None</span>,
<span class="sig-arg">location</span>=<span class="sig-default">None</span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">DEFAULT_ALPHABET</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.__init__">source code</a></span>
</td>
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<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__hash__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Hashing function)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.__hash__">source code</a></span>
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<p>hash(x)</p>
<dl class="fields">
<dt>Overrides:
object.__hash__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<a name="__str__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
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><span class="codelink"><a href="Bio.GFF-pysrc.html#Feature.__str__">source code</a></span>
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<p>str(x)</p>
<dl class="fields">
<dt>Overrides:
object.__str__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
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