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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.UniGene-module.html">Package UniGene</a> ::
Module UniGene
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<h1 class="epydoc">Source Code for <a href="Bio.UniGene.UniGene-module.html">Module Bio.UniGene.UniGene</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Permission to use, copy, modify, and distribute this software and</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># its documentation with or without modifications and for any purpose</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># and without fee is hereby granted, provided that any copyright</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># notices appear in all copies and that both those copyright notices</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># and this permission notice appear in supporting documentation, and</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># that the names of the contributors or copyright holders not be used</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># in advertising or publicity pertaining to distribution of the software</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># without specific prior permission.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"># THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"># WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"># WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"># CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"># OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"># LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"># NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"># WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">operator</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sgmllib</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">UserDict</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-keyword">import</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-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser"></a><div id="UniGeneParser-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="UniGeneParser-toggle" onclick="return toggle('UniGeneParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html">UniGeneParser</a><tt class="py-op">(</tt> <tt class="py-base-class">sgmllib</tt><tt class="py-op">.</tt><tt class="py-base-class">SGMLParser</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UniGeneParser-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.reset"></a><div id="UniGeneParser.reset-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="UniGeneParser.reset-toggle" onclick="return toggle('UniGeneParser.reset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#reset">reset</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="UniGeneParser.reset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.reset-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">sgmllib</tt><tt class="py-op">.</tt><tt class="py-name">SGMLParser</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Blast.NCBIXML.BlastParser.reset()=Bio.Blast.NCBIXML.BlastParser-class.html#reset,Method Bio.UniGene.UniGene.UniGeneParser.reset()=Bio.UniGene.UniGene.UniGeneParser-class.html#reset"><a title="Bio.Blast.NCBIXML.BlastParser.reset
Bio.UniGene.UniGene.UniGeneParser.reset" class="py-name" href="#" onclick="return doclink('link-2', 'reset', 'link-2');">reset</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt> <tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt> <tt class="py-op">=</tt> <tt class="py-name">UserDict</tt><tt class="py-op">.</tt><tt class="py-name">UserDict</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_html'</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">=</tt> <tt class="py-string">'general_info'</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.parse"></a><div id="UniGeneParser.parse-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="UniGeneParser.parse-toggle" onclick="return toggle('UniGeneParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#parse">parse</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.parse-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Blast.NCBIXML.BlastParser.reset
Bio.UniGene.UniGene.UniGeneParser.reset" class="py-name" href="#" onclick="return doclink('link-3', 'reset', 'link-2');">reset</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ExPASy.ScanProsite.Parser.feed()=Bio.ExPASy.ScanProsite.Parser-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.UniGene.UniGene.UniGeneParser.feed()=Bio.UniGene.UniGene.UniGeneParser-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ExPASy.ScanProsite.Parser.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.UniGene.UniGene.UniGeneParser.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-4', 'feed', 'link-4');">feed</a></tt><tt class="py-op">(</tt> <tt id="link-5" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-5', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">key</tt> <tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">key</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-number">15</tt> <tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'UniGene Cluster'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-string">'UniGene Cluster'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">key</tt><tt class="py-op">[</tt> <tt class="py-number">16</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">key</tt> <tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</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">queue</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-comment"># Assumes an empty line between records</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="UniGeneParser.feed"></a><div id="UniGeneParser.feed-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="UniGeneParser.feed-toggle" onclick="return toggle('UniGeneParser.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#feed">feed</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.feed-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-6', 'handle', 'link-5');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-8', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-9', 'UndoHandle', 'link-9');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-10', 'handle', 'link-5');">handle</a></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-11', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-12', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-13', 'UndoHandle', 'link-9');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-5');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</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="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-15', 'readline', 'link-15');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-16', 'strip', 'link-16');">strip</a></tt><tt class="py-op">(</tt> <tt class="py-name">line</tt> <tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">sgmllib</tt><tt class="py-op">.</tt><tt class="py-name">SGMLParser</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ExPASy.ScanProsite.Parser.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.UniGene.UniGene.UniGeneParser.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-17', 'feed', 'link-4');">feed</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">text</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.handle_data"></a><div id="UniGeneParser.handle_data-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="UniGeneParser.handle_data-toggle" onclick="return toggle('UniGeneParser.handle_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#handle_data">handle_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">newtext</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.handle_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.handle_data-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">newtext</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-18', 'strip', 'link-16');">strip</a></tt><tt class="py-op">(</tt> <tt class="py-name">newtext</tt> <tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">+</tt> <tt class="py-name">newtext</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.start_a"></a><div id="UniGeneParser.start_a-def"><a name="L75"></a><tt class="py-lineno"> 75</tt> <a class="py-toggle" href="#" id="UniGeneParser.start_a-toggle" onclick="return toggle('UniGeneParser.start_a');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#start_a">start_a</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.start_a-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.start_a-expanded"><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'seq_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">!=</tt> <tt class="py-string">'open_b'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><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"># self.queue.append( attrs )</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.end_a"></a><div id="UniGeneParser.end_a-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="UniGeneParser.end_a-toggle" onclick="return toggle('UniGeneParser.end_a');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#end_a">end_a</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="UniGeneParser.end_a-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.end_a-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'seq_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">!=</tt> <tt class="py-string">'open_b'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.start_b"></a><div id="UniGeneParser.start_b-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="UniGeneParser.start_b-toggle" onclick="return toggle('UniGeneParser.start_b');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#start_b">start_b</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.start_b-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.start_b-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-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"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-19', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_b'</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.end_b"></a><div id="UniGeneParser.end_b-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="UniGeneParser.end_b-toggle" onclick="return toggle('UniGeneParser.end_b');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#end_b">end_b</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="UniGeneParser.end_b-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.end_b-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-number">15</tt> <tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'UniGene Cluster'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-string">'UniGene Cluster'</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">text</tt><tt class="py-op">[</tt> <tt class="py-number">16</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.UniGene.UniGene.UniGeneParser.extract_key()=Bio.UniGene.UniGene.UniGeneParser-class.html#extract_key"><a title="Bio.UniGene.UniGene.UniGeneParser.extract_key" class="py-name" href="#" onclick="return doclink('link-20', 'extract_key', 'link-20');">extract_key</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.extract_key"></a><div id="UniGeneParser.extract_key-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="UniGeneParser.extract_key-toggle" onclick="return toggle('UniGeneParser.extract_key');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#extract_key">extract_key</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="UniGeneParser.extract_key-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.extract_key-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-21', 'strip', 'link-16');">strip</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">key</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-22', 'split', 'link-22');">split</a></tt><tt class="py-op">(</tt> <tt class="py-name">text</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-23', 'split', 'link-22');">split</a></tt><tt class="py-op">(</tt> <tt class="py-name">key</tt> <tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">key</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt class="py-name">words</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>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop,Method Bio.SeqIO._index._IndexedSeqFileDict.pop()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#pop"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-24', 'pop', 'link-24');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_html'</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">==</tt> <tt class="py-string">'open_table_data'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'general_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">=</tt> <tt class="py-name">key</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'seq_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">text</tt> <tt class="py-op">==</tt> <tt class="py-string">'Key to Symbols'</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">=</tt> <tt class="py-string">'legend'</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</tt> <tt class="py-op">=</tt> <tt class="py-name">key</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'general_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</tt> <tt class="py-op">=</tt> <tt class="py-name">key</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="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.Seq.Seq.find()=Bio.Seq.Seq-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.Seq.Seq.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-25', 'find', 'link-25');">find</a></tt><tt class="py-op">(</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-string">'SEQUENCE'</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>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">=</tt> <tt class="py-string">'seq_info'</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">key</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">UserDict</tt><tt class="py-op">.</tt><tt class="py-name">UserDict</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'seq_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">key</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">UserDict</tt><tt class="py-op">.</tt><tt class="py-name">UserDict</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</tt> <tt class="py-op">=</tt> <tt class="py-name">key</tt> </tt>
</div><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.start_table"></a><div id="UniGeneParser.start_table-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="UniGeneParser.start_table-toggle" onclick="return toggle('UniGeneParser.start_table');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#start_table">start_table</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.start_table-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.start_table-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-26', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_table'</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.end_table"></a><div id="UniGeneParser.end_table-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="UniGeneParser.end_table-toggle" onclick="return toggle('UniGeneParser.end_table');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#end_table">end_table</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="UniGeneParser.end_table-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.end_table-expanded"><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-27', 'pop', 'link-24');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_html'</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.start_tr"></a><div id="UniGeneParser.start_tr-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="UniGeneParser.start_tr-toggle" onclick="return toggle('UniGeneParser.start_tr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#start_tr">start_tr</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.start_tr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.start_tr-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-28', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_table_row'</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.end_tr"></a><div id="UniGeneParser.end_tr-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="UniGeneParser.end_tr-toggle" onclick="return toggle('UniGeneParser.end_tr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#end_tr">end_tr</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="UniGeneParser.end_tr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.end_tr-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-29', 'pop', 'link-24');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">except</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">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_html'</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">text</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 class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">text</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-string">':'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">text</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="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-30', 'split', 'link-22');">split</a></tt><tt class="py-op">(</tt> <tt class="py-name">text</tt> <tt class="py-op">)</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">if</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">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'general_info'</tt> <tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'seq_info'</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">contents</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</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">key_waiting</tt> <tt class="py-op">]</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-31" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type,Method Bio.Phylo.PhyloXMLIO.Writer.type()=Bio.Phylo.PhyloXMLIO.Writer-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-31', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">contents</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-32" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-32', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">contents</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-33', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">text</tt> <tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</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">key_waiting</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-op">[</tt> <tt class="py-name">contents</tt> <tt class="py-op">,</tt> <tt class="py-name">text</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">except</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">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">master_key</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">key_waiting</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_waiting</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.start_td"></a><div id="UniGeneParser.start_td-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="UniGeneParser.start_td-toggle" onclick="return toggle('UniGeneParser.start_td');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#start_td">start_td</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.start_td-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.start_td-expanded"><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-34', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_table_data'</tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.end_td"></a><div id="UniGeneParser.end_td-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="UniGeneParser.end_td-toggle" onclick="return toggle('UniGeneParser.end_td');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#end_td">end_td</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="UniGeneParser.end_td-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.end_td-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag_stack</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-35', 'pop', 'link-24');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">open_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">'open_html'</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">context</tt> <tt class="py-op">==</tt> <tt class="py-string">'seq_info'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> </tt>
</div><a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.print_item"></a><div id="UniGeneParser.print_item-def"><a name="L190"></a><tt class="py-lineno">190</tt> <a class="py-toggle" href="#" id="UniGeneParser.print_item-toggle" onclick="return toggle('UniGeneParser.print_item');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#print_item">print_item</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">item</tt><tt class="py-op">,</tt> <tt class="py-param">level</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UniGeneParser.print_item-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.print_item-expanded"><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">indent</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt id="link-36" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-36', 'range', 'link-36');">range</a></tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">indent</tt> <tt class="py-op">=</tt> <tt class="py-name">indent</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-37" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-37', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">item</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-38" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-38', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">item</tt> <tt class="py-op">!=</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'%s%s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt class="py-name">item</tt> <tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-39" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-39', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">item</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-40" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-40', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subitem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">item</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.UniGene.UniGene.UniGeneParser.print_item()=Bio.UniGene.UniGene.UniGeneParser-class.html#print_item"><a title="Bio.UniGene.UniGene.UniGeneParser.print_item" class="py-name" href="#" onclick="return doclink('link-41', 'print_item', 'link-41');">print_item</a></tt><tt class="py-op">(</tt> <tt class="py-name">subitem</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt> <tt class="py-name">item</tt><tt class="py-op">,</tt> <tt class="py-name">UserDict</tt><tt class="py-op">.</tt><tt class="py-name">UserDict</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subitem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">item</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'%skey is %s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt class="py-name">subitem</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 id="link-42" class="py-name"><a title="Bio.UniGene.UniGene.UniGeneParser.print_item" class="py-name" href="#" onclick="return doclink('link-42', 'print_item', 'link-41');">print_item</a></tt><tt class="py-op">(</tt> <tt class="py-name">item</tt><tt class="py-op">[</tt> <tt class="py-name">subitem</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">item</tt> </tt>
</div><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="UniGeneParser.print_tags"></a><div id="UniGeneParser.print_tags-def"><a name="L207"></a><tt class="py-lineno">207</tt> <a class="py-toggle" href="#" id="UniGeneParser.print_tags-toggle" onclick="return toggle('UniGeneParser.print_tags');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UniGene.UniGeneParser-class.html#print_tags">print_tags</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="UniGeneParser.print_tags-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UniGeneParser.print_tags-expanded"><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'key %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">key</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.UniGene.UniGene.UniGeneParser.print_item" class="py-name" href="#" onclick="return doclink('link-43', 'print_item', 'link-41');">print_item</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queue</tt><tt class="py-op">[</tt> <tt class="py-name">key</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-44', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt> <tt class="py-string">'Hs13225.htm'</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt id="link-45" class="py-name" targets="Variable Bio.UniGene.UniGene.undo_handle=Bio.UniGene.UniGene-module.html#undo_handle"><a title="Bio.UniGene.UniGene.undo_handle" class="py-name" href="#" onclick="return doclink('link-45', 'undo_handle', 'link-45');">undo_handle</a></tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-46', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-47', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-48', 'UndoHandle', 'link-9');">UndoHandle</a></tt><tt class="py-op">(</tt> <tt id="link-49" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-49', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt id="link-50" class="py-name" targets="Variable Bio.UniGene.UniGene.unigene_parser=Bio.UniGene.UniGene-module.html#unigene_parser"><a title="Bio.UniGene.UniGene.unigene_parser" class="py-name" href="#" onclick="return doclink('link-50', 'unigene_parser', 'link-50');">unigene_parser</a></tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name" targets="Class Bio.UniGene.UniGene.UniGeneParser=Bio.UniGene.UniGene.UniGeneParser-class.html"><a title="Bio.UniGene.UniGene.UniGeneParser" class="py-name" href="#" onclick="return doclink('link-51', 'UniGeneParser', 'link-51');">UniGeneParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Bio.UniGene.UniGene.unigene_parser" class="py-name" href="#" onclick="return doclink('link-52', 'unigene_parser', 'link-50');">unigene_parser</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-53', 'parse', 'link-53');">parse</a></tt><tt class="py-op">(</tt> <tt id="link-54" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-54', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt id="link-55" class="py-name"><a title="Bio.UniGene.UniGene.unigene_parser" class="py-name" href="#" onclick="return doclink('link-55', 'unigene_parser', 'link-50');">unigene_parser</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.UniGene.UniGene.UniGeneParser.print_tags()=Bio.UniGene.UniGene.UniGeneParser-class.html#print_tags"><a title="Bio.UniGene.UniGene.UniGeneParser.print_tags" class="py-name" href="#" onclick="return doclink('link-56', 'print_tags', 'link-56');">print_tags</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt><script type="text/javascript">
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