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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.WWW-module.html">Package&nbsp;WWW</a> ::
        Module&nbsp;ExPASy
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<h1 class="epydoc">Source Code for <a href="Bio.WWW.ExPASy-module.html">Module Bio.WWW.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">_open</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>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</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.ExPASy is deprecated. The functions in Bio.WWW.ExPASy  are now available from Bio.ExPASy."</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">              <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"> </tt>
<a name="get_prodoc_entry"></a><div id="get_prodoc_entry-def"><a name="L27"></a><tt class="py-lineno"> 27</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.WWW.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="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-docstring">"""get_prodoc_entry(id,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry') -&gt; handle</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 class="py-docstring">    Get a handle to a PRODOC entry at ExPASy in HTML format. </tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">    For a non-existing key XXX, ExPASy returns a web page containing</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">    this line:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring">    'There is no PROSITE documentation entry XXX. Please try again.'</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-comment"># XXX need to check to see if the entry exists!</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">return</tt> <tt id="link-0" 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-0', '_open', 'link-0');">_open</a></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>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"> </tt>
<a name="get_prosite_entry"></a><div id="get_prosite_entry-def"><a name="L40"></a><tt class="py-lineno"> 40</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.WWW.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="L41"></a><tt class="py-lineno"> 41</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="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-docstring">"""get_prosite_entry(id,</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">    cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -&gt; handle</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">    Get a handle to a PROSITE entry at ExPASy in HTML format.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    For a non-existing key XXX, ExPASy returns a web page containing</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">    this line:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">    'There is currently no PROSITE entry for XXX. Please try again.'</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-comment"># XXX need to check to see if the entry exists!</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">return</tt> <tt id="link-2" 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-2', '_open', 'link-0');">_open</a></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-3" 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-3', 'id', 'link-1');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"> </tt>
<a name="get_prosite_raw"></a><div id="get_prosite_raw-def"><a name="L54"></a><tt class="py-lineno"> 54</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.WWW.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="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-docstring">"""get_prosite_raw(id,</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-docstring">                       cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl')</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">    -&gt; handle</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">    Get a handle to a raw PROSITE or PRODOC entry at ExPASy.</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 class="py-docstring">    For a non-existing key, ExPASy returns nothing.</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-keyword">import</tt> <tt class="py-name">urllib</tt><tt class="py-op">,</tt> <tt class="py-name">socket</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt id="link-4" 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-4', 'handle', 'link-4');">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-5" 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-5', 'id', 'link-1');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-comment"># Peek at the first character to see if anything is available.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># ExPASy returns nothing for non-existing keys</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt id="link-6" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-6', 'start', 'link-6');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-7', 'handle', 'link-4');">handle</a></tt><tt class="py-op">.</tt><tt class="py-name">fp</tt><tt class="py-op">.</tt><tt class="py-name">_sock</tt><tt class="py-op">.</tt><tt class="py-name">recv</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">socket</tt><tt class="py-op">.</tt><tt class="py-name">MSG_PEEK</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-8" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-8', 'start', 'link-6');">start</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># ExPASy returned nothing</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</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">"no results"</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <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-4');">handle</a></tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"> </tt>
<a name="get_sprot_raw"></a><div id="get_sprot_raw-def"><a name="L75"></a><tt class="py-lineno"> 75</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.WWW.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="L76"></a><tt class="py-lineno"> 76</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="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">    -&gt; handle</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">    Get a handle to a raw SwissProt entry at ExPASy.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">    For a non-existing key XXX, ExPASy returns a web page containing</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">    this line:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">    'XXX is not a valid identifier.'</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-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-0');">_open</a></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-11" 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-11', 'id', 'link-1');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"> </tt>
<a name="sprot_search_ful"></a><div id="sprot_search_ful-def"><a name="L87"></a><tt class="py-lineno"> 87</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.WWW.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="L88"></a><tt class="py-lineno"> 88</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="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">    <tt class="py-docstring">"""sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None,</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-docstring">    cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -&gt; handle</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">    Search SwissProt by full text.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">    """</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 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="L96"></a><tt class="py-lineno"> 96</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="L97"></a><tt class="py-lineno"> 97</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="L98"></a><tt class="py-lineno"> 98</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="L99"></a><tt class="py-lineno"> 99</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="L100"></a><tt class="py-lineno">100</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="L101"></a><tt class="py-lineno">101</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="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-14" 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-14', '_open', 'link-0');">_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="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"> </tt>
<a name="sprot_search_de"></a><div id="sprot_search_de-def"><a name="L104"></a><tt class="py-lineno">104</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.WWW.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="L105"></a><tt class="py-lineno">105</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="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    <tt class="py-docstring">"""sprot_search_de(text, swissprot=1, trembl=None,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring">    cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -&gt; handle</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">    Search SwissProt by name, description, gene name, species, or</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring">    organelle.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</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-15" 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-15', 'text', 'link-12');">text</a></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">if</tt> <tt id="link-16" 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-16', 'swissprot', 'link-13');">swissprot</a></tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</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="L116"></a><tt class="py-lineno">116</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="L117"></a><tt class="py-lineno">117</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="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-17" 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-17', '_open', 'link-0');">_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="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt>
<a name="scanprosite1"></a><div id="scanprosite1-def"><a name="L120"></a><tt class="py-lineno">120</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.WWW.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="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">                 <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://expasy.cbr.nrc.ca/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="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-docstring">"""scanprosite1(seq=None, id=None, exclude_frequent=None, </tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">    cgi='http://expasy.cbr.nrc.ca/cgi-bin/scanprosite/scanprosite?1') -&gt; handle</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">    Scan a sequence for a Prosite pattern.  Either a sequence or a SwissProt/</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-docstring">    trEMBL sequence can be passed.  exclude_frequent specifies whether to</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-docstring">    exclude patterns with high probability.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"><tt class="py-docstring">    </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-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-18" 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-18', 'seq', 'link-18');">seq</a></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">'SEQ'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-19" 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-19', 'seq', 'link-18');">seq</a></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-20" 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-20', 'id', 'link-1');">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 class="py-string">'ID'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-21" 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-21', 'id', 'link-1');">id</a></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</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="L136"></a><tt class="py-lineno">136</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="L137"></a><tt class="py-lineno">137</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-0');">_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 id="link-23" 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-23', 'get', 'link-23');">get</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"> </tt>
<a name="_open"></a><div id="_open-def"><a name="L139"></a><tt class="py-lineno">139</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.ExPASy-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="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">    <tt class="py-docstring">"""_open(cgi, params={}, get=1) -&gt; UndoHandle</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">    Open a handle to ExPASy.  cgi is the URL for the cgi script to access.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</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="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"><tt class="py-docstring">    that describes whether a GET should be used.  Does some</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</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="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-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-24" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-24', 'Bio', 'link-24');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-25" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-25', 'File', 'link-25');">File</a></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-comment"># Open a handle to ExPASy.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</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="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-26" class="py-name"><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-26', 'get', 'link-23');">get</a></tt><tt class="py-op">:</tt>  <tt class="py-comment"># do a GET</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</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="L155"></a><tt class="py-lineno">155</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="L156"></a><tt class="py-lineno">156</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="L157"></a><tt class="py-lineno">157</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-4');">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="L158"></a><tt class="py-lineno">158</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="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">        <tt id="link-28" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-28', 'handle', 'link-4');">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="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-comment"># Wrap the handle inside an UndoHandle.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-29', 'File', 'link-25');">File</a></tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'UndoHandle', 'link-30');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-31', 'handle', 'link-4');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">    <tt class="py-comment"># If the key doesn't exist, ExPASy returns nothing.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.File.UndoHandle.peekline()=Bio.File.UndoHandle-class.html#peekline"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-32', 'peekline', 'link-32');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"no results"</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">     </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">uhandle</tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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