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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqFeature-module.html">Module SeqFeature</a> ::
Class SeqFeature
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SeqFeature</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">SeqFeature</strong>
</pre>
<hr />
<p>Represent a Sequence Feature on an object.</p>
<p>Attributes: o location - the location of the feature on the sequence
(FeatureLocation) o type - the specified type of the feature (ie. CDS,
exon, repeat...) o location_operator - a string specifying how this
SeqFeature may be related to others. For example, in the example GenBank
feature shown below, the location_operator would be "join" o
strand - A value specifying on which strand (of a DNA sequence, for
instance) the feature deals with. 1 indicates the plus strand, -1
indicates the minus strand, 0 indicates stranded but unknown (? in GFF3),
while the default of None indicates that strand doesn't apply (dot in
GFF3, e.g. features on proteins) o id - A string identifier for the
feature. o ref - A reference to another sequence. This could be an
accession number for some different sequence. o ref_db - A different
database for the reference accession number. o qualifiers - A dictionary
of qualifiers on the feature. These are analagous to the qualifiers from
a GenBank feature table. The keys of the dictionary are qualifier names,
the values are the qualifier values. o sub_features - Additional
SeqFeatures which fall under this 'parent' feature. For instance, if we
having something like:</p>
<p>CDS join(1..10,30..40,50..60)</p>
<p>Then the top level feature would be of type 'CDS' from 1 to 60
(actually 0 to 60 in Python counting) with location_operator='join', and
the three sub- features would also be of type 'CDS', and would be from 1
to 10, 30 to 40 and 50 to 60, respectively (although actually using
Python counting).</p>
<p>To get the nucleotide sequence for this CDS, you would need to take
the parent sequence and do seq[0:10]+seq[29:40]+seq[49:60] (Python
counting). Things are more complicated with strands and fuzzy positions.
To save you dealing with all these special cases, the SeqFeature provides
an extract method to do this for you.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.SeqFeature.SeqFeature-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">location</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">type</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">location_operator</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">strand</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown id></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">qualifiers</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">sub_features</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">ref</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">ref_db</span>=<span class="summary-sig-default">None</span>)</span><br />
Initialize a SeqFeature on a Sequence.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__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.SeqFeature.SeqFeature-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span><br />
A string representation of the record for debugging.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__repr__">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.SeqFeature.SeqFeature-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
A readable summary of the feature intended to be printed to screen.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__str__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.SeqFeature-class.html#_shift" class="summary-sig-name" onclick="show_private();">_shift</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">offset</span>)</span><br />
Returns a copy of the feature with its location shifted (PRIVATE).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature._shift">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.SeqFeature-class.html#_flip" class="summary-sig-name" onclick="show_private();">_flip</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">length</span>)</span><br />
Returns a copy of the feature with its location flipped (PRIVATE).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature._flip">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.SeqFeature.SeqFeature-class.html#extract" class="summary-sig-name">extract</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">parent_sequence</span>)</span><br />
Extract feature sequence from the supplied parent sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.extract">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.SeqFeature.SeqFeature-class.html#__nonzero__" class="summary-sig-name">__nonzero__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns True regardless of the length of the feature.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__nonzero__">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.SeqFeature.SeqFeature-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the length of the region described by a feature.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__len__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.SeqFeature-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over the parent positions within the feature.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__iter__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.SeqFeature-class.html#__contains__" class="summary-sig-name">__contains__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span><br />
Check if an integer position is within the feature.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__contains__">source code</a></span>
</td>
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<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>
</p>
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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>
</td>
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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">location</span>=<span class="sig-default">None</span>,
<span class="sig-arg">type</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">location_operator</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">strand</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown id></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">qualifiers</span>=<span class="sig-default">None</span>,
<span class="sig-arg">sub_features</span>=<span class="sig-default">None</span>,
<span class="sig-arg">ref</span>=<span class="sig-default">None</span>,
<span class="sig-arg">ref_db</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.SeqFeature-pysrc.html#SeqFeature.__init__">source code</a></span>
</td>
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<p>Initialize a SeqFeature on a Sequence.</p>
<p>location can either be a FeatureLocation (with strand argument also
given if required), or None.</p>
<p>e.g. With no strand, on the forward strand, and on the reverse
strand:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> SeqFeature, FeatureLocation
<span class="py-prompt">>>> </span>f1 = SeqFeature(FeatureLocation(5,10), type=<span class="py-string">"domain"</span>)
<span class="py-prompt">>>> </span>f2 = SeqFeature(FeatureLocation(7,110), strand=1, type=<span class="py-string">"CDS"</span>)
<span class="py-prompt">>>> </span>f3 = SeqFeature(FeatureLocation(9,108), strand=-1, type=<span class="py-string">"CDS"</span>)</pre>
<p>An invalid strand will trigger an exception:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>f4 = SeqFeature(FeatureLocation(50,60), strand=2)
<span class="py-except">Traceback (most recent call last):</span>
<span class="py-except"> ...</span>
<span class="py-except">ValueError: Strand should be +1, -1, 0 or None, not 2</span></pre>
<p>For exact start/end positions, an integer can be used (as shown above)
as shorthand for the ExactPosition object. For non-exact locations, the
FeatureLocation must be specified via the appropriate position
objects.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
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</div>
<a name="__repr__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__repr__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__repr__">source code</a></span>
</td>
</tr></table>
<p>A string representation of the record for debugging.</p>
<dl class="fields">
<dt>Overrides:
object.__repr__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
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<tr valign="top"><td>
<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>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__str__">source code</a></span>
</td>
</tr></table>
<p>A readable summary of the feature intended to be printed to
screen.</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
<a name="_shift"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_shift</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">offset</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature._shift">source code</a></span>
</td>
</tr></table>
<p>Returns a copy of the feature with its location shifted (PRIVATE).</p>
<p>The annotation qaulifiers are copied.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_flip"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_flip</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">length</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature._flip">source code</a></span>
</td>
</tr></table>
<p>Returns a copy of the feature with its location flipped (PRIVATE).</p>
<p>The argument length gives the length of the parent sequence. For
example a location 0..20 (+1 strand) with parent length 30 becomes after
flipping 10..30 (-1 strand). Strandless (None) or unknown strand (0)
remain like that - just their end points are changed.</p>
<p>The annotation qaulifiers are copied.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="extract"></a>
<div>
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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">extract</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">parent_sequence</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.extract">source code</a></span>
</td>
</tr></table>
<p>Extract feature sequence from the supplied parent sequence.</p>
<p>The parent_sequence can be a Seq like object or a string, and will
generally return an object of the same type. The exception to this is a
MutableSeq as the parent sequence will return a Seq object.</p>
<p>This should cope with complex locations including complements, joins
and fuzzy positions. Even mixed strand features should work! This also
covers features on protein sequences (e.g. domains), although here
reverse strand features are not permitted.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Seq <span class="py-keyword">import</span> Seq
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet <span class="py-keyword">import</span> generic_protein
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> SeqFeature, FeatureLocation
<span class="py-prompt">>>> </span>seq = Seq(<span class="py-string">"MKQHKAMIVALIVICITAVVAAL"</span>, generic_protein)
<span class="py-prompt">>>> </span>f = SeqFeature(FeatureLocation(8,15), type=<span class="py-string">"domain"</span>)
<span class="py-prompt">>>> </span>f.extract(seq)
<span class="py-output">Seq('VALIVIC', ProteinAlphabet())</span></pre>
<p>Note - currently only sub-features of type "join" are
supported.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__nonzero__"></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">__nonzero__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Boolean test operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__nonzero__">source code</a></span>
</td>
</tr></table>
<p>Returns True regardless of the length of the feature.</p>
<p>This behaviour is for backwards compatibility, since until the __len__
method was added, a SeqFeature always evaluated as True.</p>
<p>Note that in comparison, Seq objects, strings, lists, etc, will all
evaluate to False if they have length zero.</p>
<p>WARNING: The SeqFeature may in future evaluate to False when its
length is zero (in order to better match normal python behaviour)!</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
<div>
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<tr><td>
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<tr valign="top"><td>
<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.SeqFeature-pysrc.html#SeqFeature.__len__">source code</a></span>
</td>
</tr></table>
<p>Returns the length of the region described by a feature.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Seq <span class="py-keyword">import</span> Seq
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet <span class="py-keyword">import</span> generic_protein
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> SeqFeature, FeatureLocation
<span class="py-prompt">>>> </span>seq = Seq(<span class="py-string">"MKQHKAMIVALIVICITAVVAAL"</span>, generic_protein)
<span class="py-prompt">>>> </span>f = SeqFeature(FeatureLocation(8,15), type=<span class="py-string">"domain"</span>)
<span class="py-prompt">>>> </span>len(f)
<span class="py-output">7</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>f.extract(seq)
<span class="py-output">Seq('VALIVIC', ProteinAlphabet())</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>len(f.extract(seq))
<span class="py-output">7</span></pre>
<p>For simple features without subfeatures this is the same as the region
spanned (end position minus start position). However, for a feature
defined by combining several subfeatures (e.g. a CDS as the join of
several exons) the gaps are not counted (e.g. introns). This ensures that
len(f) == len(f.extract(parent_seq)), and also makes sure things work
properly with features wrapping the origin etc.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__iter__"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__iter__">source code</a></span>
</td>
</tr></table>
<p>Iterate over the parent positions within the feature.</p>
<p>The iteration order is strand aware, and can be thought of as moving
along the feature using the parent sequence coordinates:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> SeqFeature, FeatureLocation
<span class="py-prompt">>>> </span>f = SeqFeature(FeatureLocation(5,10), type=<span class="py-string">"domain"</span>, strand=-1)
<span class="py-prompt">>>> </span>len(f)
<span class="py-output">5</span>
<span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">for</span> i <span class="py-keyword">in</span> f: <span class="py-keyword">print</span> i
<span class="py-output">9</span>
<span class="py-output">8</span>
<span class="py-output">7</span>
<span class="py-output">6</span>
<span class="py-output">5</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>list(f)
<span class="py-output">[9, 8, 7, 6, 5]</span></pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__contains__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__contains__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">value</span>)</span>
<br /><em class="fname">(In operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__contains__">source code</a></span>
</td>
</tr></table>
<p>Check if an integer position is within the feature.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> SeqFeature, FeatureLocation
<span class="py-prompt">>>> </span>f = SeqFeature(FeatureLocation(5,10), type=<span class="py-string">"domain"</span>, strand=-1)
<span class="py-prompt">>>> </span>len(f)
<span class="py-output">5</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>[i <span class="py-keyword">for</span> i <span class="py-keyword">in</span> range(15) <span class="py-keyword">if</span> i <span class="py-keyword">in</span> f]
<span class="py-output">[5, 6, 7, 8, 9]</span></pre>
<p>For example, to see which features include a SNP position, you could
use this:</p>
<pre class="py-doctest">
<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 = SeqIO.read(<span class="py-string">"GenBank/NC_000932.gb"</span>, <span class="py-string">"gb"</span>)
<span class="py-prompt">>>> </span><span class="py-keyword">for</span> f <span class="py-keyword">in</span> record.features:
<span class="py-more">... </span> <span class="py-keyword">if</span> 1750 <span class="py-keyword">in</span> f:
<span class="py-more">... </span> <span class="py-keyword">print</span> f.type, f.strand, f.location
<span class="py-output">source 1 [0:154478]</span>
<span class="py-output">gene -1 [1716:4347]</span>
<span class="py-output">tRNA -1 [1716:4347]</span></pre>
<p>Note that for a feature defined as a join of several subfeatures (e.g.
the union of several exons) the gaps are not checked (e.g. introns). In
this example, the tRNA location is defined in the GenBank file as
complement(join(1717..1751,4311..4347)), so that position 1760 falls in
the gap:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">for</span> f <span class="py-keyword">in</span> record.features:
<span class="py-more">... </span> <span class="py-keyword">if</span> 1760 <span class="py-keyword">in</span> f:
<span class="py-more">... </span> <span class="py-keyword">print</span> f.type, f.strand, f.location
<span class="py-output">source 1 [0:154478]</span>
<span class="py-output">gene -1 [1716:4347]</span></pre>
<p>Note that additional care may be required with fuzzy locations, for
example just before a BeforePosition:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> SeqFeature, FeatureLocation
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.SeqFeature <span class="py-keyword">import</span> BeforePosition
<span class="py-prompt">>>> </span>f = SeqFeature(FeatureLocation(BeforePosition(3),8), type=<span class="py-string">"domain"</span>)
<span class="py-prompt">>>> </span>len(f)
<span class="py-output">5</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>[i <span class="py-keyword">for</span> i <span class="py-keyword">in</span> range(10) <span class="py-keyword">if</span> i <span class="py-keyword">in</span> f]
<span class="py-output">[3, 4, 5, 6, 7]</span></pre>
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