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<a href="Bio-module.html">Package Bio</a> ::
Module SeqFeature
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<h1 class="epydoc">Module SeqFeature</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqFeature-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Represent a Sequence Feature holding info about a part of a sequence.
This is heavily modeled after the Biocorba SeqFeature objects, and
may be pretty biased towards GenBank stuff since I'm writing it
for the GenBank parser output...
What's here:
Base class to hold a Feature.
----------------------------
classes:
o SeqFeature
Hold information about a Reference.
----------------------------------
This is an attempt to create a General class to hold Reference type
information.
classes:
o Reference
Specify locations of a feature on a Sequence.
---------------------------------------------
This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in
much the same way as Biocorba. This has the advantages of allowing us
to handle fuzzy stuff in case anyone needs it, and also be compatible
with Biocorba.
classes:
o FeatureLocation - Specify the start and end location of a feature.
o ExactPosition - Specify the position as being exact.
o WithinPosition - Specify a position occuring within some range.
o BetweenPosition - Specify a position occuring between a range (OBSOLETE?).
o BeforePosition - Specify the position as being found before some base.
o AfterPosition - Specify the position as being found after some base.
o OneOfPosition - Specify a position where the location can be multiple positions.
</pre>
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<a href="Bio.SeqFeature.SeqFeature-class.html" class="summary-name">SeqFeature</a><br />
Represent a Sequence Feature on an object.
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Represent a Generic Reference object.
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<a href="Bio.SeqFeature.FeatureLocation-class.html" class="summary-name">FeatureLocation</a><br />
Specify the location of a feature along a sequence.
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<a href="Bio.SeqFeature.AbstractPosition-class.html" class="summary-name">AbstractPosition</a><br />
Abstract base class representing a position.
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<a href="Bio.SeqFeature.ExactPosition-class.html" class="summary-name">ExactPosition</a><br />
Specify the specific position of a boundary.
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<a href="Bio.SeqFeature.UncertainPosition-class.html" class="summary-name">UncertainPosition</a><br />
Specify a specific position which is uncertain.
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<a href="Bio.SeqFeature.UnknownPosition-class.html" class="summary-name">UnknownPosition</a><br />
Specify a specific position which is unknown (has no position).
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Specify the position of a boundary within some coordinates.
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Specify the position of a boundary between two coordinates
(OBSOLETE?).
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<a href="Bio.SeqFeature.BeforePosition-class.html" class="summary-name">BeforePosition</a><br />
Specify a position where the actual location occurs before it.
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<a href="Bio.SeqFeature.AfterPosition-class.html" class="summary-name">AfterPosition</a><br />
Specify a position where the actual location is found after it.
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<a href="Bio.SeqFeature.OneOfPosition-class.html" class="summary-name">OneOfPosition</a><br />
Specify a position where the location can be multiple positions.
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<a href="Bio.SeqFeature.PositionGap-class.html" class="summary-name">PositionGap</a><br />
Simple class to hold information about a gap between positions.
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<td><span class="summary-sig"><a href="Bio.SeqFeature-module.html#_test" class="summary-sig-name" onclick="show_private();">_test</a>()</span><br />
Run the Bio.SeqFeature module's doctests (PRIVATE).</td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio'"><code class="variable-quote">'</code><code class="variable-string">Bio</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_test</span>()</span>
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<p>Run the Bio.SeqFeature module's doctests (PRIVATE).</p>
<p>This will try and locate the unit tests directory, and run the
doctests from there in order that the relative paths used in the examples
work.</p>
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