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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SCOP-module.html">Package SCOP</a> ::
Module Hie
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<h1 class="epydoc">Source Code for <a href="Bio.SCOP.Hie-module.html">Module Bio.SCOP.Hie</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 2001 by Gavin E. Crooks. 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>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">""" Handle the SCOP HIErarchy files, which describe the SCOP hierarchy in</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">terms of SCOP unique identifiers (sunid).</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">The file format is described in the scop</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">"release notes.":http://scop.berkeley.edu/release-notes-1.55.html </tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">The latest HIE file can be found</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">"Release 1.55":http://scop.berkeley.edu/parse/dir.hie.scop.txt_1.55 (July 2001)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Record-class.html">Record</a><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information for one node in the SCOP hierarchy.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> sunid -- SCOP unique identifiers of this node</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> parent -- Parents sunid</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> children -- Sequence of childrens sunids</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Record-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">line</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="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.children()=Bio.Pathway.Rep.Graph.Graph-class.html#children,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.children()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#children"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-0', 'children', 'link-0');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</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 id="link-1" class="py-name" targets="Method Bio.SCOP.Cla.Record._process()=Bio.SCOP.Cla.Record-class.html#_process,Method Bio.SCOP.Des.Record._process()=Bio.SCOP.Des.Record-class.html#_process,Method Bio.SCOP.Dom.Record._process()=Bio.SCOP.Dom.Record-class.html#_process,Method Bio.SCOP.Hie.Record._process()=Bio.SCOP.Hie.Record-class.html#_process,Method Bio.SCOP.Raf.SeqMap._process()=Bio.SCOP.Raf.SeqMap-class.html#_process"><a title="Bio.SCOP.Cla.Record._process
Bio.SCOP.Des.Record._process
Bio.SCOP.Dom.Record._process
Bio.SCOP.Hie.Record._process
Bio.SCOP.Raf.SeqMap._process" class="py-name" href="#" onclick="return doclink('link-1', '_process', 'link-1');">_process</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="Record._process"></a><div id="Record._process-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="Record._process-toggle" onclick="return toggle('Record._process');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Record-class.html#_process">_process</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record._process-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._process-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses HIE records.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> Records consist of 3 tab deliminated fields; node's sunid,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> parent's sunid, and a list of children's sunids.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-comment">#For example ::</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">#</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#0 - 46456,48724,51349,53931,56572,56835,56992,57942</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#21953 49268 -</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">#49267 49266 49268,49269</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># no trailing whitespace</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">columns</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-2" 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-2', 'split', 'link-2');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'\t'</tt><tt class="py-op">)</tt> <tt class="py-comment"># separate the tab-delineated cols</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</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">columns</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">3</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I don't understand the format of %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<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-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-3', 'children', 'link-0');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-name">columns</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sunid</tt> <tt class="py-op">==</tt><tt class="py-string">'-'</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">else</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">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parent</tt><tt class="py-op">==</tt><tt class="py-string">'-'</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">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</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">else</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">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-4" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-4', 'children', 'link-0');">children</a></tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-5', 'children', 'link-0');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-6', 'children', 'link-0');">children</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-7', 'children', 'link-0');">children</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-8', 'split', 'link-2');">split</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-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-9', 'children', 'link-0');">children</a></tt> <tt class="py-op">=</tt> <tt id="link-10" 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-10', 'map', 'link-10');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-11', 'children', 'link-0');">children</a></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="Record.__str__"></a><div id="Record.__str__-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="Record.__str__-toggle" onclick="return toggle('Record.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Record-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="Record.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__str__-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt id="link-12" 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-12', 's', 'link-12');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <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-12');">s</a></tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'append', 'link-14');">append</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 class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <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-12');">s</a></tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'append', 'link-14');">append</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 class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">else</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <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-12');">s</a></tt><tt class="py-op">.</tt><tt id="link-18" 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-18', 'append', 'link-14');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'0'</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <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-12');">s</a></tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'append', 'link-14');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-21', 'children', 'link-0');">children</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">child_str</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-22', 'map', 'link-10');">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-23" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-23', 'children', 'link-0');">children</a></tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-24', 's', 'link-12');">s</a></tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'append', 'link-14');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">child_str</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-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-26', 's', 'link-12');">s</a></tt><tt class="py-op">.</tt><tt id="link-27" 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-27', 'append', 'link-14');">append</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-keyword">return</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-28', 's', 'link-12');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
</div></div><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>
<a name="parse"></a><div id="parse-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie-module.html#parse">parse</a><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="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterates over a HIE file, returning a Hie record for each line</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> in the file.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> handle -- file-like object.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-29" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-29', 'handle', 'link-29');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-30" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-30', 'Record', 'link-30');">Record</a></tt><tt class="py-op">(</tt><tt class="py-name">line</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="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="Iterator-toggle" onclick="return toggle('Iterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Iterator-class.html">Iterator</a><tt class="py-op">:</tt> </tt>
</div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterates over a HIE file.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="Iterator.__init__-toggle" onclick="return toggle('Iterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Iterator-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">handle</tt><tt class="py-op">,</tt> <tt class="py-param">parser</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="Iterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__init__-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-docstring">"""Create an object that iterates over a HIE file.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> handle -- file-like object.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> parser -- an optional Parser object to change the results into</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> another form. If set to None, then the raw contents</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> of the file will be returned.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.SCOP.Hie.Iterator is deprecated. Please use Bio.SCOP.Hie.parse() instead."</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-name">FileType</tt><tt class="py-op">,</tt> <tt class="py-name">InstanceType</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</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"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-31', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-32', 'handle', 'link-29');">handle</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">FileType</tt> <tt class="py-keyword">and</tt> <tt id="link-33" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-33', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-34', 'handle', 'link-29');">handle</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">InstanceType</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">"I expected a file handle or file-like object"</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">_handle</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-35', 'handle', 'link-29');">handle</a></tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="Iterator.next-toggle" onclick="return toggle('Iterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Iterator-class.html#next">next</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="Iterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.next-expanded"><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve the next HIE record."""</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</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="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'readline', 'link-36');">readline</a></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-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</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-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-keyword">break</tt> <tt class="py-comment"># Not a comment line</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</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">_parser</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="L132"></a><tt class="py-lineno">132</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">_parser</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-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,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.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,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.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,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.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.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-37', 'parse', 'link-37');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="Iterator.__iter__-toggle" onclick="return toggle('Iterator.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Iterator-class.html#__iter__">__iter__</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="Iterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__iter__-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-38', 'next', 'link-38');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="Parser"></a><div id="Parser-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="Parser-toggle" onclick="return toggle('Parser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Parser-class.html">Parser</a><tt class="py-op">:</tt> </tt>
</div><div id="Parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Parser-expanded"><a name="Parser.__init__"></a><div id="Parser.__init__-def"><a name="L140"></a><tt class="py-lineno">140</tt> <a class="py-toggle" href="#" id="Parser.__init__-toggle" onclick="return toggle('Parser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Parser-class.html#__init__">__init__</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="Parser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.__init__-expanded"><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"""Bio.SCOP.Hie.Parser is deprecated.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-string"> Instead of</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-string"> parser = Hie.Parser()</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-string"> record = parser.parse(entry)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-string"> please use</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-string"> record = Hie.Record(entry)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-string"> """</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
</div><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="Parser.parse"></a><div id="Parser.parse-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="Parser.parse-toggle" onclick="return toggle('Parser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Hie.Parser-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">entry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.parse-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a Hie Record """</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-39" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-39', 'Record', 'link-30');">Record</a></tt><tt class="py-op">(</tt><tt class="py-name">entry</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> </tt><script type="text/javascript">
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