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<?xml version="1.0" encoding="ascii"?>
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<a href="core-module.html">Package core</a> ::
Module insert_mutations
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module insert_mutations</h1><p class="nomargin-top"></p>
<p>Created 2012 core Script for the generation of the artificial
reference genome</p>
<p>The functions purpose is to to go through a list of positions and find
balanced mutations which fulfill the demands on the artificial reference
genome. Once a initial start positions is randomly selected all possible
triplets with hamming distance 1 are generated and looked up in a
dictionary which contains all triplet positions in the input genome. If a
suitable partner is found for the initial mutation the next start
positions is chosen randomly. Else: try all other triplets with hamming
distance 1 until no one is left. This process can be accelerated by
allowing unbalanced mutations, but this will cause differences in the
NUC/AA distribution and the AA neighborhood.</p>
<hr />
<div class="fields"> <p><strong>Author:</strong>
Sven Giese
</p>
</div><!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
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<td align="left"><span class="table-header">Functions</span></td>
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<span class="summary-type">list,list</span>
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<tr>
<td><span class="summary-sig"><a href="core.insert_mutations-module.html#getMutation" class="summary-sig-name">getMutation</a>(<span class="summary-sig-arg">AA</span>,
<span class="summary-sig-arg">Codon</span>)</span><br />
Returns a random mutation for a given AA and its Codon(DNA).</td>
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</td>
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</td>
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<span class="summary-type">Char,Char,int</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="core.insert_mutations-module.html#getdifference" class="summary-sig-name">getdifference</a>(<span class="summary-sig-arg">triplet_old</span>,
<span class="summary-sig-arg">triplet_new</span>)</span><br />
Given two triplets, returns the differences between them plus the
position</td>
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<span class="summary-type">Bool</span>
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<td><span class="summary-sig"><a href="core.insert_mutations-module.html#isvalidposition" class="summary-sig-name">isvalidposition</a>(<span class="summary-sig-arg">pdic</span>,
<span class="summary-sig-arg">iprime</span>,
<span class="summary-sig-arg">distance</span>)</span><br />
Checks if a position is valid for mutation.</td>
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<span class="summary-type">list</span>
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<tr>
<td><span class="summary-sig"><a href="core.insert_mutations-module.html#mutate_random" class="summary-sig-name">mutate_random</a>(<span class="summary-sig-arg">DNA</span>,
<span class="summary-sig-arg">AminoAcid</span>,
<span class="summary-sig-arg">distance</span>,
<span class="summary-sig-arg">pdic</span>,
<span class="summary-sig-arg">rev</span>,
<span class="summary-sig-arg">header</span>,
<span class="summary-sig-arg">Random</span>,
<span class="summary-sig-arg">outputpath</span>)</span><br />
Mutates a given DNA(AminoAcid) Genomesequence on several positions
(distance based on DISTANCE var.</td>
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</td>
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<!-- ==================== VARIABLES ==================== -->
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<span class="summary-type"> </span>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'core'"><code class="variable-quote">'</code><code class="variable-string">core</code><code class="variable-quote">'</code></code>
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<a name="getMutation"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">getMutation</span>(<span class="sig-arg">AA</span>,
<span class="sig-arg">Codon</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
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<p>Returns a random mutation for a given AA and its Codon(DNA). The
mutation is done in a way which supports the equilibrium of the
nucleotide distribution by only regarding hamming distance=1 Codons as
possible mutations</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>AA</code></strong> (string) - Single AA.</li>
<li><strong class="pname"><code>Codon</code></strong> (string) - 3-letter dna code.</li>
</ul></dd>
<dt>Returns: list,list</dt>
<dd>A list of all valid mutations (triplet) and the coresponding AA.</dd>
</dl>
</td></tr></table>
</div>
<a name="getdifference"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">getdifference</span>(<span class="sig-arg">triplet_old</span>,
<span class="sig-arg">triplet_new</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Given two triplets, returns the differences between them plus the
position</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>triplet_old</code></strong> (string) - AA triplet.</li>
<li><strong class="pname"><code>triplet_new</code></strong> (string) - AA triplet.</li>
</ul></dd>
<dt>Returns: Char,Char,int</dt>
<dd>The new aminoacid, the old aminoacid and the position.</dd>
</dl>
</td></tr></table>
</div>
<a name="isvalidposition"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">isvalidposition</span>(<span class="sig-arg">pdic</span>,
<span class="sig-arg">iprime</span>,
<span class="sig-arg">distance</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Checks if a position is valid for mutation. It queries all neighboring
positions (iprime +-distance) to check whether there already was a
mutation in pdic</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>pdic</code></strong> (dictionary) - Diciontary containing mutations and start/ stop codons..</li>
<li><strong class="pname"><code>iprime</code></strong> (int) - Position of the prospective mutation (DNA level)</li>
<li><strong class="pname"><code>distance</code></strong> (int) - User defined parameter which limits the distance between two
mutations.</li>
</ul></dd>
<dt>Returns: Bool</dt>
<dd>Boolean which decides if the position is valid (1= yes,0 = no)</dd>
</dl>
</td></tr></table>
</div>
<a name="mutate_random"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">mutate_random</span>(<span class="sig-arg">DNA</span>,
<span class="sig-arg">AminoAcid</span>,
<span class="sig-arg">distance</span>,
<span class="sig-arg">pdic</span>,
<span class="sig-arg">rev</span>,
<span class="sig-arg">header</span>,
<span class="sig-arg">Random</span>,
<span class="sig-arg">outputpath</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Mutates a given DNA(AminoAcid) Genomesequence on several positions
(distance based on DISTANCE var. If one mutation is done a compareable
Triplet is searched to "reverse" the changes made in AA
distribution, N distribution, AA neighborhood</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>DNA</code></strong> (list) - DNA sequence of the reference genome.</li>
<li><strong class="pname"><code>AminoAcid</code></strong> (list) - AA sequence of the reference genome.</li>
<li><strong class="pname"><code>rev</code></strong> (Bool) - Boolean which decides if unbalanced mutations are allowed (only
initial mutation is performed)</li>
<li><strong class="pname"><code>pdic</code></strong> (dictionary) - Diciontary containing mutations and start/ stop codons..</li>
<li><strong class="pname"><code>header</code></strong> (string) - Header for the resulting artificial reference file (fasta
format).</li>
<li><strong class="pname"><code>Random</code></strong> (Bool) - Boolean for choosing on of the mutation modes (linear = 0,random
= 1)</li>
<li><strong class="pname"><code>distance</code></strong> (int) - User defined parameter which limits the distance between two
mutations.</li>
</ul></dd>
<dt>Returns: list</dt>
<dd>Artificial reference genome sequence.</dd>
</dl>
</td></tr></table>
</div>
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