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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._Update-module.html">Package _Update</a> ::
Module RestrictionCompiler
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module RestrictionCompiler</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction._Update.RestrictionCompiler-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Convert a serie of Rebase files into a Restriction_Dictionary.py module.
The Rebase files are in the emboss format :
emboss_e.### -> contains informations about the restriction sites.
emboss_r.### -> contains general informations about the enzymes.
emboss_s.### -> contains informations about the suppliers.
### is a 3 digit number. The first digit is the year and the two last the month.
</pre>
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<a href="Bio.Restriction._Update.RestrictionCompiler.OverhangError-class.html" class="summary-name">OverhangError</a><br />
Exception for dealing with overhang.
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construct the attributes of the enzyme corresponding to 'name'.
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<a href="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html" class="summary-name">TypeCompiler</a><br />
Build the different types possible for Restriction Enzymes
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<td><span class="summary-sig"><a href="Bio.Restriction._Update.RestrictionCompiler-module.html#BaseExpand" class="summary-sig-name">BaseExpand</a>(<span class="summary-sig-arg">base</span>)</span><br />
given a degenerated base, returns its meaning in IUPAC alphabet.</td>
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<td><span class="summary-sig"><a href="Bio.Restriction._Update.RestrictionCompiler-module.html#regex" class="summary-sig-name">regex</a>(<span class="summary-sig-arg">site</span>)</span><br />
Construct a regular expression from a DNA sequence.</td>
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<td><span class="summary-sig"><a name="Antiparallel"></a><span class="summary-sig-name">Antiparallel</span>(<span class="summary-sig-arg">sequence</span>)</span><br />
returns a string which represents the reverse complementary strand of
a DNA sequence.</td>
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<span class="summary-type">bool</span>
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<td><span class="summary-sig"><a href="Bio.Restriction._Update.RestrictionCompiler-module.html#is_palindrom" class="summary-sig-name">is_palindrom</a>(<span class="summary-sig-arg">sequence</span>)</span><br />
True is the sequence is a palindrom.</td>
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<td><span class="summary-sig"><a name="LocalTime"></a><span class="summary-sig-name">LocalTime</span>()</span><br />
LocalTime calculate the extension for emboss file for the current
year and month.</td>
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<a name="DNA"></a><span class="summary-name">DNA</span> = <code title="Seq">Seq</code>
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<a href="Bio.Restriction._Update.RestrictionCompiler-module.html#dna_alphabet" class="summary-name">dna_alphabet</a> = <code title="{'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'R': 'AG', 'Y': 'CT', 'W': 'A\
T', 'S': 'CG', 'M': 'AC', 'K': 'GT', 'H': 'ACT', 'B': 'CGT', 'V': 'ACG\
', 'D': 'AGT', 'N': 'ACGT', 'a': 'a', 'c': 'c', 'g': 'g', 't': 't', 'r\
': 'ag', 'y': 'ct', 'w': 'at', 's': 'cg', 'm': 'ac', 'k': 'gt', 'h': '\
act', 'b': 'cgt', 'v': 'acg', 'd': 'agt', 'n': 'acgt'}">{'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'R': '<code class="variable-ellipsis">...</code></code>
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<a href="Bio.Restriction._Update.RestrictionCompiler-module.html#complement_alphabet" class="summary-name">complement_alphabet</a> = <code title="{'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', 'R': 'Y', 'Y': 'R', 'W': 'W',\
'S': 'S', 'M': 'K', 'K': 'M', 'H': 'D', 'D': 'H', 'B': 'V', 'V': 'B',\
'N': 'N', 'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'r': 'y', 'y': 'r',\
'w': 'w', 's': 's', 'm': 'k', 'k': 'm', 'h': 'd', 'd': 'h', 'b': 'v',\
'v': 'b', 'n': 'n'}">{'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C',<code class="variable-ellipsis">...</code></code>
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<a name="enzymedict"></a><span class="summary-name">enzymedict</span> = <code title="{}">{}</code>
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<a name="suppliersdict"></a><span class="summary-name">suppliersdict</span> = <code title="{}">{}</code>
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<a name="classdict"></a><span class="summary-name">classdict</span> = <code title="{}">{}</code>
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<a href="Bio.Restriction._Update.RestrictionCompiler-module.html#start" class="summary-name">start</a> = <code title="'\n\
#!/usr/bin/env python\n\
#\n\
# Restriction Analysis Libraries.\n\
# Copyright (C) 2004. Frederic Sohm.\n\
#\n\
# This code is part of the Biopython distribution and governed by its\\
n\
...">'<code class="variable-ellipsis">...</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">BaseExpand</span>(<span class="sig-arg">base</span>)</span>
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<pre class="literalblock">
given a degenerated base, returns its meaning in IUPAC alphabet.
i.e:
b= 'A' -> 'A'
b= 'N' -> 'ACGT'
etc...
</pre>
<dl class="fields">
<dt>Returns: string</dt>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">regex</span>(<span class="sig-arg">site</span>)</span>
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<pre class="literalblock">
Construct a regular expression from a DNA sequence.
i.e. :
site = 'ABCGN' -> 'A[CGT]CG.'
</pre>
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<dt>Returns: string</dt>
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<p>True is the sequence is a palindrom. sequence is a DNA object.</p>
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<dt>Returns: bool</dt>
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<dl class="fields">
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<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
{'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'R': 'AG', 'Y': 'CT', 'W': 'A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
T', 'S': 'CG', 'M': 'AC', 'K': 'GT', 'H': 'ACT', 'B': 'CGT', 'V': 'ACG<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
', 'D': 'AGT', 'N': 'ACGT', 'a': 'a', 'c': 'c', 'g': 'g', 't': 't', 'r<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
': 'ag', 'y': 'ct', 'w': 'at', 's': 'cg', 'm': 'ac', 'k': 'gt', 'h': '<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
act', 'b': 'cgt', 'v': 'acg', 'd': 'agt', 'n': 'acgt'}
</pre></td></tr></table>
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<h3 class="epydoc">complement_alphabet</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
{'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', 'R': 'Y', 'Y': 'R', 'W': 'W',<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
'S': 'S', 'M': 'K', 'K': 'M', 'H': 'D', 'D': 'H', 'B': 'V', 'V': 'B',<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
'N': 'N', 'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'r': 'y', 'y': 'r',<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
'w': 'w', 's': 's', 'm': 'k', 'k': 'm', 'h': 'd', 'd': 'h', 'b': 'v',<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
'v': 'b', 'n': 'n'}
</pre></td></tr></table>
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<h3 class="epydoc">start</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
'\n\
#!/usr/bin/env python\n\
#\n\
# Restriction Analysis Libraries.\n\
# Copyright (C) 2004. Frederic Sohm.\n\
#\n\
# This code is part of the Biopython distribution and governed by its\<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
n\
<code class="variable-ellipsis">...</code>
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