<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.WWW.ExPASy</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.WWW-module.html">Package WWW</a> :: Module ExPASy </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.WWW.ExPASy-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module ExPASy</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html">source code</a></span></p> <p>This module provides code to access resources at ExPASy over the WWW. http://www.expasy.ch/</p> <p>Functions: get_prodoc_entry Interface to the get-prodoc-entry CGI script. get_prosite_entry Interface to the get-prosite-entry CGI script. get_prosite_raw Interface to the get-prosite-raw CGI script. get_sprot_raw Interface to the get-sprot-raw CGI script. sprot_search_ful Interface to the sprot-search-ful CGI script. sprot_search_de Interface to the sprot-search-de CGI script. _open</p> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.WWW.ExPASy-module.html#get_prodoc_entry" class="summary-sig-name">get_prodoc_entry</a>(<span class="summary-sig-arg">id</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.expasy.ch/cgi-bin/get-prodoc-entry'</span>)</span><br /> Get a handle to a PRODOC entry at ExPASy in HTML format.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_prodoc_entry">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.WWW.ExPASy-module.html#get_prosite_entry" class="summary-sig-name">get_prosite_entry</a>(<span class="summary-sig-arg">id</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.expasy.ch/cgi-bin/get-prosite-entry'</span>)</span><br /> Get a handle to a PROSITE entry at ExPASy in HTML format.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_prosite_entry">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.WWW.ExPASy-module.html#get_prosite_raw" class="summary-sig-name">get_prosite_raw</a>(<span class="summary-sig-arg">id</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.expasy.ch/cgi-bin/get-prosite-raw.pl'</span>)</span><br /> Get a handle to a raw PROSITE or PRODOC entry at ExPASy.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_prosite_raw">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.WWW.ExPASy-module.html#get_sprot_raw" class="summary-sig-name">get_sprot_raw</a>(<span class="summary-sig-arg">id</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.expasy.ch/cgi-bin/get-sprot-raw.pl'</span>)</span><br /> Get a handle to a raw SwissProt entry at ExPASy.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_sprot_raw">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="sprot_search_ful"></a><span class="summary-sig-name">sprot_search_ful</span>(<span class="summary-sig-arg">text</span>, <span class="summary-sig-arg">make_wild</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">swissprot</span>=<span class="summary-sig-default">1</span>, <span class="summary-sig-arg">trembl</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.expasy.ch/cgi-bin/sprot-search-ful'</span>)</span><br /> Search SwissProt by full text.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#sprot_search_ful">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="sprot_search_de"></a><span class="summary-sig-name">sprot_search_de</span>(<span class="summary-sig-arg">text</span>, <span class="summary-sig-arg">swissprot</span>=<span class="summary-sig-default">1</span>, <span class="summary-sig-arg">trembl</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.expasy.ch/cgi-bin/sprot-search-de'</span>)</span><br /> Search SwissProt by name, description, gene name, species, or organelle.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#sprot_search_de">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">handle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.WWW.ExPASy-module.html#scanprosite1" class="summary-sig-name">scanprosite1</a>(<span class="summary-sig-arg">seq</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">exclude_frequent</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://expasy.cbr.nrc.ca/cgi-bin/scanprosite/scanprosite?1'</span>)</span><br /> Scan a sequence for a Prosite pattern.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#scanprosite1">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">UndoHandle</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.WWW.ExPASy-module.html#_open" class="summary-sig-name" onclick="show_private();">_open</a>(<span class="summary-sig-arg">cgi</span>, <span class="summary-sig-arg">params</span>=<span class="summary-sig-default">{}</span>, <span class="summary-sig-arg">get</span>=<span class="summary-sig-default">1</span>)</span><br /> Open a handle to ExPASy.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#_open">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.WWW.ExPASy-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.WWW.ExPASy is deprecated. The functions in Bio.WWW.ExPASy are \ now available from Bio.ExPASy.', <type 'exceptions.DeprecationWarning'>, 24): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.WWW.ExPASy is deprecated. The fun</code><code class="variable-ellipsis">...</code></code> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="get_prodoc_entry"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">get_prodoc_entry</span>(<span class="sig-arg">id</span>, <span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.expasy.ch/cgi-bin/get-prodoc-entry'</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_prodoc_entry">source code</a></span> </td> </tr></table> <p>Get a handle to a PRODOC entry at ExPASy in HTML format.</p> <p>For a non-existing key XXX, ExPASy returns a web page containing this line: 'There is no PROSITE documentation entry XXX. Please try again.'</p> <dl class="fields"> <dt>Returns: handle</dt> </dl> </td></tr></table> </div> <a name="get_prosite_entry"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">get_prosite_entry</span>(<span class="sig-arg">id</span>, <span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.expasy.ch/cgi-bin/get-prosite-entry'</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_prosite_entry">source code</a></span> </td> </tr></table> <p>Get a handle to a PROSITE entry at ExPASy in HTML format.</p> <p>For a non-existing key XXX, ExPASy returns a web page containing this line: 'There is currently no PROSITE entry for XXX. Please try again.'</p> <dl class="fields"> <dt>Returns: handle</dt> </dl> </td></tr></table> </div> <a name="get_prosite_raw"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">get_prosite_raw</span>(<span class="sig-arg">id</span>, <span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.expasy.ch/cgi-bin/get-prosite-raw.pl'</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_prosite_raw">source code</a></span> </td> </tr></table> <p>Get a handle to a raw PROSITE or PRODOC entry at ExPASy.</p> <p>For a non-existing key, ExPASy returns nothing.</p> <dl class="fields"> <dt>Returns: handle</dt> </dl> </td></tr></table> </div> <a name="get_sprot_raw"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">get_sprot_raw</span>(<span class="sig-arg">id</span>, <span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.expasy.ch/cgi-bin/get-sprot-raw.pl'</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#get_sprot_raw">source code</a></span> </td> </tr></table> <p>Get a handle to a raw SwissProt entry at ExPASy.</p> <p>For a non-existing key XXX, ExPASy returns a web page containing this line: 'XXX is not a valid identifier.'</p> <dl class="fields"> <dt>Returns: handle</dt> </dl> </td></tr></table> </div> <a name="scanprosite1"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">scanprosite1</span>(<span class="sig-arg">seq</span>=<span class="sig-default">None</span>, <span class="sig-arg">id</span>=<span class="sig-default">None</span>, <span class="sig-arg">exclude_frequent</span>=<span class="sig-default">None</span>, <span class="sig-arg">cgi</span>=<span class="sig-default">'http://expasy.cbr.nrc.ca/cgi-bin/scanprosite/scanprosite?1'</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#scanprosite1">source code</a></span> </td> </tr></table> <p>Scan a sequence for a Prosite pattern. Either a sequence or a SwissProt/ trEMBL sequence can be passed. exclude_frequent specifies whether to exclude patterns with high probability.</p> <dl class="fields"> <dt>Returns: handle</dt> </dl> </td></tr></table> </div> <a name="_open"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_open</span>(<span class="sig-arg">cgi</span>, <span class="sig-arg">params</span>=<span class="sig-default">{}</span>, <span class="sig-arg">get</span>=<span class="sig-default">1</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.WWW.ExPASy-pysrc.html#_open">source code</a></span> </td> </tr></table> <p>Open a handle to ExPASy. cgi is the URL for the cgi script to access. params is a dictionary with the options to pass to it. get is a boolean that describes whether a GET should be used. Does some simple error checking, and will raise an IOError if it encounters one.</p> <dl class="fields"> <dt>Returns: UndoHandle</dt> </dl> </td></tr></table> </div> <br /> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="__warningregistry__"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">__warningregistry__</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.WWW.ExPASy is deprecated. The functions in Bio.WWW.ExPASy are </code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">now available from Bio.ExPASy.</code><code class="variable-quote">'</code><code class="variable-op">,</code> <type 'exceptions.DeprecationWarning'><code class="variable-op">,</code> 24<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:26 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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