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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.WWW-module.html">Package WWW</a> ::
Module NCBI
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<h1 class="epydoc">Source Code for <a href="Bio.WWW.NCBI-module.html">Module Bio.WWW.NCBI</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">"""Provides code to access NCBI over the WWW.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">The main Entrez web page is available at:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/Entrez/</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">A list of the Entrez utilities is available at:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html</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">Documentation for the e-utilies are available at:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html</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">The main Blast web page is available at:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/BLAST/</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">query Query Entrez; retrieve results in HTML format.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">pmfetch Retrieve results using a unique identifier.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">pmqty Search PubMed.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">pmneighbor Return a list of related articles for a PubMed entry.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">efetch Access the efetch script.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">_open</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.WWW.NCBI is deprecated. The functions in Bio.WWW.NCBI are now available from Bio.Entrez; except for the pm* functions which the NCBI have retired."</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</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="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="query"></a><div id="query-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="query-toggle" onclick="return toggle('query');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#query">query</a><tt class="py-op">(</tt><tt class="py-param">cmd</tt><tt class="py-op">,</tt> <tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/sites/entrez'</tt><tt class="py-op">,</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="query-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="query-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-docstring">"""query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/sites/entrez',</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> **keywds) -> handle</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-docstring"> Query Entrez and return a handle to the results, consisting of</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> a web page in HTML format.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> See the online documentation for an explanation of the parameters:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'cmd'</tt> <tt class="py-op">:</tt> <tt class="py-name">cmd</tt><tt class="py-op">,</tt> <tt class="py-string">'db'</tt> <tt class="py-op">:</tt> <tt id="link-2" 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-2', 'db', 'link-2');">db</a></tt><tt class="py-op">}</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-3', 'update', 'link-3');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-4" class="py-name" targets="Function Bio.Entrez._open()=Bio.Entrez-module.html#_open,Function Bio.Mindy.BerkeleyDB._open()=Bio.Mindy.BerkeleyDB-module.html#_open,Function Bio.SCOP._open()=Bio.SCOP-module.html#_open,Function Bio.WWW.ExPASy._open()=Bio.WWW.ExPASy-module.html#_open,Function Bio.WWW.NCBI._open()=Bio.WWW.NCBI-module.html#_open"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-4', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="pmfetch"></a><div id="pmfetch-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="pmfetch-toggle" onclick="return toggle('pmfetch');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#pmfetch">pmfetch</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">report</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">mode</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">"http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="pmfetch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="pmfetch-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-docstring">"""pmfetch(db, id, report=None, mode=None,</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi")</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> Query PmFetch and return a handle to the results. See the</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> online documentation for an explanation of the parameters:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch_help.html</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># NCBI has retired PmFetch!!!</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'db'</tt> <tt class="py-op">:</tt> <tt id="link-5" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-5', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> <tt class="py-string">'id'</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="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">report</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="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'report'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">report</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">mode</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="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'mode'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">mode</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-7" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-7', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="pmqty"></a><div id="pmqty-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="pmqty-toggle" onclick="return toggle('pmqty');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#pmqty">pmqty</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">term</tt><tt class="py-op">,</tt> <tt class="py-param">dopt</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi'</tt><tt class="py-op">,</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="pmqty-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="pmqty-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">"""pmqty(db, term, dopt=None,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi') -> handle</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> Query PmQty and return a handle to the results. See the</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> online documentation for an explanation of the parameters:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty_help.html</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-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-comment"># NCBI has retired PmQty!!!</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'db'</tt> <tt class="py-op">:</tt> <tt id="link-8" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-8', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> <tt class="py-string">'term'</tt> <tt class="py-op">:</tt> <tt class="py-name">term</tt><tt class="py-op">}</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dopt</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="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'dopt'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">dopt</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-9', 'update', 'link-3');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-10', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="pmneighbor"></a><div id="pmneighbor-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="pmneighbor-toggle" onclick="return toggle('pmneighbor');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#pmneighbor">pmneighbor</a><tt class="py-op">(</tt><tt class="py-param">pmid</tt><tt class="py-op">,</tt> <tt class="py-param">display</tt><tt class="py-op">,</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="pmneighbor-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="pmneighbor-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-docstring">"""pmneighbor(pmid, display,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi') -> handle</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> Query PMNeighbor and return a handle to the results. See the</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> online documentation for an explanation of the parameters:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor_help.html</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-comment"># NCBI has retired PmNeighbor!!!</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Warning: HUGE HACK HERE! pmneighbor expects the display</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># parameter to be passed as just a tag, with no value.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Unfortunately, _open doesn't support these types of parameters,</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># so I'm building my own cgi string. This is really due to the</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># limitations of urllib.urlencode. We'll have to figure out a</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># good workaround.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fullcgi</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s?pmid=%s&%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">pmid</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name" targets="Method Bio.Nexus.Trees.Tree.display()=Bio.Nexus.Trees.Tree-class.html#display"><a title="Bio.Nexus.Trees.Tree.display" class="py-name" href="#" onclick="return doclink('link-11', 'display', 'link-11');">display</a></tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-12" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-12', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">fullcgi</tt><tt class="py-op">)</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"># XXX retmode?</tt> </tt>
<a name="epost"></a><div id="epost-def"><a name="L122"></a><tt class="py-lineno">122</tt> <a class="py-toggle" href="#" id="epost-toggle" onclick="return toggle('epost');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#epost">epost</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'</tt><tt class="py-op">,</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="epost-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="epost-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-docstring">"""epost(db, id[, cgi]) -> handle</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> Query Entrez and return a handle to the results. See the online</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> documentation for an explanation of the parameters:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'db'</tt> <tt class="py-op">:</tt> <tt id="link-13" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-13', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> <tt class="py-string">'id'</tt> <tt class="py-op">:</tt> <tt id="link-14" 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-14', 'id', 'link-6');">id</a></tt><tt class="py-op">}</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-15', 'update', 'link-3');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</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">return</tt> <tt id="link-16" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-16', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="efetch"></a><div id="efetch-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="efetch-toggle" onclick="return toggle('efetch');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#efetch">efetch</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'</tt><tt class="py-op">,</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="efetch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="efetch-expanded"><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-docstring">"""efetch(db[, cgi][...]) -> handle</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> Query Entrez and return a handle to the results. See the online</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> documentation for an explanation of the parameters:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'db'</tt> <tt class="py-op">:</tt> <tt id="link-17" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-17', 'db', 'link-2');">db</a></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">variables</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-18', 'update', 'link-3');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-19" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-19', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="esearch"></a><div id="esearch-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="esearch-toggle" onclick="return toggle('esearch');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#esearch">esearch</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">term</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="esearch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="esearch-expanded"><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-docstring">"""esearch(db, term[, cgi][...]) -> handle</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> Query Entrez and return a handle to the results. See the online</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> documentation for an explanation of the parameters:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'db'</tt> <tt class="py-op">:</tt> <tt id="link-20" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-20', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-string">'term'</tt> <tt class="py-op">:</tt> <tt class="py-name">term</tt><tt class="py-op">}</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-21', 'update', 'link-3');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-22" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-22', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="elink"></a><div id="elink-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="elink-toggle" onclick="return toggle('elink');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#elink">elink</a><tt class="py-op">(</tt><tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'</tt><tt class="py-op">,</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="elink-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="elink-expanded"><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-docstring">"""elink([, cgi][...]) -> handle</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> Query Entrez and return a handle to the results. See the online</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> documentation for an explanation of the parameters:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError exception if there's a network error.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-23', 'update', 'link-3');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-24" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-24', '_open', 'link-4');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="_open"></a><div id="_open-def"><a name="L184"></a><tt class="py-lineno">184</tt> <a class="py-toggle" href="#" id="_open-toggle" onclick="return toggle('_open');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.WWW.NCBI-module.html#_open">_open</a><tt class="py-op">(</tt><tt class="py-param">cgi</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">get</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_open-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_open-expanded"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-docstring">"""_open(cgi, params={}, get=1) -> UndoHandle</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> Open a handle to Entrez. cgi is the URL for the cgi script to access.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> params is a dictionary with the options to pass to it. get is a boolean</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> that describes whether a GET should be used. Does some</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> simple error checking, and will raise an IOError if it encounters one.</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-docstring"> """</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-comment"># Open a handle to Entrez.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">options</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlencode</tt><tt class="py-op">(</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-25" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-25', 'get', 'link-25');">get</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># do a GET</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">fullcgi</tt> <tt class="py-op">=</tt> <tt class="py-name">cgi</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">fullcgi</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s?%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-comment"># print fullcgi</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-26" 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-26', 'handle', 'link-26');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">fullcgi</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># do a POST</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-27', 'handle', 'link-26');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-comment"># Wrap the handle inside an UndoHandle.</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-28', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-29', 'UndoHandle', 'link-29');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-30', 'handle', 'link-26');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment"># Check for errors in the first 5 lines.</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># This is kind of ugly.</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lines</tt> <tt class="py-op">=</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-keyword">for</tt> <tt id="link-31" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-31', 'i', 'link-31');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'append', 'link-32');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-33', 'readline', 'link-33');">readline</a></tt><tt class="py-op">(</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-keyword">for</tt> <tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-31');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.File.UndoHandle.saveline()=Bio.File.UndoHandle-class.html#saveline"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-35', 'saveline', 'link-35');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">[</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-36', 'i', 'link-31');">i</a></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 id="link-37" 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-37', 'data', 'link-37');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-38', 'find', 'link-38');">find</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-39', 'data', 'link-37');">data</a></tt><tt class="py-op">,</tt> <tt class="py-string">"500 Proxy Error"</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-comment"># Sometimes Entrez returns a Proxy Error instead of results</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"500 Proxy Error (NCBI busy?)"</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-40', 'find', 'link-38');">find</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-41', 'data', 'link-37');">data</a></tt><tt class="py-op">,</tt> <tt class="py-string">"502 Proxy Error"</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"502 Proxy Error (NCBI busy?)"</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-42', 'find', 'link-38');">find</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-43', 'data', 'link-37');">data</a></tt><tt class="py-op">,</tt> <tt class="py-string">"WWW Error 500 Diagnostic"</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"WWW Error 500 Diagnostic (NCBI busy?)"</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-44" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-44', 'data', 'link-37');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"ERROR"</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-comment"># XXX Possible bug here, because I don't know whether this really</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># occurs on the first line. I need to check this!</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"ERROR, possibly because id not available?"</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-comment"># Should I check for 404? timeout? etc?</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">uhandle</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt><script type="text/javascript">
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