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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 TwoCuts
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<!-- ==================== TYPE DESCRIPTION ==================== -->
<h1 class="epydoc">Type TwoCuts</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts">source code</a></span></p>
<pre class="base-tree">
object --+
|
type --+
|
<a href="Bio.Restriction.Restriction.RestrictionType-class.html" onclick="show_private();">RestrictionType</a> --+
|
<a href="Bio.Restriction.Restriction.AbstractCut-class.html" onclick="show_private();">AbstractCut</a> --+
|
<strong class="uidshort">TwoCuts</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.Restriction.Restriction.AjuI-class.html">AjuI</a></li><li>, <a href="Bio.Restriction.Restriction.AlfI-class.html">AlfI</a></li><li>, <a href="Bio.Restriction.Restriction.AloI-class.html">AloI</a></li><li>, <a href="Bio.Restriction.Restriction.ArsI-class.html">ArsI</a></li><li>, <a href="Bio.Restriction.Restriction.BaeI-class.html">BaeI</a></li><li>, <a href="Bio.Restriction.Restriction.BarI-class.html">BarI</a></li><li>, <a href="Bio.Restriction.Restriction.BcgI-class.html">BcgI</a></li><li>, <a href="Bio.Restriction.Restriction.BdaI-class.html">BdaI</a></li><li>, <a href="Bio.Restriction.Restriction.BplI-class.html">BplI</a></li><li>, <a href="Bio.Restriction.Restriction.BsaXI-class.html">BsaXI</a></li><li>, <a href="Bio.Restriction.Restriction.Bsp24I-class.html">Bsp24I</a></li><li>, <a href="Bio.Restriction.Restriction.CjeI-class.html">CjeI</a></li><li>, <a href="Bio.Restriction.Restriction.CjePI-class.html">CjePI</a></li><li>, <a href="Bio.Restriction.Restriction.CspCI-class.html">CspCI</a></li><li>, <a href="Bio.Restriction.Restriction.FalI-class.html">FalI</a></li><li>, <a href="Bio.Restriction.Restriction.Hin4I-class.html">Hin4I</a></li><li>, <a href="Bio.Restriction.Restriction.NgoAVIII-class.html">NgoAVIII</a></li><li>, <a href="Bio.Restriction.Restriction.NmeDI-class.html">NmeDI</a></li><li>, <a href="Bio.Restriction.Restriction.PpiI-class.html">PpiI</a></li><li>, <a href="Bio.Restriction.Restriction.PsrI-class.html">PsrI</a></li><li>, <a href="Bio.Restriction.Restriction.SdeOSI-class.html">SdeOSI</a></li><li class="private">, <a href="Bio.Restriction.Restriction.T-class.html" onclick="show_private();">T</a></li><li>, <a href="Bio.Restriction.Restriction.TstI-class.html">TstI</a></li> </ul>
</dd></dl>
<hr />
<p>Implement the methods specific to the enzymes that cut the DNA
twice</p>
<p>Correspond to ncuts values of 4 in emboss_e.###</p>
<p>Internal use only. Not meant to be instantiated.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html" onclick="show_private();">RestrictionType</a></code></b>:
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__add__">__add__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__div__">__div__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__eq__">__eq__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__floordiv__">__floordiv__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__ge__">__ge__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__gt__">__gt__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__hash__">__hash__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__init__">__init__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__le__">__le__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__len__">__len__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__lt__">__lt__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__mod__">__mod__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__ne__">__ne__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rdiv__">__rdiv__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__repr__">__repr__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rfloordiv__">__rfloordiv__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rshift__">__rshift__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rtruediv__">__rtruediv__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__str__">__str__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__truediv__">__truediv__</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>type</code></b>:
<code>__call__</code>,
<code>__delattr__</code>,
<code>__getattribute__</code>,
<code>__instancecheck__</code>,
<code>__new__</code>,
<code>__setattr__</code>,
<code>__subclasscheck__</code>,
<code>__subclasses__</code>,
<code>mro</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
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<!-- ==================== CLASS METHODS ==================== -->
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<td align="left"><span class="table-header">Class Methods</span></td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">bool</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="cut_once"></a><span class="summary-sig-name">cut_once</span>(<span class="summary-sig-arg">RE</span>)</span><br />
True if the enzyme cut the sequence one time on each strand.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts.cut_once">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">bool</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="cut_twice"></a><span class="summary-sig-name">cut_twice</span>(<span class="summary-sig-arg">RE</span>)</span><br />
True if the enzyme cut the sequence twice on each strand.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts.cut_twice">source code</a></span>
</td>
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</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">int</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.TwoCuts-class.html#_modify" class="summary-sig-name" onclick="show_private();">_modify</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">location</span>)</span><br />
for internal use only.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts._modify">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">generator of int</span>
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.TwoCuts-class.html#_rev_modify" class="summary-sig-name" onclick="show_private();">_rev_modify</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">location</span>)</span><br />
for internal use only.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts._rev_modify">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">tuple</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="characteristic"></a><span class="summary-sig-name">characteristic</span>(<span class="summary-sig-arg">RE</span>)</span><br />
the tuple contains the attributes:
fst5 -> first 5' cut ((current strand) or None
fst3 -> first 3' cut (complementary strand) or None
scd5 -> second 5' cut (current strand) or None
scd5 -> second 3' cut (complementary strand) or None
site -> recognition site.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts.characteristic">source code</a></span>
</td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html" onclick="show_private();">AbstractCut</a></code></b>:
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#all_suppliers">all_suppliers</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#equischizomers">equischizomers</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#frequency">frequency</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#is_equischizomer">is_equischizomer</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#is_isoschizomer">is_isoschizomer</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#is_neoschizomer">is_neoschizomer</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#isoschizomers">isoschizomers</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#neoschizomers">neoschizomers</a></code>,
<code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#search">search</a></code>
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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>type</code></b>:
<code>__abstractmethods__</code>,
<code>__base__</code>,
<code>__bases__</code>,
<code>__basicsize__</code>,
<code>__dictoffset__</code>,
<code>__flags__</code>,
<code>__itemsize__</code>,
<code>__mro__</code>,
<code>__name__</code>,
<code>__weakrefoffset__</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<!-- ==================== METHOD DETAILS ==================== -->
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<td align="left"><span class="table-header">Method Details</span></td>
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<a name="_modify"></a>
<div class="private">
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_modify</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">location</span>)</span>
<br /><em class="fname">Class Method</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts._modify">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
for internal use only.
location is an integer corresponding to the location of the match for
the enzyme pattern in the sequence.
_modify returns the real place where the enzyme will cut.
example:
EcoRI pattern : GAATTC
EcoRI will cut after the G.
so in the sequence:
______
GAATACACGGAATTCGA
|
10
dna.finditer(GAATTC, 6) will return 10 as G is the 10th base
EcoRI cut after the G so:
EcoRI._modify(10) -> 11.
if the enzyme cut twice _modify will returns two integer corresponding
to each cutting site.
</pre>
<dl class="fields">
<dt>Returns: int</dt>
</dl>
</td></tr></table>
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<a name="_rev_modify"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_rev_modify</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">location</span>)</span>
<br /><em class="fname">Class Method</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#TwoCuts._rev_modify">source code</a></span>
</td>
</tr></table>
<p>for internal use only.</p>
<p>as _modify for site situated on the antiparallel strand when the
enzyme is not palindromic</p>
<dl class="fields">
<dt>Returns: generator of int</dt>
</dl>
</td></tr></table>
</div>
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