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<a href="Bio-module.html">Package Bio</a> ::
Module ExPASy
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<h1 class="epydoc">Source Code for <a href="Bio.ExPASy-module.html">Module Bio.ExPASy</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000 by 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 access resources at ExPASy over the WWW.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">http://www.expasy.ch/</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"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">get_prodoc_entry Interface to the get-prodoc-entry CGI script.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">get_prosite_entry Interface to the get-prosite-entry CGI script.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">get_prosite_raw Interface to the get-prosite-raw CGI script.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">get_sprot_raw Interface to the get-sprot-raw CGI script.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">sprot_search_ful Interface to the sprot-search-ful CGI script.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">sprot_search_de Interface to the sprot-search-de CGI script.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">scanprosite1 Interface to the scanprosite CGI script.</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>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="get_prodoc_entry"></a><div id="get_prodoc_entry-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="get_prodoc_entry-toggle" onclick="return toggle('get_prodoc_entry');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#get_prodoc_entry">get_prodoc_entry</a><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.expasy.ch/cgi-bin/get-prodoc-entry'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_prodoc_entry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_prodoc_entry-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-docstring">"""get_prodoc_entry(id,</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry') -> handle</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> Get a handle to a PRODOC entry at ExPASy in HTML format. </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"> For a non-existing key XXX, ExPASy returns an HTML-formatted page</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> containing this line:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> 'There is no PROSITE documentation entry XXX. Please try again.'</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-comment"># Open a handle to ExPASy.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-0" 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-0', 'handle', 'link-0');">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-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 id="link-1" 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-1', 'id', 'link-1');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-2" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-2', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="get_prosite_entry"></a><div id="get_prosite_entry-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="get_prosite_entry-toggle" onclick="return toggle('get_prosite_entry');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#get_prosite_entry">get_prosite_entry</a><tt class="py-op">(</tt><tt class="py-param">id</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.expasy.ch/cgi-bin/get-prosite-entry'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_prosite_entry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_prosite_entry-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-docstring">"""get_prosite_entry(id,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -> handle</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> Get a handle to a PROSITE entry at ExPASy in HTML format.</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"> For a non-existing key XXX, ExPASy returns an HTML-formatted page</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> containing this line:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> 'There is currently no PROSITE entry for XXX. Please try again.'</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt id="link-3" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-3', 'handle', 'link-0');">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-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 id="link-4" 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-4', 'id', 'link-1');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-5" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-5', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="get_prosite_raw"></a><div id="get_prosite_raw-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="get_prosite_raw-toggle" onclick="return toggle('get_prosite_raw');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#get_prosite_raw">get_prosite_raw</a><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.expasy.ch/cgi-bin/get-prosite-raw.pl'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_prosite_raw-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_prosite_raw-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""get_prosite_raw(id,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl')</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> -> handle</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> Get a handle to a raw PROSITE or PRODOC entry at ExPASy.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> For a non-existing key, ExPASy returns nothing.</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-6', 'handle', 'link-0');">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-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 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-1');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-8', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
<a name="get_sprot_raw"></a><div id="get_sprot_raw-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="get_sprot_raw-toggle" onclick="return toggle('get_sprot_raw');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#get_sprot_raw">get_sprot_raw</a><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.expasy.ch/cgi-bin/get-sprot-raw.pl'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_sprot_raw-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_sprot_raw-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-docstring">"""get_sprot_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-sprot-raw.pl')</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> -> handle</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> Get a handle to a raw SwissProt entry at ExPASy.</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-docstring"> For a non-existing key XXX, ExPASy returns an HTML-formatted page</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> containing this line:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> 'XXX is not a valid identifier.'</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-9', 'handle', 'link-0');">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-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 id="link-10" 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-10', 'id', 'link-1');">id</a></tt><tt class="py-op">)</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 id="link-11" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-11', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="sprot_search_ful"></a><div id="sprot_search_ful-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="sprot_search_ful-toggle" onclick="return toggle('sprot_search_ful');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#sprot_search_ful">sprot_search_ful</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">make_wild</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">swissprot</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">trembl</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.expasy.ch/cgi-bin/sprot-search-ful'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="sprot_search_ful-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="sprot_search_ful-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-docstring">"""sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None,</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -> handle</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> Search SwissProt by full text.</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"> """</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</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">'SEARCH'</tt> <tt class="py-op">:</tt> <tt id="link-12" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-12', 'text', 'link-12');">text</a></tt><tt class="py-op">}</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">make_wild</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'makeWild'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'on'</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-13" class="py-name" targets="Module Bio.dbdefs.swissprot=Bio.dbdefs.swissprot-module.html,Variable Bio.dbdefs.swissprot.swissprot=Bio.dbdefs.swissprot-module.html#swissprot,Package Bio.expressions.swissprot=Bio.expressions.swissprot-module.html,Module Bio.formatdefs.swissprot=Bio.formatdefs.swissprot-module.html,Variable Bio.formatdefs.swissprot.swissprot=Bio.formatdefs.swissprot-module.html#swissprot"><a title="Bio.dbdefs.swissprot
Bio.dbdefs.swissprot.swissprot
Bio.expressions.swissprot
Bio.formatdefs.swissprot
Bio.formatdefs.swissprot.swissprot" class="py-name" href="#" onclick="return doclink('link-13', 'swissprot', 'link-13');">swissprot</a></tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'S'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'on'</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">trembl</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'T'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'on'</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <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">variables</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</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="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-0');">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="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="sprot_search_de"></a><div id="sprot_search_de-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="sprot_search_de-toggle" onclick="return toggle('sprot_search_de');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#sprot_search_de">sprot_search_de</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">swissprot</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">trembl</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.expasy.ch/cgi-bin/sprot-search-de'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="sprot_search_de-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="sprot_search_de-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""sprot_search_de(text, swissprot=1, trembl=None,</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -> handle</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> Search SwissProt by name, description, gene name, species, or</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> organelle.</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"> """</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</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">'SEARCH'</tt> <tt class="py-op">:</tt> <tt id="link-16" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-16', 'text', 'link-12');">text</a></tt><tt class="py-op">}</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-17" class="py-name"><a title="Bio.dbdefs.swissprot
Bio.dbdefs.swissprot.swissprot
Bio.expressions.swissprot
Bio.formatdefs.swissprot
Bio.formatdefs.swissprot.swissprot" class="py-name" href="#" onclick="return doclink('link-17', 'swissprot', 'link-13');">swissprot</a></tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'S'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'on'</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">trembl</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'T'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'on'</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <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">variables</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</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="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <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-0');">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="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-19" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-19', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> </tt>
<a name="scanprosite1"></a><div id="scanprosite1-def"><a name="L116"></a><tt class="py-lineno">116</tt> <a class="py-toggle" href="#" id="scanprosite1-toggle" onclick="return toggle('scanprosite1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ExPASy-module.html#scanprosite1">scanprosite1</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">exclude_frequent</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://www.expasy.org/cgi-bin/scanprosite/scanprosite?1'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="scanprosite1-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="scanprosite1-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-docstring">"""scanprosite1(seq=None, id=None, exclude_frequent=None, </tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://www.expasy.org/cgi-bin/scanprosite/scanprosite?1') -> handle</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> Scan a sequence for a Prosite pattern. Either a sequence or a SwissProt/</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> trEMBL sequence can be passed. exclude_frequent specifies whether to</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> exclude patterns with high probability.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> </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-name">variables</tt> <tt class="py-op">=</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-keyword">if</tt> <tt id="link-20" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-20', 'seq', 'link-20');">seq</a></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">variables</tt><tt class="py-op">[</tt><tt class="py-string">'SEQ'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-21', 'seq', 'link-20');">seq</a></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-22" 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-22', 'id', 'link-1');">id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'ID'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-23" 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-23', 'id', 'link-1');">id</a></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">exclude_frequent</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-string">'box'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'ok'</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <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">variables</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-24', 'handle', 'link-0');">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="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-25" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-25', 'handle', 'link-0');">handle</a></tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt><script type="text/javascript">
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