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<a href="Bio-module.html">Package Bio</a> ::
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Module Signature
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<h1 class="epydoc">Source Code for <a href="Bio.NeuralNetwork.Gene.Signature-module.html">Module Bio.NeuralNetwork.Gene.Signature</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Find and deal with signatures in biological sequence data.</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">In addition to representing sequences according to motifs (see Motif.py</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">for more information), we can also use Signatures, which are conserved</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">regions that are not necessarily consecutive. This may be useful in</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">the case of very diverged sequences, where signatures may pick out</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">important conservation that can't be found by motifs (hopefully!).</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># biopython</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.GenBank.utils=Bio.GenBank.utils-module.html,Module Bio.utils=Bio.utils-module.html"><a title="Bio.GenBank.utils
Bio.utils" class="py-name" href="#" onclick="return doclink('link-1', 'utils', 'link-1');">utils</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-3', 'Seq', 'link-3');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-4', 'Seq', 'link-3');">Seq</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"># local stuff</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name" targets="Module Bio.NeuralNetwork.Gene.Pattern=Bio.NeuralNetwork.Gene.Pattern-module.html,Module Bio.Prosite.Pattern=Bio.Prosite.Pattern-module.html,Class Martel.msre_parse.Pattern=Martel.msre_parse.Pattern-class.html"><a title="Bio.NeuralNetwork.Gene.Pattern
Bio.Prosite.Pattern
Martel.msre_parse.Pattern" class="py-name" href="#" onclick="return doclink('link-5', 'Pattern', 'link-5');">Pattern</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class Bio.NeuralNetwork.Gene.Pattern.PatternRepository=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html"><a title="Bio.NeuralNetwork.Gene.Pattern.PatternRepository" class="py-name" href="#" onclick="return doclink('link-6', 'PatternRepository', 'link-6');">PatternRepository</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="SignatureFinder"></a><div id="SignatureFinder-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="SignatureFinder-toggle" onclick="return toggle('SignatureFinder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html">SignatureFinder</a><tt class="py-op">:</tt> </tt>
</div><div id="SignatureFinder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SignatureFinder-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-docstring">"""Find Signatures in a group of sequence records.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> In this simple implementation, signatures are just defined as a</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> two motifs separated by a gap. We need something a lot smarter than</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> this to find more complicated signatures.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SignatureFinder.__init__"></a><div id="SignatureFinder.__init__-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="SignatureFinder.__init__-toggle" onclick="return toggle('SignatureFinder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureFinder-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">alphabet_strict</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SignatureFinder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SignatureFinder.__init__-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a finder to get signatures.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> o alphabet_strict - Specify whether signatures should be required</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> to have all letters in the signature be consistent with the</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> alphabet of the original sequence. This requires that all Seqs</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> used have a consistent alphabet. This helps protect against getting</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> useless signatures full of ambiguity signals.</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">_alphabet_strict</tt> <tt class="py-op">=</tt> <tt class="py-name">alphabet_strict</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="SignatureFinder.find"></a><div id="SignatureFinder.find-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="SignatureFinder.find-toggle" onclick="return toggle('SignatureFinder.find');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find">find</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq_records</tt><tt class="py-op">,</tt> <tt class="py-param">signature_size</tt><tt class="py-op">,</tt> <tt class="py-param">max_gap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SignatureFinder.find-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SignatureFinder.find-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-docstring">"""Find all signatures in a group of sequences.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</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-docstring"> o seq_records - A list of SeqRecord objects we'll use the sequences</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> from to find signatures.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> o signature_size - The size of each half of a signature (ie. if this</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> is set at 3, then the signature could be AGC-----GAC)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> o max_gap - The maximum gap size between two parts of a signature.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">sig_info</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder._get_signature_dict()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#_get_signature_dict"><a title="Bio.NeuralNetwork.Gene.Signature.SignatureFinder._get_signature_dict" class="py-name" href="#" onclick="return doclink('link-7', '_get_signature_dict', 'link-7');">_get_signature_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">seq_records</tt><tt class="py-op">,</tt> <tt class="py-name">signature_size</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">max_gap</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><a title="Bio.NeuralNetwork.Gene.Pattern.PatternRepository" class="py-name" href="#" onclick="return doclink('link-8', 'PatternRepository', 'link-6');">PatternRepository</a></tt><tt class="py-op">(</tt><tt class="py-name">sig_info</tt><tt class="py-op">)</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="SignatureFinder._get_signature_dict"></a><div id="SignatureFinder._get_signature_dict-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="SignatureFinder._get_signature_dict-toggle" onclick="return toggle('SignatureFinder._get_signature_dict');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#_get_signature_dict">_get_signature_dict</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq_records</tt><tt class="py-op">,</tt> <tt class="py-param">sig_size</tt><tt class="py-op">,</tt> <tt class="py-param">max_gap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SignatureFinder._get_signature_dict-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SignatureFinder._get_signature_dict-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a dictionary with all signatures and their counts.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> This internal function does all of the hard work for the</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> find_signatures function.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alphabet_strict</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt id="link-9" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-9', 'alphabet', 'link-9');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seq_records</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-10', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'alphabet', 'link-9');">alphabet</a></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-12', 'alphabet', 'link-9');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment"># loop through all records to find signatures</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">all_sigs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seq_record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seq_records</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-comment"># if we are working with alphabets, make sure we are consistent</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-13" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-13', 'alphabet', 'link-9');">alphabet</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-14', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-15', 'alphabet', 'link-9');">alphabet</a></tt> <tt class="py-op">==</tt> <tt id="link-16" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-16', 'alphabet', 'link-9');">alphabet</a></tt><tt class="py-op">,</tt> \ </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-string">"Working with alphabet %s and got %s"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-17', 'alphabet', 'link-9');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-18', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-19', 'alphabet', 'link-9');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment"># now start finding signatures in the sequence</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">largest_sig_size</tt> <tt class="py-op">=</tt> <tt class="py-name">sig_size</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> <tt class="py-op">+</tt> <tt class="py-name">max_gap</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-20" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-20', 'start', 'link-20');">start</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-21', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">largest_sig_size</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-comment"># find the first part of the signature</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">first_sig</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-22', 'seq', 'link-10');">seq</a></tt><tt class="py-op">[</tt><tt id="link-23" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-23', 'start', 'link-20');">start</a></tt><tt class="py-op">:</tt><tt id="link-24" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-24', 'start', 'link-20');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">sig_size</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-25', 'data', 'link-25');">data</a></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment"># now find all of the second parts of the signature</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">second</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-26', 'start', 'link-20');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-27', 'start', 'link-20');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">max_gap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">second_sig</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-28', 'seq', 'link-10');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">second</tt><tt class="py-op">:</tt> <tt class="py-name">second</tt> <tt class="py-op">+</tt> <tt class="py-name">sig_size</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-29', 'data', 'link-25');">data</a></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># if we are being alphabet strict, make sure both parts</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># of the sig fall within the specified alphabet</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-30" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-30', 'alphabet', 'link-9');">alphabet</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">first_seq</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-31', 'Seq', 'link-3');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">first_sig</tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-32', 'alphabet', 'link-9');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">second_seq</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-33', 'Seq', 'link-3');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">second_sig</tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-34', 'alphabet', 'link-9');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-35" class="py-name"><a title="Bio.GenBank.utils
Bio.utils" class="py-name" href="#" onclick="return doclink('link-35', 'utils', 'link-1');">utils</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Function Bio.utils.verify_alphabet()=Bio.utils-module.html#verify_alphabet"><a title="Bio.utils.verify_alphabet" class="py-name" href="#" onclick="return doclink('link-36', 'verify_alphabet', 'link-36');">verify_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">first_seq</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.GenBank.utils
Bio.utils" class="py-name" href="#" onclick="return doclink('link-37', 'utils', 'link-1');">utils</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.utils.verify_alphabet" class="py-name" href="#" onclick="return doclink('link-38', 'verify_alphabet', 'link-36');">verify_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">second_seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">all_sigs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder._add_sig()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#_add_sig"><a title="Bio.NeuralNetwork.Gene.Signature.SignatureFinder._add_sig" class="py-name" href="#" onclick="return doclink('link-39', '_add_sig', 'link-39');">_add_sig</a></tt><tt class="py-op">(</tt><tt class="py-name">all_sigs</tt><tt class="py-op">,</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">first_sig</tt><tt class="py-op">,</tt> <tt class="py-name">second_sig</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-comment"># if we are not being strict, just add the motif</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">all_sigs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.NeuralNetwork.Gene.Signature.SignatureFinder._add_sig" class="py-name" href="#" onclick="return doclink('link-40', '_add_sig', 'link-39');">_add_sig</a></tt><tt class="py-op">(</tt><tt class="py-name">all_sigs</tt><tt class="py-op">,</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">first_sig</tt><tt class="py-op">,</tt> <tt class="py-name">second_sig</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">all_sigs</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="SignatureFinder._add_sig"></a><div id="SignatureFinder._add_sig-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="SignatureFinder._add_sig-toggle" onclick="return toggle('SignatureFinder._add_sig');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#_add_sig">_add_sig</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sig_dict</tt><tt class="py-op">,</tt> <tt class="py-param">sig_to_add</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SignatureFinder._add_sig-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SignatureFinder._add_sig-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a signature to the given dictionary.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># incrememt the count of the signature if it is already present</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">sig_dict</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-41', 'has_key', 'link-41');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sig_to_add</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">sig_dict</tt><tt class="py-op">[</tt><tt class="py-name">sig_to_add</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-comment"># otherwise add it to the dictionary</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">sig_dict</tt><tt class="py-op">[</tt><tt class="py-name">sig_to_add</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sig_dict</tt> </tt>
</div></div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="SignatureCoder"></a><div id="SignatureCoder-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="SignatureCoder-toggle" onclick="return toggle('SignatureCoder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureCoder-class.html">SignatureCoder</a><tt class="py-op">:</tt> </tt>
</div><div id="SignatureCoder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SignatureCoder-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert a Sequence into its signature representatives.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> This takes a sequence and a set of signatures, and converts the</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> sequence into a list of numbers representing the relative amounts</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> each signature is seen in the sequence. This allows a sequence to</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> serve as input into a neural network.</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SignatureCoder.__init__"></a><div id="SignatureCoder.__init__-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="SignatureCoder.__init__-toggle" onclick="return toggle('SignatureCoder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureCoder-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">signatures</tt><tt class="py-op">,</tt> <tt class="py-param">max_gap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SignatureCoder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SignatureCoder.__init__-expanded"><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize with the signatures to look for.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> o signatures - A complete list of signatures, in order, that</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> are to be searched for in the sequences. The signatures should</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> be represented as a tuple of (first part of the signature,</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> second_part of the signature) -- ('GATC', 'GATC').</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> o max_gap - The maximum gap we can have between the two</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> elements of the signature.</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt> <tt class="py-op">=</tt> <tt class="py-name">signatures</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_max_gap</tt> <tt class="py-op">=</tt> <tt class="py-name">max_gap</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment"># check to be sure the signatures are all the same size</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># only do this if we actually have signatures</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">first_sig_size</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">second_sig_size</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">first_sig_size</tt> <tt class="py-op">==</tt> <tt class="py-name">second_sig_size</tt><tt class="py-op">,</tt> \ </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-string">"Ends of the signature do not match: %s"</tt> \ </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sig</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sig</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">first_sig_size</tt><tt class="py-op">,</tt> \ </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-string">"Got first part of signature %s, expected size %s"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">sig</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">first_sig_size</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sig</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">second_sig_size</tt><tt class="py-op">,</tt> \ </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-string">"Got second part of signature %s, expected size %s"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">sig</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">second_sig_size</tt><tt class="py-op">)</tt> </tt>
</div><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="SignatureCoder.representation"></a><div id="SignatureCoder.representation-def"><a name="L155"></a><tt class="py-lineno">155</tt> <a class="py-toggle" href="#" id="SignatureCoder.representation-toggle" onclick="return toggle('SignatureCoder.representation');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Gene.Signature.SignatureCoder-class.html#representation">representation</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SignatureCoder.representation-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SignatureCoder.representation-expanded"><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert a sequence into a representation of its signatures.</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> o sequence - A Seq object we are going to convert into a set of</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> signatures.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> Returns:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> A list of relative signature representations. Each item in the</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"> list corresponds to the signature passed in to the initializer and</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> is the number of times that the signature was found, divided by the</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> total number of signatures found in the sequence.</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-comment"># check to be sure we have signatures to deal with,</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># otherwise just return an empty list</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-comment"># initialize a dictionary to hold the signature counts</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sequence_sigs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sig</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">sequence_sigs</tt><tt class="py-op">[</tt><tt class="py-name">sig</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment"># get a list of all of the first parts of the signatures</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">all_first_sigs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sig_start</tt><tt class="py-op">,</tt> <tt class="py-name">sig_end</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">all_first_sigs</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-42', 'append', 'link-42');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">sig_start</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-comment"># count all of the signatures we are looking for in the sequence</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sig_size</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">smallest_sig_size</tt> <tt class="py-op">=</tt> <tt class="py-name">sig_size</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-43" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-43', 'start', 'link-20');">start</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-44" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-44', 'sequence', 'link-44');">sequence</a></tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">smallest_sig_size</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-comment"># if the first part matches any of the signatures we are looking</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># for, then expand out to look for the second part</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">first_sig</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-45', 'sequence', 'link-44');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-46', 'start', 'link-20');">start</a></tt><tt class="py-op">:</tt><tt id="link-47" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-47', 'start', 'link-20');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">sig_size</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-48', 'data', 'link-25');">data</a></tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">first_sig</tt> <tt class="py-keyword">in</tt> <tt class="py-name">all_first_sigs</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">second</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-49', 'start', 'link-20');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">sig_size</tt><tt class="py-op">,</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-50', 'start', 'link-20');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">sig_size</tt> <tt class="py-op">+</tt> <tt class="py-number">1</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">_max_gap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">second_sig</tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-51', 'sequence', 'link-44');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">second</tt><tt class="py-op">:</tt><tt class="py-name">second</tt> <tt class="py-op">+</tt> <tt class="py-name">sig_size</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-52', 'data', 'link-25');">data</a></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-comment"># if we find the motif, increase the counts for it</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">sequence_sigs</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-53', 'has_key', 'link-41');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">first_sig</tt><tt class="py-op">,</tt> <tt class="py-name">second_sig</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">sequence_sigs</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">first_sig</tt><tt class="py-op">,</tt> <tt class="py-name">second_sig</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment"># -- normalize the signature info to go between zero and one</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">min_count</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">sequence_sigs</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-54', 'values', 'link-54');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">max_count</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">sequence_sigs</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-55', 'values', 'link-54');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-comment"># as long as we have some signatures present, normalize them</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># otherwise we'll just return 0 for everything </tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">max_count</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sig</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sequence_sigs</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-56', 'keys', 'link-56');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">sequence_sigs</tt><tt class="py-op">[</tt><tt class="py-name">sig</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">sequence_sigs</tt><tt class="py-op">[</tt><tt class="py-name">sig</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">min_count</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-op">/</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">max_count</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-comment"># return the relative signature info in the specified order</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sig_amounts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sig</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_signatures</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">sig_amounts</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-57', 'append', 'link-42');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">sequence_sigs</tt><tt class="py-op">[</tt><tt class="py-name">sig</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sig_amounts</tt> </tt>
</div></div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt><script type="text/javascript">
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