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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GA-module.html">Package GA</a> ::
<a href="Bio.GA.Repair-module.html">Package Repair</a> ::
Module Stabilizing
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<h1 class="epydoc">Source Code for <a href="Bio.GA.Repair.Stabilizing-module.html">Module Bio.GA.Repair.Stabilizing</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Methods for performing repairs that will Stabilize genomes.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">These methods perform repair to keep chromosomes from drifting too far in</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">any direction -- ie. bring them back to a stabilizing center. This may be</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">useful in cases where fitness functions alone won't keep chromosomes in</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">check.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="AmbiguousRepair"></a><div id="AmbiguousRepair-def"><a name="L11"></a><tt class="py-lineno">11</tt> <a class="py-toggle" href="#" id="AmbiguousRepair-toggle" onclick="return toggle('AmbiguousRepair');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html">AmbiguousRepair</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AmbiguousRepair-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="AmbiguousRepair-expanded"><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform repair to reduce the number of Ambiguous genes in a genome.</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"> In cases where ambiguous genes are allowed in a genome (for example,</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring"> where you have a wild card character like '*' that will match</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> anything), these can come to dominate a genome since, really, the</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> best fitness is someting like '*******'. This repair protects against</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> that by changing ambiguous characters into some non-ambiguous gene.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="AmbiguousRepair.__init__"></a><div id="AmbiguousRepair.__init__-def"><a name="L20"></a><tt class="py-lineno">20</tt> <a class="py-toggle" href="#" id="AmbiguousRepair.__init__-toggle" onclick="return toggle('AmbiguousRepair.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ambig_finder</tt><tt class="py-op">,</tt> <tt class="py-param">num_ambiguous</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AmbiguousRepair.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="AmbiguousRepair.__init__-expanded"><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the repair class.</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> o ambig_finder - A class implementing the function find_ambiguous</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> which will return a list of all ambiguous positions in a sequence.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> It also must have the function all_unambiguous, which will return</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> all allowed unambiguous letters.</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> o num_ambiguous - The minimum number of ambiguous items that are</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> allowed in a genome. If there are more than this present, repair</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> will be performed.</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ambig_finder</tt> <tt class="py-op">=</tt> <tt class="py-name">ambig_finder</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_num_ambiguous</tt> <tt class="py-op">=</tt> <tt id="link-0" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Schema.Schema.num_ambiguous()=Bio.NeuralNetwork.Gene.Schema.Schema-class.html#num_ambiguous"><a title="Bio.NeuralNetwork.Gene.Schema.Schema.num_ambiguous" class="py-name" href="#" onclick="return doclink('link-0', 'num_ambiguous', 'link-0');">num_ambiguous</a></tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alphabet_letters</tt> <tt class="py-op">=</tt> <tt class="py-name">ambig_finder</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Schema.Schema.all_unambiguous()=Bio.NeuralNetwork.Gene.Schema.Schema-class.html#all_unambiguous"><a title="Bio.NeuralNetwork.Gene.Schema.Schema.all_unambiguous" class="py-name" href="#" onclick="return doclink('link-1', 'all_unambiguous', 'link-1');">all_unambiguous</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="AmbiguousRepair.repair"></a><div id="AmbiguousRepair.repair-def"><a name="L38"></a><tt class="py-lineno">38</tt> <a class="py-toggle" href="#" id="AmbiguousRepair.repair-toggle" onclick="return toggle('AmbiguousRepair.repair');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html#repair">repair</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">organism</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AmbiguousRepair.repair-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="AmbiguousRepair.repair-expanded"><a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform a repair to remove excess ambiguous genes.</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">new_org</tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.organism()=Bio.GenBank._FeatureConsumer-class.html#organism,Method Bio.GenBank._RecordConsumer.organism()=Bio.GenBank._RecordConsumer-class.html#organism"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism" class="py-name" href="#" onclick="return doclink('link-2', 'organism', 'link-2');">organism</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.SeqIO._index._IndexedSeqFileDict.copy()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.PDB.Vector'.Vector.copy
Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-3', 'copy', 'link-3');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-comment"># start getting rid of ambiguous items</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-comment"># first find all of the ambigous items</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">seq_genome</tt> <tt class="py-op">=</tt> <tt class="py-name">new_org</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Seq.MutableSeq.toseq()=Bio.Seq.MutableSeq-class.html#toseq,Method BioSQL.BioSeq.DBSeq.toseq()=BioSQL.BioSeq.DBSeq-class.html#toseq"><a title="Bio.Seq.MutableSeq.toseq
BioSQL.BioSeq.DBSeq.toseq" class="py-name" href="#" onclick="return doclink('link-4', 'toseq', 'link-4');">toseq</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">all_ambiguous</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ambig_finder</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Schema.Schema.find_ambiguous()=Bio.NeuralNetwork.Gene.Schema.Schema-class.html#find_ambiguous"><a title="Bio.NeuralNetwork.Gene.Schema.Schema.find_ambiguous" class="py-name" href="#" onclick="return doclink('link-5', 'find_ambiguous', 'link-5');">find_ambiguous</a></tt><tt class="py-op">(</tt><tt class="py-name">seq_genome</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-6', 'tostring', 'link-6');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-comment"># if we have less then the number of ambiguous allowed, stop</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">all_ambiguous</tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_num_ambiguous</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-comment"># remove an ambiguous item and replace it with a non-ambiguous</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-name">to_change</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">choice</tt><tt class="py-op">(</tt><tt class="py-name">all_ambiguous</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">new_gene</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">choice</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alphabet_letters</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-name">new_org</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">[</tt><tt class="py-name">to_change</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">new_gene</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">new_org</tt> </tt>
</div></div><a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> </tt><script type="text/javascript">
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