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<a href="Bio-module.html">Package Bio</a> ::
Module PubMed
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<h1 class="epydoc">Source Code for <a href="Bio.PubMed-module.html">Module Bio.PubMed</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 1999-2000 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to work with PubMed from the NCBI.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/PubMed/</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">Online documentation for linking to PubMed is available at:</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/PubMed/linking.html</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">Dictionary Access PubMed articles using a dictionary interface.</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 class="py-docstring">Functions:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">search_for Search PubMed.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">find_related Find related articles in PubMed.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">download_many Download many articles from PubMed in batch mode.</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">"""</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </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">re</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sgmllib</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 class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.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="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Package Bio.Entrez=Bio.Entrez-module.html"><a title="Bio.Entrez" class="py-name" href="#" onclick="return doclink('link-3', 'Entrez', 'link-3');">Entrez</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Package Bio.Medline=Bio.Medline-module.html"><a title="Bio.Medline" class="py-name" href="#" onclick="return doclink('link-5', 'Medline', 'link-5');">Medline</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="Dictionary"></a><div id="Dictionary-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="Dictionary-toggle" onclick="return toggle('Dictionary');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html">Dictionary</a><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Dictionary-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-docstring">"""Access PubMed using a read-only dictionary interface.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Dictionary.__init__"></a><div id="Dictionary.__init__-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="Dictionary.__init__-toggle" onclick="return toggle('Dictionary.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-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">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="Dictionary.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__init__-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-docstring">"""Dictionary(parser=None)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> Create a new Dictionary to access PubMed. parser is an optional</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> parser (e.g. Medline.RecordParser) object to change the results</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> into another form. If set to None, then the raw contents of the</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> file will be returned.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</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="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="Dictionary.__len__"></a><div id="Dictionary.__len__-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="Dictionary.__len__-toggle" onclick="return toggle('Dictionary.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__len__-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"PubMed contains lots of entries"</tt> </tt>
</div><a name="Dictionary.clear"></a><div id="Dictionary.clear-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="Dictionary.clear-toggle" onclick="return toggle('Dictionary.clear');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#clear">clear</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="Dictionary.clear-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.clear-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"This is a read-only dictionary"</tt> </tt>
</div><a name="Dictionary.__setitem__"></a><div id="Dictionary.__setitem__-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="Dictionary.__setitem__-toggle" onclick="return toggle('Dictionary.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">item</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__setitem__-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"This is a read-only dictionary"</tt> </tt>
</div><a name="Dictionary.update"></a><div id="Dictionary.update-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="Dictionary.update-toggle" onclick="return toggle('Dictionary.update');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#update">update</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="Dictionary.update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.update-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"This is a read-only dictionary"</tt> </tt>
</div><a name="Dictionary.copy"></a><div id="Dictionary.copy-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="Dictionary.copy-toggle" onclick="return toggle('Dictionary.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#copy">copy</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.copy-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't need to do this..."</tt> </tt>
</div><a name="Dictionary.keys"></a><div id="Dictionary.keys-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="Dictionary.keys-toggle" onclick="return toggle('Dictionary.keys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#keys">keys</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="Dictionary.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.keys-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't really want to do this..."</tt> </tt>
</div><a name="Dictionary.items"></a><div id="Dictionary.items-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="Dictionary.items-toggle" onclick="return toggle('Dictionary.items');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#items">items</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="Dictionary.items-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.items-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't really want to do this..."</tt> </tt>
</div><a name="Dictionary.values"></a><div id="Dictionary.values-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="Dictionary.values-toggle" onclick="return toggle('Dictionary.values');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#values">values</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="Dictionary.values-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.values-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't really want to do this..."</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="Dictionary.has_key"></a><div id="Dictionary.has_key-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="Dictionary.has_key-toggle" onclick="return toggle('Dictionary.has_key');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#has_key">has_key</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.has_key-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.has_key-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-docstring">"""S.has_key(id) -> bool"""</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-6" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-6', 'id', 'link-6');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="Dictionary.get"></a><div id="Dictionary.get-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="Dictionary.get-toggle" onclick="return toggle('Dictionary.get');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#get">get</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">failobj</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="Dictionary.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.get-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-7" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-7', 'id', 'link-6');">id</a></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">except</tt> <tt class="py-name">KeyError</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">return</tt> <tt class="py-name">failobj</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">"How did I get here?"</tt> </tt>
</div><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="Dictionary.__getitem__"></a><div id="Dictionary.__getitem__-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="Dictionary.__getitem__-toggle" onclick="return toggle('Dictionary.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed.Dictionary-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__getitem__-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">"""S.__getitem__(id) -> object</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> Return the Medline entry. id is either the Medline Unique ID</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> or the Pubmed ID of the article. Raises a KeyError if there's an</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> error.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt id="link-8" 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-8', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.Entrez" class="py-name" href="#" onclick="return doclink('link-9', 'Entrez', 'link-3');">Entrez</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch()=Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html#efetch,Method Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch()=Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html#efetch,Method Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch()=Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html#efetch,Method Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch()=Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html#efetch,Function Bio.Entrez.efetch()=Bio.Entrez-module.html#efetch,Function Bio.WWW.NCBI.efetch()=Bio.WWW.NCBI-module.html#efetch"><a title="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch
Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch
Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch
Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch
Bio.Entrez.efetch
Bio.WWW.NCBI.efetch" class="py-name" href="#" onclick="return doclink('link-10', 'efetch', 'link-10');">efetch</a></tt><tt class="py-op">(</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-11" class="py-name" targets="Variable Bio.LocusLink.locus_format.db=Bio.LocusLink.locus_format-module.html#db,Variable Bio.config.DBRegistry.db=Bio.config.DBRegistry-module.html#db"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-11', 'db', 'link-11');">db</a></tt><tt class="py-op">=</tt><tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-12', 'id', 'link-6');">id</a></tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-13', 'id', 'link-6');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">retmode</tt><tt class="py-op">=</tt><tt class="py-string">'text'</tt><tt class="py-op">,</tt> <tt class="py-name">rettype</tt><tt class="py-op">=</tt><tt class="py-string">'medlars'</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-14', 'x', 'link-14');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-comment"># raise a KeyError instead of an IOError</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># XXX I really should distinguish between a real IOError and</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># if the id is not in the database.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-15', 'x', 'link-14');">x</a></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</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="L97"></a><tt class="py-lineno"> 97</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-16" 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-16', 'parse', 'link-16');">parse</a></tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-17', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-18" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-18', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-19', 'read', 'link-19');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="search_for"></a><div id="search_for-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="search_for-toggle" onclick="return toggle('search_for');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed-module.html#search_for">search_for</a><tt class="py-op">(</tt><tt class="py-param">search</tt><tt class="py-op">,</tt> <tt class="py-param">reldate</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">mindate</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">maxdate</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-param">batchsize</tt><tt class="py-op">=</tt><tt class="py-number">100</tt><tt class="py-op">,</tt> <tt class="py-param">callback_fn</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">start_id</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">max_ids</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="search_for-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="search_for-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-docstring">"""search_for(search[, reldate][, mindate][, maxdate]</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> [, batchsize][, callback_fn][, start_id][, max_ids]) -> ids</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> Search PubMed and return a list of the PMID's that match the</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> criteria. search is the search string used to search the</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> database. reldate is the number of dates prior to the current</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> date to restrict the search. mindate and maxdate are the dates to</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> restrict the search, e.g. 2002/01/01. batchsize specifies the</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> number of ids to return at one time. By default, it is set to</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> 10000, the maximum. callback_fn is an optional callback function</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> that will be called as passed a PMID as results are retrieved.</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> start_id specifies the index of the first id to retrieve and</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> max_ids specifies the maximum number of id's to retrieve.</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"> XXX The date parameters don't seem to be working with NCBI's</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> script. Please let me know if you can get it to work.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">class</tt> <tt class="py-def-name">ResultParser</tt><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>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment"># Parse the ID's out of the XML-formatted page that PubMed</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># returns. The format of the page is:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># [...]</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <Id>...</Id></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># [...]</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <tt class="py-def-name">__init__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</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-20" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method 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Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-20', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-21', 'ids', 'link-21');">ids</a></tt> <tt class="py-op">=</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">in_id</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">start_id</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attributes</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_id</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">end_id</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_id</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">_not_pmid_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-22', 'compile', 'link-22');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r'\D'</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">handle_data</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_id</tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment"># If data is just whitespace, then ignore it.</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-23" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-23', 'data', 'link-23');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-24', 'data', 'link-23');">data</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-25', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-26" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-26', 'data', 'link-23');">data</a></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">return</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment"># Everything here should be a PMID. Check and make sure</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># data really is one. A PMID should be a string consisting</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># of only integers. Should I check to make sure it</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># meets a certain minimum length?</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_not_pmid_re</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-27', 'search', 'link-27');">search</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-28', 'data', 'link-23');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> \ </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-string">"I expected an ID, but %s doesn't look like one."</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-29', 'data', 'link-23');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-30', 'ids', 'link-21');">ids</a></tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-32', 'data', 'link-23');">data</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">params</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-string">'db'</tt> <tt class="py-op">:</tt> <tt class="py-string">'pubmed'</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-string">'term'</tt> <tt class="py-op">:</tt> <tt id="link-33" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-33', 'search', 'link-27');">search</a></tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-string">'reldate'</tt> <tt class="py-op">:</tt> <tt class="py-name">reldate</tt><tt class="py-op">,</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-string">'mindate'</tt> <tt class="py-op">:</tt> <tt class="py-name">mindate</tt><tt class="py-op">,</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-string">'maxdate'</tt> <tt class="py-op">:</tt> <tt class="py-name">maxdate</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-34', 'v', 'link-34');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">params</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-35', 'items', 'link-35');">items</a></tt><tt class="py-op">(</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-keyword">if</tt> <tt id="link-36" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-36', 'v', 'link-34');">v</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</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">del</tt> <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-37', 'ids', 'link-21');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">max_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-38', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">max_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">ResultParser</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>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-39" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-39', 'start', 'link-39');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">start_id</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-40', 'ids', 'link-21');">ids</a></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">max</tt> <tt class="py-op">=</tt> <tt class="py-name">batchsize</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">max_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">max</tt> <tt class="py-op">></tt> <tt class="py-name">max_ids</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-41', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-name">max_ids</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-42', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'retstart'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-43', 'start', 'link-39');">start</a></tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'retmax'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">h</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.Entrez" class="py-name" href="#" onclick="return doclink('link-44', 'Entrez', 'link-3');">Entrez</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.esearch()=Bio.EUtils.ThinClient.ThinClient-class.html#esearch,Function Bio.Entrez.esearch()=Bio.Entrez-module.html#esearch,Function Bio.WWW.NCBI.esearch()=Bio.WWW.NCBI-module.html#esearch"><a title="Bio.EUtils.ThinClient.ThinClient.esearch
Bio.Entrez.esearch
Bio.WWW.NCBI.esearch" class="py-name" href="#" onclick="return doclink('link-45', 'esearch', 'link-45');">esearch</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-46', 'feed', 'link-46');">feed</a></tt><tt class="py-op">(</tt><tt class="py-name">h</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-47', 'read', 'link-19');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-48', 'ids', 'link-21');">ids</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-49', 'extend', 'link-49');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-50', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">callback_fn</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="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-comment"># Call the callback function with each of the new ID's.</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-51" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-51', 'id', 'link-6');">id</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-52', 'ids', 'link-21');">ids</a></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">callback_fn</tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-53', 'id', 'link-6');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-54', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">max</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-55', 'ids', 'link-21');">ids</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># no more id's to read</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-56" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-56', 'ids', 'link-21');">ids</a></tt> </tt>
</div><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> </tt>
<a name="find_related"></a><div id="find_related-def"><a name="L185"></a><tt class="py-lineno">185</tt> <a class="py-toggle" href="#" id="find_related-toggle" onclick="return toggle('find_related');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed-module.html#find_related">find_related</a><tt class="py-op">(</tt><tt class="py-param">pmid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="find_related-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="find_related-expanded"><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-docstring">"""find_related(pmid) -> ids</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> Search PubMed for a list of citations related to pmid. pmid can</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> be a PubMed ID, a MEDLINE UID, or a list of those.</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">class</tt> <tt class="py-def-name">ResultParser</tt><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>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-comment"># Parse the ID's out of the HTML-formatted page that PubMed</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># returns. The format of the page is:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># [...]</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <Link></tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <Id>######</Id></tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <Score>######</Score></tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># [...]</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </Link></tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># [...]</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <tt class="py-def-name">__init__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">sgmllib</tt><tt class="py-op">.</tt><tt class="py-name">SGMLParser</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-57', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-58', 'ids', 'link-21');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_link</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_id</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">start_id</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attributes</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_id</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">end_id</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</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 class="py-name">in_id</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">start_link</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attributes</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_link</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">end_link</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_link</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">_not_pmid_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-59', 'compile', 'link-22');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r'\D'</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">handle_data</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_link</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">in_id</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-comment"># Everything here should be a PMID. Check and make sure</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># data really is one. A PMID should be a string consisting</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># of only integers. Should I check to make sure it</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># meets a certain minimum length?</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_not_pmid_re</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-60', 'search', 'link-27');">search</a></tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-61', 'data', 'link-23');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> \ </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-string">"I expected an ID, but '%s' doesn't look like one."</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-62', 'data', 'link-23');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-63', 'ids', 'link-21');">ids</a></tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-65', 'data', 'link-23');">data</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">ResultParser</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-66" 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-66', 'type', 'link-66');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">pmid</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt id="link-67" 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-67', 'type', 'link-66');">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>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">pmid</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">pmid</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">h</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Bio.Entrez" class="py-name" href="#" onclick="return doclink('link-68', 'Entrez', 'link-3');">Entrez</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup.elink()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#elink,Method Bio.EUtils.HistoryClient.HistoryLookup.elink()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#elink,Function Bio.Entrez.elink()=Bio.Entrez-module.html#elink,Function Bio.WWW.NCBI.elink()=Bio.WWW.NCBI-module.html#elink"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.elink
Bio.EUtils.HistoryClient.HistoryLookup.elink
Bio.Entrez.elink
Bio.WWW.NCBI.elink" class="py-name" href="#" onclick="return doclink('link-69', 'elink', 'link-69');">elink</a></tt><tt class="py-op">(</tt><tt class="py-name">dbfrom</tt><tt class="py-op">=</tt><tt class="py-string">'pubmed'</tt><tt class="py-op">,</tt> <tt id="link-70" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-70', 'id', 'link-6');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">pmid</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-71', 'feed', 'link-46');">feed</a></tt><tt class="py-op">(</tt><tt class="py-name">h</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-72', 'read', 'link-19');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-73', 'ids', 'link-21');">ids</a></tt> </tt>
</div><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> </tt>
<a name="download_many"></a><div id="download_many-def"><a name="L236"></a><tt class="py-lineno">236</tt> <a class="py-toggle" href="#" id="download_many-toggle" onclick="return toggle('download_many');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PubMed-module.html#download_many">download_many</a><tt class="py-op">(</tt><tt class="py-param">ids</tt><tt class="py-op">,</tt> <tt class="py-param">callback_fn</tt><tt class="py-op">,</tt> <tt class="py-param">broken_fn</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-param">batchsize</tt><tt class="py-op">=</tt><tt class="py-number">500</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="download_many-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="download_many-expanded"><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-docstring">"""download_many(ids, callback_fn[, broken_fn][, batchsize])</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> Download many records from PubMed. ids is a list of either the</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> Medline Unique ID or the PubMed ID's of the articles. Each time a</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> record is downloaded, callback_fn is called with the text of the</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> record. broken_fn is an optional function that is called with the</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> id of records that were not able to be downloaded. batchsize is the</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> number of records to request each time.</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-comment"># parser is an undocumented parameter that allows people to</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># specify an optional parser to handle each record. This is</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># dangerous because the results may be malformed, and exceptions</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the parser may disrupt the whole download process.</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">batchsize</tt> <tt class="py-op">></tt> <tt class="py-number">500</tt> <tt class="py-keyword">or</tt> <tt class="py-name">batchsize</tt> <tt class="py-op"><</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</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">"batchsize must be between 1 and 500"</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">current_batchsize</tt> <tt class="py-op">=</tt> <tt class="py-name">batchsize</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-comment"># Loop until all the ids are processed. We want to process as</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># many as possible with each request. Unfortunately, errors can</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># occur. Some id may be incorrect, or the server may be</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># unresponsive. In addition, one broken id out of a list of id's</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># can cause a non-specific error. Thus, the strategy I'm going to</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># take, is to start by downloading as many as I can. If the</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># request fails, I'm going to half the number of records I try to</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># get. If there's only one more record, then I'll report it as</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># broken and move on. If the request succeeds, I'll double the</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># number of records until I get back up to the batchsize.</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">nsuccesses</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-74" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-74', 'ids', 'link-21');">ids</a></tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op">></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-75', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">current_batchsize</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-76', 'ids', 'link-21');">ids</a></tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">id_str</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 id="link-77" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-77', 'ids', 'link-21');">ids</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">current_batchsize</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-comment"># Query PubMed. If one or more of the id's are broken,</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># this will raise an IOError.</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-78" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-78', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name"><a title="Bio.Entrez" class="py-name" href="#" onclick="return doclink('link-79', 'Entrez', 'link-3');">Entrez</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch
Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch
Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch
Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch
Bio.Entrez.efetch
Bio.WWW.NCBI.efetch" class="py-name" href="#" onclick="return doclink('link-80', 'efetch', 'link-10');">efetch</a></tt><tt class="py-op">(</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-81', 'db', 'link-11');">db</a></tt><tt class="py-op">=</tt><tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> <tt id="link-82" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-82', 'id', 'link-6');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">id_str</tt><tt class="py-op">,</tt> <tt class="py-name">retmode</tt><tt class="py-op">=</tt><tt class="py-string">'text'</tt><tt class="py-op">,</tt> <tt class="py-name">rettype</tt><tt class="py-op">=</tt><tt class="py-string">'medlars'</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-comment"># I'm going to check to make sure PubMed returned the same</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># number of id's as I requested. If it didn't then I'm going</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># to raise an exception. This could take a lot of memory if</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the batchsize is large.</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-83', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-84', 'read', 'link-19');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">num_ids</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-85" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-85', 'x', 'link-14');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-86" class="py-name"><a title="Bio.Medline" class="py-name" href="#" onclick="return doclink('link-86', 'Medline', 'link-5');">Medline</a></tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Class Bio.Blast.NCBIStandalone.Iterator=Bio.Blast.NCBIStandalone.Iterator-class.html,Class Bio.CDD.Iterator=Bio.CDD.Iterator-class.html,Class Bio.Compass.Iterator=Bio.Compass.Iterator-class.html,Class Bio.ECell.Iterator=Bio.ECell.Iterator-class.html,Class Bio.Enzyme.Iterator=Bio.Enzyme.Iterator-class.html,Class Bio.Fasta.Iterator=Bio.Fasta.Iterator-class.html,Class Bio.GenBank.Iterator=Bio.GenBank.Iterator-class.html,Class Bio.Gobase.Iterator=Bio.Gobase.Iterator-class.html,Class Bio.IntelliGenetics.Iterator=Bio.IntelliGenetics.Iterator-class.html,Class Bio.LocusLink.Iterator=Bio.LocusLink.Iterator-class.html,Class Bio.Medline.Iterator=Bio.Medline.Iterator-class.html,Class Bio.MetaTool.Iterator=Bio.MetaTool.Iterator-class.html,Class Bio.NBRF.Iterator=Bio.NBRF.Iterator-class.html,Class Bio.Prosite.Iterator=Bio.Prosite.Iterator-class.html,Class Bio.Prosite.Prodoc.Iterator=Bio.Prosite.Prodoc.Iterator-class.html,Class Bio.Rebase.Iterator=Bio.Rebase.Iterator-class.html,Class Bio.SCOP.Cla.Iterator=Bio.SCOP.Cla.Iterator-class.html,Class Bio.SCOP.Des.Iterator=Bio.SCOP.Des.Iterator-class.html,Class Bio.SCOP.Dom.Iterator=Bio.SCOP.Dom.Iterator-class.html,Class Bio.SCOP.Hie.Iterator=Bio.SCOP.Hie.Iterator-class.html,Class Bio.SCOP.Raf.Iterator=Bio.SCOP.Raf.Iterator-class.html,Class Bio.Saf.Iterator=Bio.Saf.Iterator-class.html,Class Bio.Sequencing.Ace.Iterator=Bio.Sequencing.Ace.Iterator-class.html,Class Bio.Sequencing.Phd.Iterator=Bio.Sequencing.Phd.Iterator-class.html,Class Bio.SwissProt.SProt.Iterator=Bio.SwissProt.SProt.Iterator-class.html,Class Bio.UniGene.Iterator=Bio.UniGene.Iterator-class.html,Module Martel.Iterator=Martel.Iterator-module.html,Class Martel.Iterator.Iterator=Martel.Iterator.Iterator-class.html"><a title="Bio.Blast.NCBIStandalone.Iterator
Bio.CDD.Iterator
Bio.Compass.Iterator
Bio.ECell.Iterator
Bio.Enzyme.Iterator
Bio.Fasta.Iterator
Bio.GenBank.Iterator
Bio.Gobase.Iterator
Bio.IntelliGenetics.Iterator
Bio.LocusLink.Iterator
Bio.Medline.Iterator
Bio.MetaTool.Iterator
Bio.NBRF.Iterator
Bio.Prosite.Iterator
Bio.Prosite.Prodoc.Iterator
Bio.Rebase.Iterator
Bio.SCOP.Cla.Iterator
Bio.SCOP.Des.Iterator
Bio.SCOP.Dom.Iterator
Bio.SCOP.Hie.Iterator
Bio.SCOP.Raf.Iterator
Bio.Saf.Iterator
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Phd.Iterator
Bio.SwissProt.SProt.Iterator
Bio.UniGene.Iterator
Martel.Iterator
Martel.Iterator.Iterator" class="py-name" href="#" onclick="return doclink('link-87', 'Iterator', 'link-87');">Iterator</a></tt><tt class="py-op">(</tt><tt id="link-88" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-88', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt class="py-name">results</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">num_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">num_ids</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">num_ids</tt> <tt class="py-op">!=</tt> <tt class="py-name">current_batchsize</tt><tt class="py-op">:</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt id="link-89" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-89', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-90', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt class="py-name">results</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> <tt class="py-comment"># Query did not work.</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-comment"># There was only 1 id in the query. Report it as</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># broken and move on.</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-91" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-91', 'id', 'link-6');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-92', 'ids', 'link-21');">ids</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-93', 'pop', 'link-93');">pop</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">broken_fn</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="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">broken_fn</tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-94', 'id', 'link-6');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-comment"># I don't know which one is broken. Try again with</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># fewer id's.</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op">=</tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">nsuccesses</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">nsuccesses</tt> <tt class="py-op">=</tt> <tt class="py-name">nsuccesses</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-comment"># Iterate through the results and pass the records to the</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># callback.</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">idnum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt id="link-95" class="py-name"><a title="Bio.Medline" class="py-name" href="#" onclick="return doclink('link-95', 'Medline', 'link-5');">Medline</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.Blast.NCBIStandalone.Iterator
Bio.CDD.Iterator
Bio.Compass.Iterator
Bio.ECell.Iterator
Bio.Enzyme.Iterator
Bio.Fasta.Iterator
Bio.GenBank.Iterator
Bio.Gobase.Iterator
Bio.IntelliGenetics.Iterator
Bio.LocusLink.Iterator
Bio.Medline.Iterator
Bio.MetaTool.Iterator
Bio.NBRF.Iterator
Bio.Prosite.Iterator
Bio.Prosite.Prodoc.Iterator
Bio.Rebase.Iterator
Bio.SCOP.Cla.Iterator
Bio.SCOP.Des.Iterator
Bio.SCOP.Dom.Iterator
Bio.SCOP.Hie.Iterator
Bio.SCOP.Raf.Iterator
Bio.Saf.Iterator
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Phd.Iterator
Bio.SwissProt.SProt.Iterator
Bio.UniGene.Iterator
Martel.Iterator
Martel.Iterator.Iterator" class="py-name" href="#" onclick="return doclink('link-96', 'Iterator', 'link-87');">Iterator</a></tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-97', 'handle', 'link-8');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">parser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">callback_fn</tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-98', 'ids', 'link-21');">ids</a></tt><tt class="py-op">[</tt><tt class="py-name">idnum</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">idnum</tt> <tt class="py-op">=</tt> <tt class="py-name">idnum</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt id="link-99" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-99', 'ids', 'link-21');">ids</a></tt> <tt class="py-op">=</tt> <tt id="link-100" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-100', 'ids', 'link-21');">ids</a></tt><tt class="py-op">[</tt><tt class="py-name">current_batchsize</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-comment"># If I'm not downloading the maximum number of articles,</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># double the number for next time.</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">nsuccesses</tt> <tt class="py-op">>=</tt> <tt class="py-number">2</tt> <tt class="py-keyword">and</tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op"><</tt> <tt class="py-name">batchsize</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">current_batchsize</tt> <tt class="py-op">=</tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_batchsize</tt> <tt class="py-op">></tt> <tt class="py-name">batchsize</tt><tt class="py-op">:</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">current_batchsize</tt> <tt class="py-op">=</tt> <tt class="py-name">batchsize</tt> </tt>
</div><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt><script type="text/javascript">
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