<?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.Prosite.Prodoc</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.Prosite-module.html">Package Prosite</a> :: Module Prodoc </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.Prosite.Prodoc-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module Prodoc</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html">source code</a></span></p> <p>This module provides code to work with the prosite.doc file from Prosite. http://www.expasy.ch/prosite/</p> <p>Tested with: Release 15.0, July 1998 Release 16.0, July 1999 Release 20.22, 13 November 2007</p> <p>Functions: parse Iterates over entries in a Prodoc file. index_file Index a Prodoc file for a Dictionary. _extract_record Extract Prodoc data from a web page.</p> <p>Classes: Record Holds Prodoc data. Reference Holds data from a Prodoc reference. Dictionary Accesses a Prodoc file using a dictionary interface. RecordParser Parses a Prodoc record into a Record object.</p> <p>_Scanner Scans Prodoc-formatted data. _RecordConsumer Consumes Prodoc data to a Record object. Iterator Iterates over entries in a Prodoc file; DEPRECATED.</p> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></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">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" 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.Prosite.Prodoc.Record-class.html" class="summary-name">Record</a><br /> Holds information from a Prodoc record. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc.Reference-class.html" class="summary-name">Reference</a><br /> Holds information from a Prodoc citation. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc.Iterator-class.html" class="summary-name">Iterator</a><br /> Returns one record at a time from a Prodoc file. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc.Dictionary-class.html" class="summary-name">Dictionary</a><br /> Accesses a Prodoc file using a dictionary interface. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html" class="summary-name">ExPASyDictionary</a><br /> Access PRODOC at ExPASy using a read-only dictionary interface. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc.RecordParser-class.html" class="summary-name">RecordParser</a><br /> Parses Prodoc data into a Record object. </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc._Scanner-class.html" class="summary-name" onclick="show_private();">_Scanner</a><br /> Scans Prodoc-formatted data. </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Prodoc._RecordConsumer-class.html" class="summary-name" onclick="show_private();">_RecordConsumer</a><br /> Consumer that converts a Prodoc record to a Record object. </td> </tr> </table> <!-- ==================== 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"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="parse"></a><span class="summary-sig-name">parse</span>(<span class="summary-sig-arg">handle</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html#parse">source code</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"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="read"></a><span class="summary-sig-name">read</span>(<span class="summary-sig-arg">handle</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html#read">source code</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"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Prosite.Prodoc-module.html#index_file" class="summary-sig-name">index_file</a>(<span class="summary-sig-arg">filename</span>, <span class="summary-sig-arg">indexname</span>, <span class="summary-sig-arg">rec2key</span>=<span class="summary-sig-default">None</span>)</span><br /> Index a Prodoc file.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html#index_file">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">str</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Prosite.Prodoc-module.html#_extract_record" class="summary-sig-name" onclick="show_private();">_extract_record</a>(<span class="summary-sig-arg">handle</span>)</span><br /> Extract PRODOC data from a web page.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html#_extract_record">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 name="xml_support"></a><span class="summary-name">xml_support</span> = <code title="1">1</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="index_file"></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">index_file</span>(<span class="sig-arg">filename</span>, <span class="sig-arg">indexname</span>, <span class="sig-arg">rec2key</span>=<span class="sig-default">None</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html#index_file">source code</a></span> </td> </tr></table> <p>Index a Prodoc file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the id name will be used.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_extract_record"></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">_extract_record</span>(<span class="sig-arg">handle</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Prosite.Prodoc-pysrc.html#_extract_record">source code</a></span> </td> </tr></table> <p>Extract PRODOC data from a web page. Raises a ValueError if no data was found in the web page.</p> <dl class="fields"> <dt>Returns: str</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 09:26:25 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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