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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Prosite-module.html">Package Prosite</a> ::
Module Pattern
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<h1 class="epydoc">Source Code for <a href="Bio.Prosite.Pattern-module.html">Module Bio.Prosite.Pattern</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000 by Andrew Dalke. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># The Prosite patterns are defined at http://www.expasy.ch/txt/prosuser.txt</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The PA (PAttern) lines contains the definition of a PROSITE pattern. The</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># patterns are described using the following conventions:</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - The standard IUPAC one-letter codes for the amino acids are used.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - The symbol `x' is used for a position where any amino acid is accepted.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - Ambiguities are indicated by listing the acceptable amino acids for a</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># given position, between square parentheses `[ ]'. For example: [ALT]</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># stands for Ala or Leu or Thr.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - Ambiguities are also indicated by listing between a pair of curly</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># brackets `{ }' the amino acids that are not accepted at a given</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># position. For example: {AM} stands for any amino acid except Ala and</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Met.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - Each element in a pattern is separated from its neighbor by a `-'.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - Repetition of an element of the pattern can be indicated by following</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># that element with a numerical value or a numerical range between</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># x-x or x-x-x or x-x-x-x.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - When a pattern is restricted to either the N- or C-terminal of a</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># sequence, that pattern either starts with a `<' symbol or respectively</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ends with a `>' symbol.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - A period ends the pattern.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># That boils down to doing these conversions</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># [] -> []</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># {} -> [^ ]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - -></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># () -> {}</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># < -> ^</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># > -> $</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># x->X</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># . -></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-comment"># Note:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># [G>] is a valid Prosite pattern, equivalent to "([G]|$)"</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"># I assume then that</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># [>G] is equivalent to "(^|[G])"</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># It is conceivable that [G>]-G-G is valid, meaning a "G" at the end</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># of the sequence or followed by two more Gs. I did not implement</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># this. I haven't gotten an answer to my query on either of these two</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># non-documented possibilities.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><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.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-1', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-2', 'Alphabet', 'link-2');">Alphabet</a></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-comment"># Syntactic conversion to two types of regular expressions</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.Prosite.Pattern._prosite_trans=Bio.Prosite.Pattern-module.html#_prosite_trans"><a title="Bio.Prosite.Pattern._prosite_trans" class="py-name" href="#" onclick="return doclink('link-3', '_prosite_trans', 'link-3');">_prosite_trans</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">maketrans</tt><tt class="py-op">(</tt><tt class="py-string">"abcdefghijklmnopqrstuvwxyzX}()<>"</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-string">"ABCDEFGHIJKLMNOPQRSTUVW.YZ.]{}^$"</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"># This does not verify that the pattern is correct - invalid patterns</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># can be converted!</tt> </tt>
<a name="prosite_to_re"></a><div id="prosite_to_re-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="prosite_to_re-toggle" onclick="return toggle('prosite_to_re');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#prosite_to_re">prosite_to_re</a><tt class="py-op">(</tt><tt class="py-param">pattern</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="prosite_to_re-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="prosite_to_re-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""convert a valid Prosite pattern into an re string"""</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">flg</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-4" class="py-name" targets="Method Bio.Prosite._RecordConsumer.pattern()=Bio.Prosite._RecordConsumer-class.html#pattern"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-4', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"[<"</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt id="link-5" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-5', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-6', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-string">"{"</tt><tt class="py-op">,</tt> <tt class="py-string">"[^"</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-7" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-7', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.GFF.Feature.translate()=Bio.GFF.Feature-class.html#translate,Method Bio.GFF.FeatureAggregate.translate()=Bio.GFF.FeatureAggregate-class.html#translate,Function Bio.Seq.translate()=Bio.Seq-module.html#translate,Function Bio.SeqUtils.translate()=Bio.SeqUtils-module.html#translate,Method Bio.Translate.Translator.translate()=Bio.Translate.Translator-class.html#translate,Function Bio.utils.translate()=Bio.utils-module.html#translate"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-8', 'translate', 'link-8');">translate</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-9', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt id="link-10" class="py-name"><a title="Bio.Prosite.Pattern._prosite_trans" class="py-name" href="#" onclick="return doclink('link-10', '_prosite_trans', 'link-3');">_prosite_trans</a></tt><tt class="py-op">,</tt> <tt class="py-string">"-."</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># special case "[<" and ">]", if they exist</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">flg</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt id="link-11" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-11', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-12', 'index', 'link-12');">index</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-13', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"]"</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-14', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"(?:^|["</tt> <tt class="py-op">+</tt> <tt id="link-15" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-15', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-16" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-16', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"])"</tt> <tt class="py-op">+</tt> <tt id="link-17" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-17', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt id="link-18" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-18', 'i', 'link-11');">i</a></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="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-19" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-19', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"$]"</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-20', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rindex</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-21', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"["</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-22', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-23', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"(?:"</tt> <tt class="py-op">+</tt> <tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-25', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt id="link-26" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-11');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"]|$)"</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-27" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-27', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"$]$"</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rindex</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-29', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"["</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-30', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-31', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-32', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"(?:"</tt> <tt class="py-op">+</tt> <tt id="link-33" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-33', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-11');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"]|$)$"</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-35" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-35', 's', 'link-5');">s</a></tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </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"># This does not verify the pattern is correct - invalid patterns can</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># be converted!</tt> </tt>
<a name="prosite_to_grouped_re"></a><div id="prosite_to_grouped_re-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="prosite_to_grouped_re-toggle" onclick="return toggle('prosite_to_grouped_re');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#prosite_to_grouped_re">prosite_to_grouped_re</a><tt class="py-op">(</tt><tt class="py-param">pattern</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="prosite_to_grouped_re-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="prosite_to_grouped_re-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-docstring">"""convert a valid Prosite pattern into an re with groups for each term"""</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">flg</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-36', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"[<"</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-37', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-38', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-string">"{"</tt><tt class="py-op">,</tt> <tt class="py-string">"[^"</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment"># Don't delete the "-" characters: use them to place the ()s</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-39" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-39', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-40', 'translate', 'link-8');">translate</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-41', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="Bio.Prosite.Pattern._prosite_trans" class="py-name" href="#" onclick="return doclink('link-42', '_prosite_trans', 'link-3');">_prosite_trans</a></tt><tt class="py-op">,</tt> <tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-comment"># Get the [< and >] terms correct</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">flg</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-44', 'index', 'link-12');">index</a></tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-45', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"]"</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt id="link-46" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-46', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"(?:^|["</tt> <tt class="py-op">+</tt> <tt id="link-47" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-47', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"])"</tt> <tt class="py-op">+</tt> <tt id="link-49" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-49', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-11');">i</a></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="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-51" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-51', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"$]"</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-52', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rindex</tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-53', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"["</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-54', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-56" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-56', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"(?:"</tt> <tt class="py-op">+</tt> <tt id="link-57" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-57', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-11');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"]|$)"</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-59', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"$]$"</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-60', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rindex</tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-61', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"["</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-62', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-63', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-64" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-64', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"(?:"</tt> <tt class="py-op">+</tt> <tt id="link-65" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-65', 's', 'link-5');">s</a></tt><tt class="py-op">[</tt><tt id="link-66" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-66', 'i', 'link-11');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"]|$)$"</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-comment"># Watch out for unescaped < and > terms</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-67" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-67', 's', 'link-5');">s</a></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 class="py-string">"^"</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-68', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"^("</tt> <tt class="py-op">+</tt> <tt id="link-69" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-69', 's', 'link-5');">s</a></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="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-70', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"("</tt> <tt class="py-op">+</tt> <tt id="link-71" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-71', 's', 'link-5');">s</a></tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-72" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-72', 's', 'link-5');">s</a></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 class="py-op">==</tt> <tt class="py-string">"$"</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-73', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-74', 's', 'link-5');">s</a></tt><tt class="py-op">[</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 class="py-string">")$"</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-75', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-76', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">")"</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-77', 's', 'link-5');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"-"</tt><tt class="py-op">,</tt> <tt class="py-string">")("</tt><tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"># Both the Prosite pattern and match result act like sequences.</tt> </tt>
<a name="PrositeAlphabet"></a><div id="PrositeAlphabet-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="PrositeAlphabet-toggle" onclick="return toggle('PrositeAlphabet');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeAlphabet-class.html">PrositeAlphabet</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeAlphabet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrositeAlphabet-expanded"><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt id="link-78" class="py-name" targets="Variable Bio.Prosite.Pattern.prosite_alphabet=Bio.Prosite.Pattern-module.html#prosite_alphabet"><a title="Bio.Prosite.Pattern.prosite_alphabet" class="py-name" href="#" onclick="return doclink('link-78', 'prosite_alphabet', 'link-78');">prosite_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name" targets="Class Bio.Prosite.Pattern.PrositeAlphabet=Bio.Prosite.Pattern.PrositeAlphabet-class.html"><a title="Bio.Prosite.Pattern.PrositeAlphabet" class="py-name" href="#" onclick="return doclink('link-79', 'PrositeAlphabet', 'link-79');">PrositeAlphabet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="compile"></a><div id="compile-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="compile-toggle" onclick="return toggle('compile');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#compile">compile</a><tt class="py-op">(</tt><tt class="py-param">pattern</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="compile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="compile-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-80" class="py-name" targets="Function Bio.Prosite.Pattern.verify_pattern()=Bio.Prosite.Pattern-module.html#verify_pattern"><a title="Bio.Prosite.Pattern.verify_pattern" class="py-name" href="#" onclick="return doclink('link-80', 'verify_pattern', 'link-80');">verify_pattern</a></tt><tt class="py-op">(</tt><tt id="link-81" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-81', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"not a legal prosite pattern"</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-82" class="py-name" targets="Package Bio.Prosite=Bio.Prosite-module.html,Class Bio.Prosite.Pattern.Prosite=Bio.Prosite.Pattern.Prosite-class.html"><a title="Bio.Prosite
Bio.Prosite.Pattern.Prosite" class="py-name" href="#" onclick="return doclink('link-82', 'Prosite', 'link-82');">Prosite</a></tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-83', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-84', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="Prosite"></a><div id="Prosite-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="Prosite-toggle" onclick="return toggle('Prosite');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html">Prosite</a><tt class="py-op">:</tt> </tt>
</div><div id="Prosite-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Prosite-expanded"><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt id="link-85" 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-85', 'alphabet', 'link-85');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Bio.Prosite.Pattern.prosite_alphabet" class="py-name" href="#" onclick="return doclink('link-86', 'prosite_alphabet', 'link-78');">prosite_alphabet</a></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># Don't like having two different types of input - not very pythonic</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># However, it is faster since I can assume the input has already been</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># verified (if it's a pattern).</tt> </tt>
<a name="Prosite.__init__"></a><div id="Prosite.__init__-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="Prosite.__init__-toggle" onclick="return toggle('Prosite.__init__');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-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">pattern</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.__init__-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">(</tt><tt id="link-87" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-87', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt id="link-88" 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-88', 'data', 'link-88');">data</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 class="py-op">^</tt> \ </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-89', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt id="link-90" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-90', 'data', 'link-88');">data</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-string">"one and only one of pattern and data can have a value"</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-91" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-91', 'pattern', 'link-4');">pattern</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="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-92', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-93', 'pattern', 'link-4');">pattern</a></tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-94" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-94', 'data', 'link-88');">data</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="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-95', 'data', 'link-88');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-96', 'data', 'link-88');">data</a></tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="Prosite.__repr__"></a><div id="Prosite.__repr__-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="Prosite.__repr__-toggle" onclick="return toggle('Prosite.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.__repr__-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Prosite(%s)"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="Prosite.__str__"></a><div id="Prosite.__str__-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="Prosite.__str__-toggle" onclick="return toggle('Prosite.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.__str__-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-97" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-97', 'map', 'link-97');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-98', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"-"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"."</tt> </tt>
</div><a name="Prosite.__len__"></a><div id="Prosite.__len__-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="Prosite.__len__-toggle" onclick="return toggle('Prosite.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-99', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="Prosite.__getitem__"></a><div id="Prosite.__getitem__-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="Prosite.__getitem__-toggle" onclick="return toggle('Prosite.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-100', 'data', 'link-88');">data</a></tt><tt class="py-op">[</tt><tt id="link-101" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-101', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="Prosite.__getslice__"></a><div id="Prosite.__getslice__-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="Prosite.__getslice__-toggle" onclick="return toggle('Prosite.__getslice__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#__getslice__">__getslice__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">,</tt> <tt class="py-param">j</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.__getslice__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.__getslice__-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt id="link-102" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-102', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt id="link-103" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-103', 'i', 'link-11');">i</a></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">j</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-104" class="py-name"><a title="Bio.Prosite
Bio.Prosite.Pattern.Prosite" class="py-name" href="#" onclick="return doclink('link-104', 'Prosite', 'link-82');">Prosite</a></tt><tt class="py-op">(</tt><tt id="link-105" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-105', 'data', 'link-88');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-106', 'data', 'link-88');">data</a></tt><tt class="py-op">[</tt><tt id="link-107" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-107', 'i', 'link-11');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="Prosite.__getattr__"></a><div id="Prosite.__getattr__-def"><a name="L148"></a><tt class="py-lineno">148</tt> <a class="py-toggle" href="#" id="Prosite.__getattr__-toggle" onclick="return toggle('Prosite.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.__getattr__-expanded"><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-comment"># Lazy creation of these elements / cache results</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-108" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-108', 'name', 'link-108');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"re"</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-109', 'compile', 'link-109');">compile</a></tt><tt class="py-op">(</tt><tt id="link-110" class="py-name" targets="Function Bio.Prosite.Pattern.prosite_to_re()=Bio.Prosite.Pattern-module.html#prosite_to_re"><a title="Bio.Prosite.Pattern.prosite_to_re" class="py-name" href="#" onclick="return doclink('link-110', 'prosite_to_re', 'link-110');">prosite_to_re</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-111', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">re</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-112" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-112', 'name', 'link-108');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"grouped_re"</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-113', 'compile', 'link-109');">compile</a></tt><tt class="py-op">(</tt><tt id="link-114" class="py-name" targets="Function Bio.Prosite.Pattern.prosite_to_grouped_re()=Bio.Prosite.Pattern-module.html#prosite_to_grouped_re"><a title="Bio.Prosite.Pattern.prosite_to_grouped_re" class="py-name" href="#" onclick="return doclink('link-114', 'prosite_to_grouped_re', 'link-114');">prosite_to_grouped_re</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-115', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-116" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-116', 'name', 'link-108');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"data"</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-117', 'data', 'link-88');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name" targets="Function Bio.Prosite.Pattern.find_terms()=Bio.Prosite.Pattern-module.html#find_terms"><a title="Bio.Prosite.Pattern.find_terms" class="py-name" href="#" onclick="return doclink('link-118', 'find_terms', 'link-118');">find_terms</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-119', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-120', 'data', 'link-88');">data</a></tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-121" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-121', 'name', 'link-108');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"pattern"</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-122', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-123', 'pattern', 'link-4');">pattern</a></tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt id="link-124" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-124', 'name', 'link-108');">name</a></tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="Prosite.tostring"></a><div id="Prosite.tostring-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="Prosite.tostring-toggle" onclick="return toggle('Prosite.tostring');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#tostring">tostring</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.tostring-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.tostring-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="Prosite.search"></a><div id="Prosite.search-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="Prosite.search-toggle" onclick="return toggle('Prosite.search');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#search">search</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">pos</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">endpos</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.search-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.search-expanded"><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">endpos</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="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-125', 'search', 'link-125');">search</a></tt><tt class="py-op">(</tt><tt class="py-name">buffer</tt><tt class="py-op">(</tt><tt id="link-126" 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-126', 'seq', 'link-126');">seq</a></tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-127', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">endpos</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-128', 'search', 'link-125');">search</a></tt><tt class="py-op">(</tt><tt class="py-name">buffer</tt><tt class="py-op">(</tt><tt id="link-129" 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-129', 'seq', 'link-126');">seq</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-130', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pos</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">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-131" class="py-name" targets="Class Bio.Prosite.Pattern.PrositeMatch=Bio.Prosite.Pattern.PrositeMatch-class.html"><a title="Bio.Prosite.Pattern.PrositeMatch" class="py-name" href="#" onclick="return doclink('link-131', 'PrositeMatch', 'link-131');">PrositeMatch</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-132" 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-132', 'seq', 'link-126');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
</div><a name="Prosite.match"></a><div id="Prosite.match-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="Prosite.match-toggle" onclick="return toggle('Prosite.match');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.Prosite-class.html#match">match</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">pos</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">endpos</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Prosite.match-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Prosite.match-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">endpos</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="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-133', 'match', 'link-133');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">buffer</tt><tt class="py-op">(</tt><tt id="link-134" 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-134', 'seq', 'link-126');">seq</a></tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-135', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">endpos</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-136', 'match', 'link-133');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">buffer</tt><tt class="py-op">(</tt><tt id="link-137" 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-137', 'seq', 'link-126');">seq</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-138', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</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">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-139" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch" class="py-name" href="#" onclick="return doclink('link-139', 'PrositeMatch', 'link-131');">PrositeMatch</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-140" 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-140', 'seq', 'link-126');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
</div></div><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"># I was thinking about adding sub, subn, findall, etc., but either</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># you just want the string (in which case, use the ".re") or</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># you could be changing to a different alphabet (eg, T->U).</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"># Elements of a Prosite pattern</tt> </tt>
<a name="PrositeTerm"></a><div id="PrositeTerm-def"><a name="L190"></a><tt class="py-lineno">190</tt> <a class="py-toggle" href="#" id="PrositeTerm-toggle" onclick="return toggle('PrositeTerm');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeTerm-class.html">PrositeTerm</a><tt class="py-op">:</tt> </tt>
</div><div id="PrositeTerm-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrositeTerm-expanded"><a name="PrositeTerm.__init__"></a><div id="PrositeTerm.__init__-def"><a name="L191"></a><tt class="py-lineno">191</tt> <a class="py-toggle" href="#" id="PrositeTerm.__init__-toggle" onclick="return toggle('PrositeTerm.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeTerm-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">letters</tt><tt class="py-op">,</tt> <tt class="py-param">ignore</tt><tt class="py-op">,</tt> <tt class="py-param">is_begin</tt><tt class="py-op">,</tt> <tt class="py-param">is_end</tt><tt class="py-op">,</tt> \ </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-param">min_count</tt><tt class="py-op">,</tt> <tt class="py-param">max_count</tt><tt class="py-op">,</tt> <tt class="py-param">can_begin</tt><tt class="py-op">,</tt> <tt class="py-param">can_end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeTerm.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeTerm.__init__-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-141', 'letters', 'link-141');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-142" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-142', 'letters', 'link-141');">letters</a></tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ignore</tt> <tt class="py-op">=</tt> <tt class="py-name">ignore</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">is_begin</tt> <tt class="py-op">=</tt> <tt class="py-name">is_begin</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">is_end</tt> <tt class="py-op">=</tt> <tt class="py-name">is_end</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">min_count</tt> <tt class="py-op">=</tt> <tt class="py-name">min_count</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_count</tt> <tt class="py-op">=</tt> <tt class="py-name">max_count</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">can_begin</tt> <tt class="py-op">=</tt> <tt class="py-name">can_begin</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">can_end</tt> <tt class="py-op">=</tt> <tt class="py-name">can_end</tt> </tt>
</div><a name="PrositeTerm.copy"></a><div id="PrositeTerm.copy-def"><a name="L201"></a><tt class="py-lineno">201</tt> <a class="py-toggle" href="#" id="PrositeTerm.copy-toggle" onclick="return toggle('PrositeTerm.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeTerm-class.html#copy">copy</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeTerm.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeTerm.copy-expanded"><a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-143" class="py-name" targets="Class Bio.Prosite.Pattern.PrositeTerm=Bio.Prosite.Pattern.PrositeTerm-class.html"><a title="Bio.Prosite.Pattern.PrositeTerm" class="py-name" href="#" onclick="return doclink('link-143', 'PrositeTerm', 'link-143');">PrositeTerm</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-144', 'letters', 'link-141');">letters</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ignore</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">is_begin</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">self</tt><tt class="py-op">.</tt><tt class="py-name">is_end</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">min_count</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_count</tt><tt class="py-op">,</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">can_begin</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">can_end</tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeTerm.__str__"></a><div id="PrositeTerm.__str__-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="PrositeTerm.__str__-toggle" onclick="return toggle('PrositeTerm.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeTerm-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeTerm.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeTerm.__str__-expanded"><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-comment"># Convert the term back into Prosite form</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-145" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-145', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeTerm.base_str()=Bio.Prosite.Pattern.PrositeTerm-class.html#base_str"><a title="Bio.Prosite.Pattern.PrositeTerm.base_str" class="py-name" href="#" onclick="return doclink('link-146', 'base_str', 'link-146');">base_str</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</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">min_count</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_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-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">min_count</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt id="link-147" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-147', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-148" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-148', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"(%d)"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">min_count</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-149" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-149', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-150" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-150', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"(%d,%d)"</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">min_count</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_count</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</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">is_end</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-151', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-152" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-152', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">">"</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-153" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-153', 's', 'link-5');">s</a></tt> </tt>
</div><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="PrositeTerm.base_str"></a><div id="PrositeTerm.base_str-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="PrositeTerm.base_str-toggle" onclick="return toggle('PrositeTerm.base_str');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeTerm-class.html#base_str">base_str</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeTerm.base_str-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeTerm.base_str-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment"># Convert the term back into Prosite form, without the repeat</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># count fields.</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</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">is_begin</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt id="link-154" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-154', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"<"</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt id="link-155" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-155', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</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">ignore</tt><tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt id="link-156" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-156', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-157" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-157', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"{"</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-158', 'letters', 'link-141');">letters</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"}"</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-159', 'letters', 'link-141');">letters</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">can_begin</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">can_end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt id="link-160" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-160', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-161" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-161', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-162', 'letters', 'link-141');">letters</a></tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt id="link-163" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-163', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-164" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-164', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"["</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</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">can_begin</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt id="link-165" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-165', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-166" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-166', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"<"</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt id="link-167" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-167', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-168" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-168', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-169', 'letters', 'link-141');">letters</a></tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</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">can_end</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt id="link-170" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-170', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-171" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-171', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">">"</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt id="link-172" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-172', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-173" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-173', 's', 'link-5');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"]"</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-174" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-174', 's', 'link-5');">s</a></tt> </tt>
</div></div><a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"># Results of a Prosite match. Wrapper to the re.MatchObj, but returns</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Seq objects instead of strings. And lookee - it implements the Seq</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># interface too!</tt> </tt>
<a name="PrositeMatch"></a><div id="PrositeMatch-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="PrositeMatch-toggle" onclick="return toggle('PrositeMatch');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html">PrositeMatch</a><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrositeMatch-expanded"><a name="PrositeMatch.__init__"></a><div id="PrositeMatch.__init__-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="PrositeMatch.__init__-toggle" onclick="return toggle('PrositeMatch.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-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">prosite</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">match</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.__init__-expanded"><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name" targets="Module Bio.dbdefs.prosite=Bio.dbdefs.prosite-module.html,Variable Bio.dbdefs.prosite.prosite=Bio.dbdefs.prosite-module.html#prosite"><a title="Bio.dbdefs.prosite
Bio.dbdefs.prosite.prosite" class="py-name" href="#" onclick="return doclink('link-175', 'prosite', 'link-175');">prosite</a></tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Bio.dbdefs.prosite
Bio.dbdefs.prosite.prosite" class="py-name" href="#" onclick="return doclink('link-176', 'prosite', 'link-175');">prosite</a></tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-177" 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-177', 'seq', 'link-126');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-178" 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-178', 'seq', 'link-126');">seq</a></tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-179', 'match', 'link-133');">match</a></tt> <tt class="py-op">=</tt> <tt id="link-180" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-180', 'match', 'link-133');">match</a></tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt id="link-181" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-181', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">endpos</tt> <tt class="py-op">=</tt> <tt id="link-182" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-182', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-comment"># for Seq.Seq initialization</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-183', 'data', 'link-88');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-184" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-184', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-185" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-185', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-186', 'alphabet', 'link-85');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-187" 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-187', 'seq', 'link-126');">seq</a></tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-188', 'alphabet', 'link-85');">alphabet</a></tt> </tt>
</div><a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
<a name="PrositeMatch.__repr__"></a><div id="PrositeMatch.__repr__-def"><a name="L258"></a><tt class="py-lineno">258</tt> <a class="py-toggle" href="#" id="PrositeMatch.__repr__-toggle" onclick="return toggle('PrositeMatch.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.__repr__-expanded"><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-comment"># XXX this isn't the right way</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-string">"<PrositeMatch instance at %x>"</tt> <tt class="py-op">%</tt> <tt id="link-189" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-189', 'id', 'link-189');">id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.__str__"></a><div id="PrositeMatch.__str__-def"><a name="L261"></a><tt class="py-lineno">261</tt> <a class="py-toggle" href="#" id="PrositeMatch.__str__-toggle" onclick="return toggle('PrositeMatch.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.__str__-expanded"><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-190', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.__len__"></a><div id="PrositeMatch.__len__-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="PrositeMatch.__len__-toggle" onclick="return toggle('PrositeMatch.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-191', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.__getitem__"></a><div id="PrositeMatch.__getitem__-def"><a name="L264"></a><tt class="py-lineno">264</tt> <a class="py-toggle" href="#" id="PrositeMatch.__getitem__-toggle" onclick="return toggle('PrositeMatch.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-192', 'data', 'link-88');">data</a></tt><tt class="py-op">[</tt><tt id="link-193" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-193', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="PrositeMatch.__getslice__"></a><div id="PrositeMatch.__getslice__-def"><a name="L265"></a><tt class="py-lineno">265</tt> <a class="py-toggle" href="#" id="PrositeMatch.__getslice__-toggle" onclick="return toggle('PrositeMatch.__getslice__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#__getslice__">__getslice__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">,</tt> <tt class="py-param">j</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.__getslice__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.__getslice__-expanded"><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt id="link-194" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-194', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-195', 'i', 'link-11');">i</a></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">j</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-196" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-196', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-197', 'data', 'link-88');">data</a></tt><tt class="py-op">[</tt><tt id="link-198" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-198', 'i', 'link-11');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-199', 'alphabet', 'link-85');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt>
<a name="PrositeMatch.mapping"></a><div id="PrositeMatch.mapping-def"><a name="L269"></a><tt class="py-lineno">269</tt> <a class="py-toggle" href="#" id="PrositeMatch.mapping-toggle" onclick="return toggle('PrositeMatch.mapping');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#mapping">mapping</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.mapping-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.mapping-expanded"><a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-docstring">"""return a list of numbers mapping to items of the original pattern</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"> For example, if the Prosite pattern is "[AP](2)-D." matched against</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> "PAD", then the mapping is [1, 1, 2], meaning the first character</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-docstring"> of the match ("P") is from the first Prosite group ("[AP]"), as</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-docstring"> is the second letter ("A"). The 3rd letter ("D") is mapped to</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-docstring"> group 2 of the pattern.</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">vals</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt id="link-200" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-200', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt id="link-201" 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-201', 'start', 'link-201');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-202" 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-202', 'start', 'link-201');">start</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</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="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt id="link-203" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-203', 'end', 'link-203');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-204', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-205', 'end', 'link-203');">end</a></tt><tt class="py-op">(</tt><tt id="link-206" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-206', 'i', 'link-11');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-207" 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-207', 'start', 'link-201');">start</a></tt> <tt class="py-op"><</tt> <tt id="link-208" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-208', 'end', 'link-203');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">vals</tt><tt class="py-op">.</tt><tt id="link-209" 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-209', 'append', 'link-209');">append</a></tt><tt class="py-op">(</tt><tt id="link-210" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-210', 'i', 'link-11');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt id="link-211" 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-211', 'start', 'link-201');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-212" 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-212', 'start', 'link-201');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt id="link-213" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-213', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-214" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-214', 'i', 'link-11');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">vals</tt> </tt>
</div><a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt>
<a name="PrositeMatch.mapped_pattern"></a><div id="PrositeMatch.mapped_pattern-def"><a name="L293"></a><tt class="py-lineno">293</tt> <a class="py-toggle" href="#" id="PrositeMatch.mapped_pattern-toggle" onclick="return toggle('PrositeMatch.mapped_pattern');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#mapped_pattern">mapped_pattern</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.mapped_pattern-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.mapped_pattern-expanded"><a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-docstring">"""returns the specific Prosite pattern used to find this sequence</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> >>> p = Prosite.compile("[AP](2,3)-D.")</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> >>> m = p.search(Seq.Seq("PAD"))</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> >>> mapping = m.mapping()</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> >>> mapped = m.mapped_pattern()</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> >>> print str(m[1]), str(p[mapping[1]]), str(mapped[1])</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> P [AP](2,3) [AP]</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> >>> print str(mapped)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> [AP]-[AP]-D.</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> >>> </tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> Note that the original term includes the count, while the</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"> mapped pattern does the expansion.</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-215" class="py-name" targets="Function Bio.Prosite.Pattern.pattern_mapping()=Bio.Prosite.Pattern-module.html#pattern_mapping"><a title="Bio.Prosite.Pattern.pattern_mapping" class="py-name" href="#" onclick="return doclink('link-215', 'pattern_mapping', 'link-215');">pattern_mapping</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><a title="Bio.dbdefs.prosite
Bio.dbdefs.prosite.prosite" class="py-name" href="#" onclick="return doclink('link-216', 'prosite', 'link-175');">prosite</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.mapping()=Bio.Prosite.Pattern.PrositeMatch-class.html#mapping"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-217', 'mapping', 'link-217');">mapping</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="PrositeMatch.start"></a><div id="PrositeMatch.start-def"><a name="L312"></a><tt class="py-lineno">312</tt> <a class="py-toggle" href="#" id="PrositeMatch.start-toggle" onclick="return toggle('PrositeMatch.start');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#start">start</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">g</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.start-expanded"><a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-218" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-218', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-219" 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-219', 'start', 'link-201');">start</a></tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.end"></a><div id="PrositeMatch.end-def"><a name="L314"></a><tt class="py-lineno">314</tt> <a class="py-toggle" href="#" id="PrositeMatch.end-toggle" onclick="return toggle('PrositeMatch.end');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#end">end</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">g</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.end-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.end-expanded"><a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-220', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-221', 'end', 'link-203');">end</a></tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.span"></a><div id="PrositeMatch.span-def"><a name="L316"></a><tt class="py-lineno">316</tt> <a class="py-toggle" href="#" id="PrositeMatch.span-toggle" onclick="return toggle('PrositeMatch.span');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#span">span</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">g</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.span-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.span-expanded"><a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-222', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-223" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.span()=Bio.Prosite.Pattern.PrositeMatch-class.html#span"><a title="Bio.Prosite.Pattern.PrositeMatch.span" class="py-name" href="#" onclick="return doclink('link-223', 'span', 'link-223');">span</a></tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.groups"></a><div id="PrositeMatch.groups-def"><a name="L318"></a><tt class="py-lineno">318</tt> <a class="py-toggle" href="#" id="PrositeMatch.groups-toggle" onclick="return toggle('PrositeMatch.groups');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#groups">groups</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">default</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.groups-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.groups-expanded"><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt id="link-224" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-224', 'alphabet', 'link-85');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-225', 'alphabet', 'link-85');">alphabet</a></tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">g</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-226', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-227" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-227', 'groups', 'link-227');">groups</a></tt><tt class="py-op">(</tt><tt id="link-228" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.default()=Bio.Parsers.spark.GenericASTTraversal-class.html#default"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-228', 'default', 'link-228');">default</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-229" 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-229', 'append', 'link-209');">append</a></tt><tt class="py-op">(</tt> <tt id="link-230" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-230', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-231', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">,</tt> <tt id="link-232" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-232', 'alphabet', 'link-85');">alphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">result</tt><tt class="py-op">)</tt> </tt>
</div><a name="PrositeMatch.group"></a><div id="PrositeMatch.group-def"><a name="L324"></a><tt class="py-lineno">324</tt> <a class="py-toggle" href="#" id="PrositeMatch.group-toggle" onclick="return toggle('PrositeMatch.group');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern.PrositeMatch-class.html#group">group</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">groups</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrositeMatch.group-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrositeMatch.group-expanded"><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-233', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-234" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-234', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt id="link-235" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-235', 'groups', 'link-227');">groups</a></tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">result</tt> <tt class="py-op">==</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</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">result</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-236" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-236', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-237', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">result</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-238" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-238', 'alphabet', 'link-85');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">retval</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-239" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-239', 'x', 'link-239');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">result</tt><tt class="py-op">:</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">retval</tt><tt class="py-op">.</tt><tt id="link-240" 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-240', 'append', 'link-209');">append</a></tt><tt class="py-op">(</tt><tt id="link-241" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-241', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-242', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-243" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-243', 'x', 'link-239');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-244', 'alphabet', 'link-85');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">retval</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> </tt>
<a name="pattern_mapping"></a><div id="pattern_mapping-def"><a name="L335"></a><tt class="py-lineno">335</tt> <a class="py-toggle" href="#" id="pattern_mapping-toggle" onclick="return toggle('pattern_mapping');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#pattern_mapping">pattern_mapping</a><tt class="py-op">(</tt><tt class="py-param">prosite</tt><tt class="py-op">,</tt> <tt class="py-param">mapping</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="pattern_mapping-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="pattern_mapping-expanded"><a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt id="link-245" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-245', 'data', 'link-88');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-246" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-246', 'i', 'link-11');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-247" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.mapping" class="py-name" href="#" onclick="return doclink('link-247', 'mapping', 'link-217');">mapping</a></tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt id="link-248" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-248', 'x', 'link-239');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-249" class="py-name"><a title="Bio.dbdefs.prosite
Bio.dbdefs.prosite.prosite" class="py-name" href="#" onclick="return doclink('link-249', 'prosite', 'link-175');">prosite</a></tt><tt class="py-op">[</tt><tt id="link-250" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-250', 'i', 'link-11');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-251" 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.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-251', 'copy', 'link-251');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt id="link-252" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-252', 'x', 'link-239');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">min_count</tt> <tt class="py-op">=</tt> <tt id="link-253" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-253', 'x', 'link-239');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">max_count</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt id="link-254" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-254', 'data', 'link-88');">data</a></tt><tt class="py-op">.</tt><tt id="link-255" 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-255', 'append', 'link-209');">append</a></tt><tt class="py-op">(</tt><tt id="link-256" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-256', 'x', 'link-239');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-257" class="py-name"><a title="Bio.Prosite
Bio.Prosite.Pattern.Prosite" class="py-name" href="#" onclick="return doclink('link-257', 'Prosite', 'link-82');">Prosite</a></tt><tt class="py-op">(</tt><tt id="link-258" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-258', 'data', 'link-88');">data</a></tt><tt class="py-op">=</tt><tt id="link-259" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-259', 'data', 'link-88');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt id="link-260" class="py-name" targets="Variable Bio.Prosite.Pattern.prosite_term_re=Bio.Prosite.Pattern-module.html#prosite_term_re"><a title="Bio.Prosite.Pattern.prosite_term_re" class="py-name" href="#" onclick="return doclink('link-260', 'prosite_term_re', 'link-260');">prosite_term_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-261', 'compile', 'link-109');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"""</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-string">(?:</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-string"> ([ABCDEFGHIKLMNPQRSTVWXYZx])| # a character OR</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-string"> \[(<?)([ABCDEFGHIKLMNPQRSTVWXYZ]+)(>?)\]| # something in []s OR</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-string"> \{([ABCDEFGHIKLMNPQRSTVWXYZ]+)\} # something in {}s</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-string">)(?:\((\d+)(,\d+)?\))? # optional count of the form "(i,j)", ",j" optional</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-string">$</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-string">"""</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">VERBOSE</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-comment"># This does not verify the pattern is correct - invalid patterns can</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># be converted!</tt> </tt>
<a name="find_terms"></a><div id="find_terms-def"><a name="L354"></a><tt class="py-lineno">354</tt> <a class="py-toggle" href="#" id="find_terms-toggle" onclick="return toggle('find_terms');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#find_terms">find_terms</a><tt class="py-op">(</tt><tt class="py-param">pattern</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="find_terms-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="find_terms-expanded"><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-262" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-262', 'pattern', 'link-4');">pattern</a></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 class="py-op">!=</tt> <tt class="py-string">"."</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"not a prosite pattern - needs a final '.'"</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt id="link-263" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-263', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt id="link-264" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-264', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">terms</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-265" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-265', 'split', 'link-265');">split</a></tt><tt class="py-op">(</tt><tt id="link-266" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-266', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-string">"-"</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt id="link-267" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-267', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt class="py-name">terms</tt><tt class="py-op">:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">can_begin</tt> <tt class="py-op">=</tt> <tt class="py-name">can_end</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-comment"># Starts with a "<"?</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">term</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 class="py-string">"<"</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</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="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">is_begin</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">is_begin</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-comment"># Ends with a ">"?</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">term</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 class="py-op">==</tt> <tt class="py-string">">"</tt><tt class="py-op">:</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">is_end</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">is_end</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt id="link-268" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-268', 'match', 'link-133');">match</a></tt> <tt class="py-op">=</tt> <tt id="link-269" class="py-name"><a title="Bio.Prosite.Pattern.prosite_term_re" class="py-name" href="#" onclick="return doclink('link-269', 'prosite_term_re', 'link-260');">prosite_term_re</a></tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-270', 'match', 'link-133');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-271" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-271', 'match', 'link-133');">match</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"not a Prosite term (%s)"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-272" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-272', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-273', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</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="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-comment"># Single letter</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ignore</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt id="link-274" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-274', 'letters', 'link-141');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-275" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-275', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-276" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-276', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-277" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-277', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-278', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</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="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-comment"># Letters inside of "[]"s</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ignore</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt id="link-279" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-279', 'letters', 'link-141');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-280" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-280', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-281', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-282" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-282', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-283" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-283', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">can_begin</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-284" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-284', 'i', 'link-11');">i</a></tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> \ </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-string">"[<] only allowed for first term (%s)"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-285" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-285', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-286', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-name">can_end</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-287" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-287', 'i', 'link-11');">i</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">terms</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> \ </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-string">"[>] only allowed for last term (%s)"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-288" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-288', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-289', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</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="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-comment"># Letters inside of "{}"s</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ignore</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt id="link-290" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-290', 'letters', 'link-141');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-291" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-291', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-292', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"not a prosite term (%s)"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-293" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-293', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-294', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">)</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="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-comment"># there is a minimum number</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</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">int</tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-295', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-296', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-comment"># no min, so it's 1</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</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-number">1</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-297" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-297', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-298', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">)</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="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-comment"># there is a maximum number</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">max_count</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-299" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-299', 'match', 'link-133');">match</a></tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-300', 'group', 'link-185');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">7</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 class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-comment"># no max specified, so use the same as the min</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">max_count</tt> <tt class="py-op">=</tt> <tt class="py-name">min_count</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-301" 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-301', 'append', 'link-209');">append</a></tt><tt class="py-op">(</tt><tt id="link-302" class="py-name"><a title="Bio.Prosite.Pattern.PrositeTerm" class="py-name" href="#" onclick="return doclink('link-302', 'PrositeTerm', 'link-143');">PrositeTerm</a></tt><tt class="py-op">(</tt><tt id="link-303" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-303', 'letters', 'link-141');">letters</a></tt><tt class="py-op">,</tt> <tt class="py-name">ignore</tt><tt class="py-op">,</tt> <tt class="py-name">is_begin</tt><tt class="py-op">,</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">is_end</tt><tt class="py-op">,</tt> <tt class="py-name">min_count</tt><tt class="py-op">,</tt> <tt class="py-name">max_count</tt><tt class="py-op">,</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-name">can_begin</tt><tt class="py-op">,</tt> <tt class="py-name">can_end</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt id="link-304" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-304', 'i', 'link-11');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-305" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-305', 'i', 'link-11');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div><a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"><tt id="link-306" class="py-name" targets="Variable Bio.Prosite.Pattern.prosite_re=Bio.Prosite.Pattern-module.html#prosite_re"><a title="Bio.Prosite.Pattern.prosite_re" class="py-name" href="#" onclick="return doclink('link-306', 'prosite_re', 'link-306');">prosite_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-307" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-307', 'compile', 'link-109');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"""</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"><tt class="py-string">^<? # starts with an optional "<"</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt class="py-string">(</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-string"> [ABCDEFGHIKLMNPQRSTVWXYZx]| # a character OR</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-string"> (\[<?[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\])| # something in []s OR</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-string"> \{[ABCDEFGHIKLMNPQRSTVWXYZ]+\} # something in {}s</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-string">)(\(\d+(,\d+)?\))? # optional count of the form "(i,j)" (",j" is optional)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-string">(- # new terms seperated by a '-'</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-string"> (</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-string"> [ABCDEFGHIKLMNPQRSTVWXYZx]| # a character OR</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-string"> \[[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\]| # something in []s OR</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-string"> \{[ABCDEFGHIKLMNPQRSTVWXYZ]+\} # something in {}s</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-string"> )(\(\d+(,\d+)?\))? # optional count</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-string">)* # repeat until done</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-string">>? # pattern ends with an optional ">"</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-string">\.$ # description ends with a required "."</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-string">"""</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">VERBOSE</tt><tt class="py-op">)</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-comment"># This verifies the pattern is correct.</tt> </tt>
<a name="verify_pattern"></a><div id="verify_pattern-def"><a name="L449"></a><tt class="py-lineno">449</tt> <a class="py-toggle" href="#" id="verify_pattern-toggle" onclick="return toggle('verify_pattern');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#verify_pattern">verify_pattern</a><tt class="py-op">(</tt><tt class="py-param">pattern</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="verify_pattern-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="verify_pattern-expanded"><a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-docstring">"""returns 1 if the Prosite pattern is syntactically correct, else 0"""</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt id="link-308" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-308', 'x', 'link-239');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-309" class="py-name"><a title="Bio.Prosite.Pattern.prosite_re" class="py-name" href="#" onclick="return doclink('link-309', 'prosite_re', 'link-306');">prosite_re</a></tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-310', 'match', 'link-133');">match</a></tt><tt class="py-op">(</tt><tt id="link-311" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-311', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-312" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-312', 'x', 'link-239');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-comment"># check there's only one [< at the beginning, or >] at the end</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-313" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-313', 'find', 'link-313');">find</a></tt><tt class="py-op">(</tt><tt id="link-314" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-314', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-string">"[<"</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-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-315', 'find', 'link-313');">find</a></tt><tt class="py-op">(</tt><tt id="link-316" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-316', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-string">">]"</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-317" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-317', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> </tt>
<a name="_verify_test"></a><div id="_verify_test-def"><a name="L461"></a><tt class="py-lineno">461</tt> <a class="py-toggle" href="#" id="_verify_test-toggle" onclick="return toggle('_verify_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Pattern-module.html#_verify_test">_verify_test</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_verify_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_verify_test-expanded"><a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-docstring">"""verify the patterns from a Prosite file handle"""</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt id="link-318" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-318', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</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="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-319" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-319', 'readline', 'link-319');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">"PA"</tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt id="link-320" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-320', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt id="link-321" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-321', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"."</tt><tt class="py-op">:</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"*"</tt> <tt class="py-op">*</tt> <tt class="py-number">60</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-322" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-322', 'pattern', 'link-4');">pattern</a></tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-323" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-323', 'compile', 'link-109');">compile</a></tt><tt class="py-op">(</tt><tt id="link-324" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-324', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-325" class="py-name"><a title="Bio.Prosite.Pattern.prosite_to_re" class="py-name" href="#" onclick="return doclink('link-325', 'prosite_to_re', 'link-110');">prosite_to_re</a></tt><tt class="py-op">(</tt><tt id="link-326" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-326', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">re</tt><tt class="py-op">)</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-327" class="py-name"><a title="Bio.Prosite.Pattern.prosite_to_grouped_re" class="py-name" href="#" onclick="return doclink('link-327', 'prosite_to_grouped_re', 'link-114');">prosite_to_grouped_re</a></tt><tt class="py-op">(</tt><tt id="link-328" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-328', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grouped_re</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-name">terms</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">terms</tt> <tt class="py-op">!=</tt> <tt id="link-329" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-329', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">:</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"DIFFER"</tt><tt class="py-op">,</tt> <tt class="py-name">terms</tt><tt class="py-op">,</tt> <tt id="link-330" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-330', 'pattern', 'link-4');">pattern</a></tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"PROBLEM"</tt><tt class="py-op">,</tt> <tt id="link-331" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-331', 'pattern', 'link-4');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt id="link-332" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-332', 'pattern', 'link-4');">pattern</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
</div><a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"><tt class="py-comment"># Commented out by jchang 4/13/00.</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Specific to Andrew's test environment.</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#if __name__ == "__main__":</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># import os</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># infile = os.popen("bzcat /home/dalke/ftps/prosite/prosite.dat.bz2 | grep ^PA")</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _verify_test(infile)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt><script type="text/javascript">
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