<?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.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> ::
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.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.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.
scanprosite1 Interface to the scanprosite CGI script.</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.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.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.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.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.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.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.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.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.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.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.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://www.expasy.org/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.ExPASy-pysrc.html#scanprosite1">source code</a></span>
</td>
</tr>
</table>
</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.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 an HTML-formatted 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.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 an HTML-formatted 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.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.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 an HTML-formatted 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://www.expasy.org/cgi-bin/scanprosite/scanprosite?1'</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.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>
<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 09:26:23 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. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
