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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Restriction-module.html">Package Restriction</a> ::
<a href="Bio.Restriction.Restriction-module.html">Module Restriction</a> ::
Class FormattedSeq
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class FormattedSeq</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">FormattedSeq</strong>
</pre>
<hr />
<pre class="literalblock">
FormattedSeq(seq, [linear=True])-> new FormattedSeq.
Translate a Bio.Seq into a formatted sequence to be used with Restriction.
Roughly:
remove anything which is not IUPAC alphabet and then add a space
in front of the sequence to get a biological index instead of a
python index (i.e. index of the first base is 1 not 0).
Retains information about the shape of the molecule linear (default)
or circular. Restriction sites are search over the edges of circular
sequence.
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<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.FormattedSeq-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">linear</span>=<span class="summary-sig-default">True</span>)</span><br />
FormattedSeq(seq, [linear=True])-> new FormattedSeq.</td>
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<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq.__len__">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.Restriction.Restriction.FormattedSeq-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span><br />
repr(x)</td>
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<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq.__repr__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__eq__"></a><span class="summary-sig-name">__eq__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span></td>
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<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq.__eq__">source code</a></span>
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<span class="summary-type">circularise FS</span>
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<td><span class="summary-sig"><a name="circularise"></a><span class="summary-sig-name">circularise</span>(<span class="summary-sig-arg">FS</span>)</span></td>
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<span class="summary-type">linearise FS</span>
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<td><span class="summary-sig"><a name="linearise"></a><span class="summary-sig-name">linearise</span>(<span class="summary-sig-arg">FS</span>)</span></td>
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<span class="summary-type">new linear FS instance</span>
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<td><span class="summary-sig"><a name="to_linear"></a><span class="summary-sig-name">to_linear</span>(<span class="summary-sig-arg">FS</span>)</span></td>
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<span class="summary-type">new circular FS instance</span>
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<td><span class="summary-sig"><a name="to_circular"></a><span class="summary-sig-name">to_circular</span>(<span class="summary-sig-arg">FS</span>)</span></td>
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<span class="summary-type">bool</span>
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<td><span class="summary-sig"><a name="is_linear"></a><span class="summary-sig-name">is_linear</span>(<span class="summary-sig-arg">FS</span>)</span><br />
True if the sequence will analysed as a linear sequence.</td>
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<span class="summary-type">list</span>
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<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.FormattedSeq-class.html#finditer" class="summary-sig-name">finditer</a>(<span class="summary-sig-arg">FS</span>,
<span class="summary-sig-arg">pattern</span>,
<span class="summary-sig-arg">size</span>)</span><br />
return a list of pattern into the sequence.</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">i</span>)</span></td>
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<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq.__getitem__">source code</a></span>
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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>__str__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
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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">seq</span>,
<span class="sig-arg">linear</span>=<span class="sig-default">True</span>)</span>
<br /><em class="fname">(Constructor)</em>
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<p>FormattedSeq(seq, [linear=True])-> new FormattedSeq.</p>
<p>seq is either a Bio.Seq, Bio.MutableSeq or a FormattedSeq. if seq is a
FormattedSeq, linear will have no effect on the shape of the
sequence.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
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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>
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><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq.__repr__">source code</a></span>
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<p>repr(x)</p>
<dl class="fields">
<dt>Overrides:
object.__repr__
<dd><em class="note">(inherited documentation)</em></dd>
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<a name="finditer"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">finditer</span>(<span class="sig-arg">FS</span>,
<span class="sig-arg">pattern</span>,
<span class="sig-arg">size</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#FormattedSeq.finditer">source code</a></span>
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<p>return a list of pattern into the sequence. the list is made of tuple
(location, pattern.group). the latter is used with non palindromic sites.
pattern is the regular expression pattern corresponding to the enzyme
restriction site. size is the size of the restriction enzyme
recognition-site size.</p>
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<dt>Returns: list</dt>
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